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 4NZR | pdb_00004nzr

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 SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
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)
A [auth H]d4nzrh_ 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

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth M]Protein M, large region / Protein M, smaller domaine4nzrM1 A: alpha arraysX: Single-stranded right-handed beta-helixH: Protein M antibody-binding regionT: Protein M antibody-binding regionF: Protein M, large region / Protein M, smaller domainECOD (v295.2)
B [auth L]Arm,Arm_3e4nzrL1 A: alpha arraysX: Repetitive alpha hairpinsH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Nicotinate/Quinolinate PRTase N-terminal domain-likeF: Arm,Arm_3ECOD (v295.2)
A [auth H]Arm,Arm_3e4nzrH1 A: alpha arraysX: Repetitive alpha hairpinsH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Nicotinate/Quinolinate PRTase N-terminal domain-likeF: Arm,Arm_3ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
C [auth M]3.30.1370.200 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8 Chain: A, domain 1CATH (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)
B [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
A [auth H]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
B [auth L]PGT135 mAb, anti-gp120 [HIV-1], broadly neutralizing L-KAPPA Homo sapiens (human) IGKV3-15*01, IGKV3D-15*01, IGKJ1*01, IGKC*01 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202636-0)
A [auth H]PGT135 mAb, anti-gp120 [HIV-1], broadly neutralizing VH-CH1 Homo sapiens (human) IGHV4-39*01, IGHV4-39*02, IGHV4-39*07, IGHV4-38-2*02, IGHJ5*01, IGHG1*03 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202636-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
B [auth L]Light ChainIGKV3 Kappaprotein m tdSAbDab (2026-09-18)
A [auth H]Heavy ChainIGHV4 -protein m tdSAbDab (2026-09-18)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
C [auth M]PF20757Protein M, large region (M_large_dom)Protein M, large regionThis 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]PF22805Protein M, smaller domain (M_smaller_dom)Protein M, smaller domainThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
C [auth M]Protein M TD- -
B [auth L]PGT135 light chain---
A [auth H]PGT135 heavy chain---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth M]IPR048475MG281-like, antibody-binding regionDomain
C [auth M]IPR030943IgG-blocking protein MFamily
C [auth M]IPR054349Protein M, smaller domainDomain
C [auth M]IPR030942IgG-blocking virulence domainDomain
C [auth M]IPR054348Protein M, C-terminalDomain