5ESZ
Crystal Structure of Broadly Neutralizing Antibody CH04, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade AE Strain A244
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
B [auth L] | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8091527 | 3000071 | SCOP2B (2022-06-29) |
F [auth B] | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8091527 | 3000071 | 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 [auth H] | PF07654 | e5eszH2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07654 | ECOD (1.6) |
A [auth H] | PF07686 | e5eszH1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
E [auth A] | PF07654 | e5eszA3 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07654 | ECOD (1.6) |
E [auth A] | PF07686 | e5eszA2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
B [auth L] | PF07654 | e5eszL2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07654 | ECOD (1.6) |
B [auth L] | PF07686 | e5eszL1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
F [auth B] | PF07654 | e5eszB1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07654 | ECOD (1.6) |
F [auth B] | PF07686 | e5eszB2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: PF07686 | ECOD (1.6) |
C | PF02542 | e5eszC1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (From Topology) | T: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF | F: PF02542 | ECOD (1.6) |
D [auth G] | PF02542 | e5eszG1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (From Topology) | T: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF | F: PF02542 | ECOD (1.6) |
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], E [auth A] | CH04 mAb, anti-gp120 [HIV-1], neutralizing | VH-CH1 | Homo sapiens (human) | IGHV3-20*01, IGHJ2*01, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202416-0) |
B [auth L], F [auth B] | CH04 mAb, anti-gp120 [HIV-1], neutralizing | L-KAPPA | Homo sapiens (human) | IGKV3-20*01, IGKJ2*01, IGKC*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202416-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
A [auth H], E [auth A] | Heavy Chain | IGHV3 | - | 2-c-methyl-d-erythritol 2,4-cyclodiphosphate synthase,envelope glycoprotein gp160 | SAbDab (2024-04-26) |
B [auth L], F [auth B] | Light Chain | IGKV3 | Kappa | 2-c-methyl-d-erythritol 2,4-cyclodiphosphate synthase,envelope glycoprotein gp160 | SAbDab (2024-04-26) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
B [auth L], F [auth B] | PF07654 | Immunoglobulin C1-set domain (C1-set) | Immunoglobulin C1-set domain | - | Domain |
C, D [auth G] | PF00516 | Envelope glycoprotein GP120 (GP120) | Envelope glycoprotein GP120 | - | Family |
C, D [auth G] | PF02542 | YgbB family (YgbB) | YgbB family | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
B [auth L], F [auth B] | IPR036179 | Immunoglobulin-like domain superfamily | Homologous Superfamily |
B [auth L], F [auth B] | IPR003597 | Immunoglobulin C1-set | Domain |
B [auth L], F [auth B] | IPR013783 | Immunoglobulin-like fold | Homologous Superfamily |
B [auth L], F [auth B] | IPR007110 | Immunoglobulin-like domain | Domain |
B [auth L], F [auth B] | IPR003006 | Immunoglobulin/major histocompatibility complex, conserved site | Conserved Site |
C, D [auth G] | IPR000777 | Human immunodeficiency virus 1, envelope glycoprotein Gp120 | Domain |
C, D [auth G] | IPR036377 | Gp120 core superfamily | Homologous Superfamily |
C, D [auth G] | IPR000328 | Retroviral envelope protein GP41-like | Domain |
C, D [auth G] | IPR037527 | Envelope glycoprotein Gp160 | Family |
C, D [auth G] | IPR036571 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily | Homologous Superfamily |
C, D [auth G] | IPR003526 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | Domain |
C, D [auth G] | IPR020555 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site | Conserved Site |