3U2S
Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain ZM109
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 H] | C1-set_1 | e3u2sH2 | 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) |
A [auth H] | V-set_12 | e3u2sH1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_12 | ECOD (1.6) |
D [auth A] | C1-set_1 | e3u2sA2 | 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) |
D [auth A] | V-set_12 | e3u2sA1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_12 | ECOD (1.6) |
B [auth L] | C1-set | e3u2sL2 | 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) |
B [auth L] | V-set_3 | e3u2sL1 | 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) |
E [auth B] | C1-set | e3u2sB2 | 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) |
E [auth B] | V-set_3 | e3u2sB1 | 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) |
C [auth G] | GP120_2nd | e3u2sG2 | A: beta barrels | X: V1/V2 domain in HIV gp120 (From Topology) | H: V1/V2 domain in HIV gp120 (From Topology) | T: V1/V2 domain in HIV gp120 | F: GP120_2nd | ECOD (1.6) |
C [auth G] | IgG_binding_B | e3u2sG1 | A: a+b two layers | X: beta-Grasp | H: Immunoglobulin-binding domains (From Topology) | T: Immunoglobulin-binding domains | F: IgG_binding_B | ECOD (1.6) |
F [auth C] | GP120_2nd | e3u2sC2 | A: beta barrels | X: V1/V2 domain in HIV gp120 (From Topology) | H: V1/V2 domain in HIV gp120 (From Topology) | T: V1/V2 domain in HIV gp120 | F: GP120_2nd | ECOD (1.6) |
F [auth C] | IgG_binding_B | e3u2sC1 | A: a+b two layers | X: beta-Grasp | H: Immunoglobulin-binding domains (From Topology) | T: Immunoglobulin-binding domains | F: IgG_binding_B | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A [auth H] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
D [auth A] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
B [auth L] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
E [auth B] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
C [auth G] | 3.10.20.10 | Alpha Beta | Roll | Ubiquitin-like (UB roll) | CATH (4.3.0) | |
F [auth C] | 3.10.20.10 | Alpha Beta | Roll | Ubiquitin-like (UB roll) | 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 |
---|---|---|---|---|---|---|---|---|
A [auth H], D [auth A] | neutralizing | VH-CH1 | Homo sapiens (human) | IGHV3-30*02, IGHV3-30*03, IGHV3-30*06, IGHV3-30*12, IGHV3-30*19, IGHV3-33*01, IGHV3-33*04, IGHV3-33*05, IGHV3-30-5*02, IGHJ6*03, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_LAMBDA | IMGT (202434-0) |
B [auth L], E [auth B] | neutralizing | L-LAMBDA | Homo sapiens (human) | IGLV2-14*01, IGLJ1*01, IGLJ2*01, IGLJ3*02, IGLJ3*01, IGLC3*03 | V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA | IG | FAB-GAMMA-1_LAMBDA | IMGT (202434-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
A [auth H], D [auth A] | Heavy Chain | IGHV3 | - | envelope glycoprotein gp120 | SAbDab (2024-08-30) |
B [auth L], E [auth B] | Light Chain | IGLV2 | Lambda | envelope glycoprotein gp120 | SAbDab (2024-08-30) |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
C [auth G], F [auth C] | IPR000777 | Human immunodeficiency virus 1, envelope glycoprotein Gp120 | Domain |
C [auth G], F [auth C] | IPR036377 | Gp120 core superfamily | Homologous Superfamily |
C [auth G], F [auth C] | IPR000328 | Retroviral envelope protein GP41-like | Domain |
C [auth G], F [auth C] | IPR037527 | Envelope glycoprotein Gp160 | Family |
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
A [auth H], D [auth A] | PCA | Parent Component: GLN :  AA0031 :  2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 |
A [auth H], D [auth A] | TYS | Parent Component: TYR :  AA0031 , AA0172 :  2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , O4'-sulfo-L-tyrosine MOD:00181 |