3TRV | pdb_00003trv

Crystal structure of quasiracemic villin headpiece subdomain containing (F5Phe17) substitution

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	VHP	e3trvA1	A: alpha arrays	X: VHP, Villin headpiece domain (From Topology)	H: VHP, Villin headpiece domain (From Topology)	T: VHP, Villin headpiece domain	F: VHP	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF02209	Villin headpiece domain (VHP)	Villin headpiece domain		Domain
A	PF02209	Villin headpiece domain (VHP)	Villin headpiece domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	D-Villin-1	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding actin filament binding anion binding phospholipid binding lipid binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding actin filament binding anion binding phospholipid binding lipid binding lysophosphatidic acid binding carbohydrate derivative binding enzyme regulator activity cysteine-type endopeptidase inhibitor activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding identical protein binding protein homodimerization activity protein dimerization activity	regulation of cytoskeleton organization regulation of biological process regulation of actin filament organization regulation of cellular component organization regulation of cellular process regulation of actin filament-based process actin cytoskeleton organization actin filament organization biological regulation regulation of organelle organization cellular component organization organelle organization regulation of actin nucleation actin filament-based process regulation of actin cytoskeleton organization regulation of cytoskeleton organization regulation of biological process regulation of actin filament organization regulation of cellular component organization regulation of cellular process regulation of actin filament-based process actin cytoskeleton organization actin filament organization biological regulation regulation of organelle organization cellular component organization organelle organization regulation of actin nucleation actin filament-based process regulation of actin cytoskeleton organization regulation of supramolecular fiber organization cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin filament severing protein polymerization actin polymerization or depolymerization actin filament polymerization protein-containing complex organization cellular component biogenesis cellular component assembly protein-containing complex assembly cellular component disassembly protein-containing complex disassembly actin filament depolymerization protein depolymerization cytoplasmic actin-based contraction involved in cell motility cell motility actin-mediated cell contraction actin filament-based movement regulation of developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell morphogenesis regulation of cell morphogenesis cell projection morphogenesis regulation of lamellipodium organization anatomical structure development regulation of lamellipodium morphogenesis regulation of anatomical structure morphogenesis developmental process plasma membrane bounded cell projection organization regulation of cell projection organization anatomical structure morphogenesis lamellipodium organization lamellipodium morphogenesis regulation of plasma membrane bounded cell projection organization regulation of cell shape regulation of biological quality positive regulation of organelle organization positive regulation of cellular component organization positive regulation of biological process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of cellular process positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization positive regulation of supramolecular fiber organization regulation of cellular component biogenesis actin filament bundle assembly cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication ERBB signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding regulation of response to wounding regulation of cellular component size negative regulation of biological process regulation of protein-containing complex disassembly regulation of actin filament depolymerization actin filament capping negative regulation of supramolecular fiber organization negative regulation of actin filament polymerization negative regulation of cellular component organization negative regulation of protein depolymerization negative regulation of protein-containing complex assembly regulation of protein polymerization regulation of protein-containing complex assembly negative regulation of protein-containing complex disassembly negative regulation of cellular process negative regulation of protein polymerization regulation of actin filament polymerization regulation of protein depolymerization negative regulation of cytoskeleton organization regulation of actin polymerization or depolymerization negative regulation of organelle organization regulation of actin filament length negative regulation of actin filament depolymerization regulation of anatomical structure size positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration locomotion biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus cellular response to endogenous stimulus response to hepatocyte growth factor cellular response to growth factor stimulus cellular response to hepatocyte growth factor stimulus response to endogenous stimulus response to growth factor cellular response to epidermal growth factor stimulus response to epidermal growth factor barbed-end actin filament capping multicellular organismal process positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration regulation of multicellular organismal process epithelial cell migration regulation of epithelial cell migration epithelium migration	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton filopodium tip actin-based cell projection cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton filopodium tip actin-based cell projection filopodium cytoplasm actin filament bundle ruffle microvillus
