6BF4 | pdb_00006bf4

Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 Familygp120 core 8080392 4002534 SCOP2 (2022-06-29)
ASCOP2 Superfamilygp120 core 8080393 3001390 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
F [auth L]C1-set_4e6bf4L1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_4ECOD (1.6)
F [auth L]V-sete6bf4L2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
CC1-set_4e6bf4C2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_4ECOD (1.6)
CV-sete6bf4C1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
E [auth H]C1-set_1e6bf4H2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
E [auth H]V-set_12e6bf4H1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_12ECOD (1.6)
BC1-set_1e6bf4B2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
BV-set_12e6bf4B1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_12ECOD (1.6)
D [auth G]GP120_3rde6bf4G2 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: GP120_3rdECOD (1.6)
D [auth G]GP120_1ste6bf4G1 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)
AGP120_3rde6bf4A1 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: GP120_3rdECOD (1.6)
AGP120_1ste6bf4A2 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
F [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
C2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
E [auth H]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
B2.60.40.10 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
C,
F [auth L]
Fab VRC-PG05, neutralizing L-KAPPA Homo sapiens (human) IGKV4-1*01, IGKJ2*03, IGKC*01 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202538-0)
B,
E [auth H]
Fab VRC-PG05, neutralizing VH-CH1 Homo sapiens (human) IGHV3-7*01, IGHV3-7*02, IGHV3-7*03, IGHJ3*01, IGHJ3*02, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05, IGHG1*12, IGHG1*14, IGHG1*13, IGHG1*09, IGHG1*10, IGHG1*07, IGHG1*11 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202538-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
C,
F [auth L]
Light ChainIGKV4 Kappahiv-1 clade ae gp120 coreSAbDab (2025-10-03)
B,
E [auth H]
Heavy ChainIGHV3 -hiv-1 clade ae gp120 coreSAbDab (2025-10-03)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A,
D [auth G]
PF00516Envelope glycoprotein GP120 (GP120)Envelope glycoprotein GP120The envelope glycoprotein Gp160 of HIV1 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. The entry of HIV requires interaction of viral GP120 with the CD4 glycoprotein (Swiss:P01730) and a chemokine receptor on the cell s ...The envelope glycoprotein Gp160 of HIV1 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. The entry of HIV requires interaction of viral GP120 with the CD4 glycoprotein (Swiss:P01730) and a chemokine receptor on the cell surface [1]. Gp160 us proteolytically cleaved n the trans-Golgi and activated by cellular furin or furin-like proteases to produce gp120 and gp41 [1,2].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
C,
F [auth L]
VRC-PG05 Fab light chain---
B,
E [auth H]
VRC-PG05 Fab heavy chain---
A,
D [auth G]
HIV-1 clade AE gp120 core