1QY9 | pdb_00001qy9

Crystal structure of E. coli Se-MET protein YDDE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1qy9a1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	PhzC/PhzF-like	Hypothetical protein YddE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1qy9c1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	PhzC/PhzF-like	Hypothetical protein YddE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1qy9d1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	PhzC/PhzF-like	Hypothetical protein YddE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1qy9b1	Alpha and beta proteins (a+b)	Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	PhzC/PhzF-like	Hypothetical protein YddE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PhzC/PhzF-like	8026233	4000604	SCOP2 (2022-06-29)
A	SCOP2 Family	PhzC/PhzF-like	8026234	4000604	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Diaminopimelate epimerase-like	8038612	3000573	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Diaminopimelate epimerase-like	8038613	3000573	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Diaminopimelate epimerase-like	8038613	3000573	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Diaminopimelate epimerase-like	8038612	3000573	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Diaminopimelate epimerase-like	8038612	3000573	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Diaminopimelate epimerase-like	8038613	3000573	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Diaminopimelate epimerase-like	8038613	3000573	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Diaminopimelate epimerase-like	8038612	3000573	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)
A	PhzC-PhzF	e1qy9A1	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: PhzC-PhzF	ECOD (1.6)
C	PhzC-PhzF	e1qy9C1	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: PhzC-PhzF	ECOD (1.6)
D	PhzC-PhzF	e1qy9D1	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: PhzC-PhzF	ECOD (1.6)
B	PhzC-PhzF	e1qy9B1	A: a+b complex topology	X: Diaminopimelate epimerase-like (From Topology)	H: Diaminopimelate epimerase-like (From Topology)	T: Diaminopimelate epimerase-like	F: PhzC-PhzF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
C	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
D	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)
B	3.10.310.10	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, D	PF02567	Phenazine biosynthesis-like protein (PhzC-PhzF)	Phenazine biosynthesis-like protein	-	Family
B	PF02567	Phenazine biosynthesis-like protein (PhzC-PhzF)	Phenazine biosynthesis-like protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, D	Uncharacterized isomerase YddE	isomerase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	biosynthetic process metabolic process cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm
B	Uncharacterized isomerase YddE	isomerase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	biosynthetic process metabolic process cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, D	IPR003719	Phenazine biosynthesis PhzF-like	Family
B	IPR003719	Phenazine biosynthesis PhzF-like	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, D	MSE	Parent Component: MET
B	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210
B	MSE	Parent Component: MET RESID: AA0205

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.