A	L-Villin-1	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding actin filament binding anion binding phospholipid binding lipid binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding actin filament binding anion binding phospholipid binding lipid binding lysophosphatidic acid binding carbohydrate derivative binding enzyme regulator activity cysteine-type endopeptidase inhibitor activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding identical protein binding protein homodimerization activity protein dimerization activity	regulation of cytoskeleton organization regulation of biological process regulation of actin filament organization regulation of cellular component organization regulation of cellular process regulation of actin filament-based process actin cytoskeleton organization actin filament organization biological regulation regulation of organelle organization cellular component organization organelle organization regulation of actin nucleation actin filament-based process regulation of actin cytoskeleton organization regulation of cytoskeleton organization regulation of biological process regulation of actin filament organization regulation of cellular component organization regulation of cellular process regulation of actin filament-based process actin cytoskeleton organization actin filament organization biological regulation regulation of organelle organization cellular component organization organelle organization regulation of actin nucleation actin filament-based process regulation of actin cytoskeleton organization regulation of supramolecular fiber organization cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin filament severing protein polymerization actin polymerization or depolymerization actin filament polymerization protein-containing complex organization cellular component biogenesis cellular component assembly protein-containing complex assembly cellular component disassembly protein-containing complex disassembly actin filament depolymerization protein depolymerization cytoplasmic actin-based contraction involved in cell motility cell motility actin-mediated cell contraction actin filament-based movement regulation of developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell morphogenesis regulation of cell morphogenesis cell projection morphogenesis regulation of lamellipodium organization anatomical structure development regulation of lamellipodium morphogenesis regulation of anatomical structure morphogenesis developmental process plasma membrane bounded cell projection organization regulation of cell projection organization anatomical structure morphogenesis lamellipodium organization lamellipodium morphogenesis regulation of plasma membrane bounded cell projection organization regulation of cell shape regulation of biological quality positive regulation of organelle organization positive regulation of cellular component organization positive regulation of biological process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of cellular process positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization positive regulation of supramolecular fiber organization regulation of cellular component biogenesis actin filament bundle assembly cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication ERBB signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding regulation of response to wounding regulation of cellular component size negative regulation of biological process regulation of protein-containing complex disassembly regulation of actin filament depolymerization actin filament capping negative regulation of supramolecular fiber organization negative regulation of actin filament polymerization negative regulation of cellular component organization negative regulation of protein depolymerization negative regulation of protein-containing complex assembly regulation of protein polymerization regulation of protein-containing complex assembly negative regulation of protein-containing complex disassembly negative regulation of cellular process negative regulation of protein polymerization regulation of actin filament polymerization regulation of protein depolymerization negative regulation of cytoskeleton organization regulation of actin polymerization or depolymerization negative regulation of organelle organization regulation of actin filament length negative regulation of actin filament depolymerization regulation of anatomical structure size positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration locomotion biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus cellular response to endogenous stimulus response to hepatocyte growth factor cellular response to growth factor stimulus cellular response to hepatocyte growth factor stimulus response to endogenous stimulus response to growth factor cellular response to epidermal growth factor stimulus response to epidermal growth factor barbed-end actin filament capping multicellular organismal process positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration regulation of multicellular organismal process epithelial cell migration regulation of epithelial cell migration epithelium migration	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton filopodium tip actin-based cell projection cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton filopodium tip actin-based cell projection filopodium cytoplasm actin filament bundle ruffle microvillus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
B	IPR007122	Villin/Gelsolin	Family
B	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
B	IPR003128	Villin headpiece	Domain
B	IPR007123	Gelsolin-like domain	Domain
B	IPR036886	Villin headpiece domain superfamily	Homologous Superfamily
A	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
A	IPR007122	Villin/Gelsolin	Family
A	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
A	IPR003128	Villin headpiece	Domain
A	IPR007123	Gelsolin-like domain	Domain
A	IPR036886	Villin headpiece domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	DAL	RESID: AA0111 , AA0191 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862
B	DAR	RESID: AA0111 , AA0191
B	DAS	RESID: AA0111 , AA0191 , AA0190 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930
B	DGL	RESID: AA0111 , AA0191 , AA0190
B	DGN	RESID: AA0111 , AA0191 , AA0190
B	DHI	RESID: AA0111 , AA0191 , AA0190
B	DLE	RESID: AA0111 , AA0191 , AA0190 , AA0197 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-leucine MOD:00204
B	DLY	RESID: AA0111 , AA0191 , AA0190 , AA0197
B	DPN	RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-leucine MOD:00204 , D-phenylalanine MOD:00201
B	DPR	RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194
B	DSG	RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194 , AA0196 , AA0622 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985
B	DSN	RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987
B	DTH	RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-allo-threonine MOD:00863
B	DTR	RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 , AA0198 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-allo-threonine MOD:00863 , D-tryptophan MOD:00205
B	DVA	RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 , AA0198 , AA0200 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-allo-threonine MOD:00863 , D-tryptophan MOD:00205 , D-valine MOD:00705
B	MED	RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 , AA0198 , AA0200 , AA0193 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-aspartic acid (Asp) MOD:01921 , D-aspartic acid (Asn) MOD:01930 , D-leucine MOD:00204 , D-phenylalanine MOD:00201 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-allo-threonine MOD:00863 , D-tryptophan MOD:00205 , D-valine MOD:00705 , D-methionine MOD:00200
A	PF5	Parent Component: PHE RESID: AA0111 , AA0191 , AA0190 , AA0197 , AA0194 , AA0196 , AA0622 , AA0195 , AA0624 , AA0199 , AA0198 , AA0200 , AA0193

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.