4NZR

Crystal structure of the antibody-binding region of Protein M (Protein M TD) in complex with anti-HIV antibody PGT135 Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
A [auth H]	d4nzrh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4nzrl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4nzrl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth H]	V-set_8	e4nzrH2	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)
A [auth H]	C1-set_1	e4nzrH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B [auth L]	C1-set_4	e4nzrL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e4nzrL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C [auth M]	prot_M_MG281	e4nzrM1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Protein M antibody-binding region (From Topology)	T: Protein M antibody-binding region	F: prot_M_MG281	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth M]	3.30.1370.200	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C [auth M]	2.160.20.180	Mainly Beta	3 Solenoid	Pectate Lyase C-like		CATH (4.3.0)
C [auth M]	3.30.110.180	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3		CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth H]	PGT135 mAb, anti-gp120 [HIV-1], broadly neutralizing	VH-CH1	Homo sapiens (human)	IGHV4-3901, IGHV4-3902, IGHV4-3907, IGHV4-38-202, IGHJ501, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202452-0)
B [auth L]	PGT135 mAb, anti-gp120 [HIV-1], broadly neutralizing	L-KAPPA	Homo sapiens (human)	IGKV3-1501, IGKV3D-1501, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202452-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV4	-	protein m td	SAbDab (2025-01-03)
B [auth L]	Light Chain	IGKV3	Kappa	protein m td	SAbDab (2025-01-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth M]	PF20757	Protein M, large region (M_large_dom)	Protein M, large region	This domain is found in proteins from Mycoplasmaceae, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains. The larger one (this entry) binds the IgG light chain t ...	This domain is found in proteins from Mycoplasmaceae, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains. The larger one (this entry) binds the IgG light chain to block the binding of antibody to antigen. It includes a leucine-rich repeat (LRR)-like subdomain, which faces away from the antibody molecule [1].	Domain
C [auth M]	PF22805	Protein M, smaller domain (M_smaller_dom)	Protein M, smaller domain	This domain is found in proteins from Mycoplasmaceae, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains. The larger one (Pfam:PF20757) binds the IgG light chain ...	This domain is found in proteins from Mycoplasmaceae, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains. The larger one (Pfam:PF20757) binds the IgG light chain to block the binding of antibody to antigen and includes a leucine-rich repeat (LRR)-like subdomain. This domain folds into two alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H]	PGT135 heavy chain	-	-	-
B [auth L]	PGT135 light chain	-	-	-
C [auth M]	Protein M TD	-	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth M]	IPR048475	MG281-like, antibody-binding region	Domain
C [auth M]	IPR030943	IgG-blocking protein M	Family
C [auth M]	IPR054349	Protein M, smaller domain	Domain
C [auth M]	IPR030942	IgG-blocking virulence domain	Domain
C [auth M]	IPR054348	Protein M, C-terminal	Domain

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.