5MP2

XcpQN012 in complex with VHH04

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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)
C	d5mp2c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d5mp2c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d5mp2d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d5mp2d2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	STN domain-like	8057219	3002388	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Secretin repeat domain-like	8057215	3002387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Secretin repeat domain-like	8057216	3002387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	STN domain-like	8057219	3002388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Secretin repeat domain-like	8057215	3002387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Secretin repeat domain-like	8057216	3002387	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	Secretin_N	e5mp2A1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
A	type_II_gspD	e5mp2A3	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: type_II_gspD	ECOD (1.6)
B	Secretin_N	e5mp2B1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
B	type_II_gspD	e5mp2B3	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: type_II_gspD	ECOD (1.6)
C	V-set_12	e5mp2C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
D	V-set_8	e5mp2D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
B	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV1	-	type ii secretion system protein d	SAbDab (2024-11-01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03958	Bacterial type II/III secretion system short domain (Secretin_N)	Bacterial type II/III secretion system short domain	This is a short, often repeated, domain found in bacterial type II/III secretory system proteins. All previous NolW-like domains fall into this family.	Domain
A, B	PF21305	GspD-like, N0 domain (type_II_gspD_N0)	GspD-like, N0 domain	GspD is a type II general secretion pathway protein involved in protein export. This is the N0 domain found at the N-terminal of GspD type II secretins and its close homologues [1-5]. These proteins form a dodecameric ring, in which the N0 domain med ...	GspD is a type II general secretion pathway protein involved in protein export. This is the N0 domain found at the N-terminal of GspD type II secretins and its close homologues [1-5]. These proteins form a dodecameric ring, in which the N0 domain mediate extensive contacts suggesting that dodecameric N0 ring is an important feature of T2SS secretins [4]. This domain is also found in virion export proteins, proteins thought to form a channel across the host outer membrane for the purposes of extruding the bacteriophage.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Type II secretion system protein D	identical protein binding protein binding binding	protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region localization secretion by cell protein transport cellular macromolecule localization protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region localization secretion by cell protein transport cellular macromolecule localization macromolecule localization cellular process protein transport across the cell outer membrane protein secretion by the type II secretion system transmembrane transport protein transmembrane transport	protein-containing complex type II protein secretion system complex cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane cellular anatomical entity
C, D	Camelid nanobody VHH04	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050810	Bacterial Secretion System Channel Protein	Family
A, B	IPR005644	NolW-like	Domain
A, B	IPR004846	Type II/III secretion system, secretin-like domain	Domain
A, B	IPR038591	NolW-like superfamily	Homologous Superfamily
A, B	IPR049371	GspD-like, N0 domain	Domain
A, B	IPR004845	Type II secretion system protein GspD, conserved site	Conserved Site
A, B	IPR013356	Type II secretion system protein GspD	Family
A, B	IPR001775	GspD/PilQ 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.