6ORO | pdb_00006oro

Modified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch antibody Ab874NHP


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
BSCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)
GSCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)
ISCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AGP41_1ste6oroA1 A: a+b duplicates or obligate multimersX: MPER trimer (From Topology)H: MPER trimer (From Topology)T: MPER trimerF: GP41_1stECOD (1.6)
CGP41_1ste6oroC1 A: a+b duplicates or obligate multimersX: MPER trimer (From Topology)H: MPER trimer (From Topology)T: MPER trimerF: GP41_1stECOD (1.6)
FGP41_1ste6oroF1 A: a+b duplicates or obligate multimersX: MPER trimer (From Topology)H: MPER trimer (From Topology)T: MPER trimerF: GP41_1stECOD (1.6)
BGP120_2nde6oroB3 A: beta barrelsX: V1/V2 domain in HIV gp120 (From Topology)H: V1/V2 domain in HIV gp120 (From Topology)T: V1/V2 domain in HIV gp120F: GP120_2ndECOD (1.6)
BGP120_3rde6oroB1 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)
BGP120_1ste6oroB2 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)
GGP120_2nde6oroG2 A: beta barrelsX: V1/V2 domain in HIV gp120 (From Topology)H: V1/V2 domain in HIV gp120 (From Topology)T: V1/V2 domain in HIV gp120F: GP120_2ndECOD (1.6)
GGP120_3rde6oroG3 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)
GGP120_1ste6oroG1 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)
IGP120_2nde6oroI2 A: beta barrelsX: V1/V2 domain in HIV gp120 (From Topology)H: V1/V2 domain in HIV gp120 (From Topology)T: V1/V2 domain in HIV gp120F: GP120_2ndECOD (1.6)
IGP120_3rde6oroI3 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)
IGP120_1ste6oroI1 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)
DV-set_8e6oroD1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
HV-set_8e6oroH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
JV-set_8e6oroJ1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
EV-set_3e6oroE1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
KV-set_3e6oroK1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
LV-set_3e6oroL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
D, H, J
Fab Ab874NHP VH-CH1 Homo sapiens (human) IGHV3-23*03, IGHV3-23*04, IGHV3-NL1*01, IGHJ1*01, IGHG1*03, IGHG1*08, IGHG1*06 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_LAMBDA IMGT (202524-0)
E, K, L
Fab Ab874NHP L-LAMBDA Homo sapiens (human) IGLV3-21*02, IGLJ2*01, IGLJ3*02, IGLJ7*01, IGLJ3*01, IGLC2*01, IGLC2*02, IGLC3*04 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-1_LAMBDA IMGT (202524-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
D, H, J
Heavy ChainIGHV3 -rc1 variant of hiv-1 env glycoprotein gp120SAbDab (2025-06-27)
E, K, L
Light ChainIGLV3 Lambdarc1 variant of hiv-1 env glycoprotein gp120SAbDab (2025-06-27)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, C, F
PF00517Retroviral envelope protein (GP41)Retroviral envelope protein- Family
B, G, I
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
A, C, F
RC1 variant of HIV-1 Env glycoprotein gp41
B, G, I
RC1 variant of HIV-1 Env glycoprotein gp120
D, H, J
Ab874NHP antibody Fab heavy chain---
E, K, L
Ab874NHP antibody Fab light chain---