5CE3

The Yersinia YopO - actin complex with MgADP

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5ce3a2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Actin/HSP70	automated matches	(Spodoptera frugiperda ) [TaxId: 7108 ],	SCOPe (2.08)
A	d5ce3a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Spodoptera frugiperda ) [TaxId: 7108 ],	SCOPe (2.08)
C	d5ce3c2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Actin/HSP70	automated matches	(Spodoptera frugiperda ) [TaxId: 7108 ],	SCOPe (2.08)
C	d5ce3c1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Spodoptera frugiperda ) [TaxId: 7108 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Rac1-binding domain-like	8045274	4004385	SCOP2 (2022-06-29)
B	SCOP2 Family	Protein kinases catalytic domain-like	8089931	4003661	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Rac1-binding domain structural repeat-like	8089930	3002403	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Protein kinase-like (PK-like)	8089932	3000066	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Rac1-binding domain structural repeat-like	8089928	3002403	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Rac1-binding domain structural repeat-like	8089929	3002403	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Rac1-binding domain structural repeat-like	8089930	3002403	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089932	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rac1-binding domain structural repeat-like	8089928	3002403	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rac1-binding domain structural repeat-like	8089929	3002403	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8092416	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8082535	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8092416	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8082535	3000092	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)
B	Rac1	e5ce3B1	A: alpha bundles	X: Yersinia protein kinase A (YpkA) Rho-GTPase binding domain (From Topology)	H: Yersinia protein kinase A (YpkA) Rho-GTPase binding domain (From Topology)	T: Yersinia protein kinase A (YpkA) Rho-GTPase binding domain	F: Rac1	ECOD (1.6)
B	Pkinase_Tyr	e5ce3B2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
D	Rac1	e5ce3D2	A: alpha bundles	X: Yersinia protein kinase A (YpkA) Rho-GTPase binding domain (From Topology)	H: Yersinia protein kinase A (YpkA) Rho-GTPase binding domain (From Topology)	T: Yersinia protein kinase A (YpkA) Rho-GTPase binding domain	F: Rac1	ECOD (1.6)
D	Pkinase_Tyr	e5ce3D1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
A	Actin_1st	e5ce3A1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Actin_1st	ECOD (1.6)
A	Actin_2nd	e5ce3A2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Actin_2nd	ECOD (1.6)
C	Actin_1st	e5ce3C1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Actin_1st	ECOD (1.6)
C	Actin_2nd	e5ce3C2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Actin_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
C	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF09632	Rac1-binding domain (Rac1)	Rac1-binding domain	The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. the N-terminal end, residues 434-615, consists of six helices organised into two three ...	The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. the N-terminal end, residues 434-615, consists of six helices organised into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end, residues 705-732. is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host [1]. It is usually found downstream of Pfam:PF00069.	Domain
B, D	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Protein kinase YopO	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	-	-
A, C	Actin	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR019093	YpkA, Rac1-binding domain	Domain
B, D	IPR043120	Rac1-binding domain, N-terminal	Homologous Superfamily
B, D	IPR000719	Protein kinase domain	Domain
B, D	IPR003547	Serine/threonine protein kinase, yersinia-type	Family
B, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B, D	IPR043119	Rac1-binding domain, C-terminal	Homologous Superfamily
A, C	IPR020902	Actin/actin-like conserved site	Conserved Site
A, C	IPR004001	Actin, conserved site	Conserved Site
A, C	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, C	IPR004000	Actin family	Family

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.