1W2M | pdb_00001w2m

Ca-substituted form of E. coli aminopeptidase P

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)
F	d1w2mf1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Creatinase/prolidase N-terminal domain	Creatinase/prolidase N-terminal domain	Aminopeptidase P	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1w2mf2	Alpha and beta proteins (a+b)	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Aminopeptidase P, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1w2me1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Creatinase/prolidase N-terminal domain	Creatinase/prolidase N-terminal domain	Aminopeptidase P	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1w2me2	Alpha and beta proteins (a+b)	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Aminopeptidase P, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1w2md1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Creatinase/prolidase N-terminal domain	Creatinase/prolidase N-terminal domain	Aminopeptidase P	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1w2md2	Alpha and beta proteins (a+b)	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Aminopeptidase P, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1w2mc1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Creatinase/prolidase N-terminal domain	Creatinase/prolidase N-terminal domain	Aminopeptidase P	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1w2mc2	Alpha and beta proteins (a+b)	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Aminopeptidase P, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1w2mb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Creatinase/prolidase N-terminal domain	Creatinase/prolidase N-terminal domain	Aminopeptidase P	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1w2mb2	Alpha and beta proteins (a+b)	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Aminopeptidase P, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1w2ma1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Creatinase/prolidase N-terminal domain	Creatinase/prolidase N-terminal domain	Aminopeptidase P	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1w2ma2	Alpha and beta proteins (a+b)	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Creatinase/aminopeptidase	Aminopeptidase P, C-terminal domain	(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)
F	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8037176	3000538	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8037177	3000126	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8037177	3000126	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8037176	3000538	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8037177	3000126	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8037176	3000538	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8037177	3000126	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8037176	3000538	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8037177	3000126	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8037176	3000538	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8037176	3000538	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8037177	3000126	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		e1w2mF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
F		e1w2mF2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Thioredoxin	F:	ECOD (20:10:01)
E		e1w2mE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
E		e1w2mE2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Thioredoxin	F:	ECOD (20:10:01)
D		e1w2mD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
D		e1w2mD2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Thioredoxin	F:	ECOD (20:10:01)
C		e1w2mC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
C		e1w2mC2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Thioredoxin	F:	ECOD (20:10:01)
B		e1w2mB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
B		e1w2mB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Thioredoxin	F:	ECOD (20:10:01)
A		e1w2mA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
A		e1w2mA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Thioredoxin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
F	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)
E	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
E	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)
D	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
D	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)
C	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
C	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)
B	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
B	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)
A	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
A	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF05195	Aminopeptidase P, N-terminal domain (AMP_N)	Aminopeptidase P, N-terminal domain	This domain is structurally very similar [1] to the creatinase N-terminal domain (Pfam:PF01321). However, little or no sequence similarity exists between the two families.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00557	Metallopeptidase family M24 (Peptidase_M24)	Metallopeptidase family M24	This family contains metallopeptidases. It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	XAA-PRO AMINOPEPTIDASE	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity metallopeptidase activity aminopeptidase activity metalloaminopeptidase activity exopeptidase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity metallopeptidase activity aminopeptidase activity metalloaminopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity identical protein binding protein binding	protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis proteolysis metabolic process primary metabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001714	Peptidase M24, methionine aminopeptidase	Family
A, B, C, D, E A, B, C, D, E, F	IPR001131	Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR007865	Aminopeptidase P, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR052433	Xaa-Pro dipeptidase-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR036005	Creatinase/aminopeptidase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000994	Peptidase M24	Domain

Protein Modification Annotation

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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.