4YDJ
Crystal structure of broadly and potently neutralizing antibody 44-VRC13.01 in complex with HIV-1 clade AE strain 93TH057 gp120
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth G] | GP120_3rd | e4ydjG2 | A: a+b two layers | X: Ribosomal protein L31e-like | H: Ribosomal protein L31e/gp120 outer domain (From Topology) | T: Ribosomal protein L31e/gp120 outer domain | F: GP120_3rd | ECOD (1.6) |
A [auth G] | GP120_1st | e4ydjG1 | A: a+b two layers | X: gp120 inner domain (From Topology) | H: gp120 inner domain (From Topology) | T: gp120 inner domain | F: GP120_1st | ECOD (1.6) |
D [auth I] | GP120_3rd | e4ydjI1 | A: a+b two layers | X: Ribosomal protein L31e-like | H: Ribosomal protein L31e/gp120 outer domain (From Topology) | T: Ribosomal protein L31e/gp120 outer domain | F: GP120_3rd | ECOD (1.6) |
D [auth I] | GP120_1st | e4ydjI2 | A: a+b two layers | X: gp120 inner domain (From Topology) | H: gp120 inner domain (From Topology) | T: gp120 inner domain | F: GP120_1st | ECOD (1.6) |
B [auth H] | V-set_8 | e4ydjH1 | 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) |
B [auth H] | C1-set_1 | e4ydjH2 | 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) |
E [auth A] | V-set_8 | e4ydjA2 | 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) |
E [auth A] | C1-set_1 | e4ydjA3 | 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) |
C [auth L] | C1-set | e4ydjL1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set | ECOD (1.6) |
C [auth L] | V-set_3 | e4ydjL2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_3 | ECOD (1.6) |
F [auth B] | C1-set | e4ydjB1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set | ECOD (1.6) |
F [auth B] | V-set_3 | e4ydjB2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_3 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A [auth G] | 2.170.40.20 | Mainly Beta | Beta Complex | HIV Envelope Protein Gp120 | Chain G | CATH (4.3.0) |
D [auth I] | 2.170.40.20 | Mainly Beta | Beta Complex | HIV Envelope Protein Gp120 | Chain G | CATH (4.3.0) |
B [auth H] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
E [auth A] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
C [auth L] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
F [auth B] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | 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 |
---|---|---|---|---|---|---|---|---|
B [auth H], E [auth A] | 44-VRC13.01 mAb, anti-gp120 [HIV-1], neutralizing | VH-CH1 | Homo sapiens (human) | IGHV1-69*01, IGHV1-69*06, IGHV1-69*12, IGHV1-69*13, IGHV1-69*14, IGHV1-69D*01, IGHJ2*01, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_LAMBDA | IMGT (202433-0) |
C [auth L], F [auth B] | 44-VRC13.01 mAb, anti-gp120 [HIV-1], neutralizing | L-LAMBDA | Homo sapiens (human) | IGLV2-14*01, IGLV2-23*02, IGLJ1*01, IGLC3*03 | V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA | IG | FAB-GAMMA-1_LAMBDA | IMGT (202433-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
C [auth L], F [auth B] | Light Chain | IGLV2 | Lambda | envelope glycoprotein gp160,envelope glycoprotein gp160 | SAbDab (2024-08-23) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth G], D [auth I] | PF00516 | Envelope glycoprotein GP120 (GP120) | Envelope glycoprotein GP120 | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
A [auth G], D [auth I] | IPR000777 | Human immunodeficiency virus 1, envelope glycoprotein Gp120 | Domain |
A [auth G], D [auth I] | IPR036377 | Gp120 core superfamily | Homologous Superfamily |
A [auth G], D [auth I] | IPR000328 | Retroviral envelope protein GP41-like | Domain |
A [auth G], D [auth I] | IPR037527 | Envelope glycoprotein Gp160 | Family |