6RXM | pdb_00006rxm

Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8041390	3001728	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	SIR2_1st	e6rxmF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
F	PTZ00408	e6rxmF1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PTZ00408	ECOD (1.6)
E	SIR2_1st	e6rxmE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
E	PTZ00408	e6rxmE1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PTZ00408	ECOD (1.6)
D	SIR2_1st	e6rxmD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
D	PTZ00408	e6rxmD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PTZ00408	ECOD (1.6)
C	SIR2_1st	e6rxmC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
C	PTZ00408	e6rxmC1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PTZ00408	ECOD (1.6)
B	SIR2_1st	e6rxmB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
B	PTZ00408	e6rxmB2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PTZ00408	ECOD (1.6)
A	SIR2_1st	e6rxmA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
A	PTZ00408	e6rxmA1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PTZ00408	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
F	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
E	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
D	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
C	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
B	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
B	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
A	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
A	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin identical protein binding	nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle transcription regulator complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure RNA polymerase I upstream activating factor complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle transcription regulator complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle membraneless organelle nuclear lumen protein-DNA complex nucleosome chromatin chromosome
A, B, C, D, E A, B, C, D, E, F	NAD-dependent protein deacylase	acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity NAD-dependent protein de-2-hydroxyisobutyrylase activity catalytic activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity NAD-dependent protein de-2-hydroxyisobutyrylase activity catalytic activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding catalytic activity, acting on a protein deacylase activity protein-succinyllysine desuccinylase activity NAD-dependent protein lysine deacylase activity guanyl nucleotide binding cyclic nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding cyclic-di-GMP binding carbohydrate derivative binding ribonucleotide binding identical protein binding protein binding protein homodimerization activity protein dimerization activity deacetylase activity protein lysine deacetylase activity histone deacetylase activity, NAD-dependent histone deacetylase activity NAD-dependent protein lysine deacetylase activity histone modifying activity protein-malonyllysine demalonylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds lipoamidase activity cation binding transition metal ion binding zinc ion binding metal ion binding pentosyltransferase activity NAD+ poly-ADP-ribosyltransferase activity glycosyltransferase activity	chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion biological process involved in interspecies interaction between organisms defense response to virus defense response response to other organism response to stress response to external biotic stimulus response to virus response to biotic stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I, J, K G, H, I, J, K, L	IPR009072	Histone-fold	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR035425	CENP-T/Histone H4, histone fold	Domain
G, H, I, J, K G, H, I, J, K, L	IPR001951	Histone H4	Family
G, H, I, J, K G, H, I, J, K, L	IPR019809	Histone H4, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR027546	Sirtuin, class III	Family
A, B, C, D, E A, B, C, D, E, F	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A, B, C, D, E A, B, C, D, E, F	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003000	Sirtuin family	Family
A, B, C, D, E A, B, C, D, E, F	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I, J, K G, H, I, J, K, L	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064

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.