Crystal structure of an HIV-1 gp120 engineered outer domain with a Man9 glycan at position N276, in complex with broadly neutralizing antibody VRC01
External Resource: Annotation
Domain Annotation: ECOD Classification ECOD Database Homepage
| Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
|---|---|---|---|---|---|---|---|---|
| I [auth G] | Ribosomal_L11_N | e5kzcG1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
| F [auth D] | Ribosomal_L11_N | e5kzcD1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
| C [auth L] | Ribosomal_L11_N | e5kzcL1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
| B [auth A] | Ribosomal_L11_N | e5kzcA1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
| H [auth F] | Ribosomal_L11_N | e5kzcF1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
| E [auth C] | Ribosomal_L11_N | e5kzcC1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
| G [auth E] | Ribosomal_L11_N | e5kzcE1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
| D [auth B] | Ribosomal_L11_N | e5kzcB1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
| A [auth H] | Ribosomal_L11_N | e5kzcH1 | A: alpha bundles | X: omega toxin-like | H: omega toxin-related | T: omega toxin-related | F: Ribosomal_L11_N | ECOD (develop294) |
Domain Annotation: CATH CATH Database Homepage
| Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
|---|---|---|---|---|---|---|
| I [auth G] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| F [auth D] | 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) |
| G [auth E] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| D [auth B] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| A [auth H] | 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 |
|---|---|---|---|---|---|---|---|---|
| C [auth L], F [auth D], I [auth G] | VRC01 mAb, anti-gp120 CD4-binding site (CD4bs) [HIV-1], broadly | L-KAPPA | Homo sapiens (human) | IGKV3-20*01, IGKJ1*01, IGKC*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202610-0) |
| A [auth H], D [auth B], G [auth E] | VRC01 mAb, anti-gp120 CD4-binding site (CD4bs) [HIV-1], broadly | VH-CH1 | Homo sapiens (human) | IGHV1-18*01, IGHV1-18*04, IGHJ1*01, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202610-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
| Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
|---|---|---|---|---|---|
| C [auth L], F [auth D], I [auth G] | Light Chain | IGKV3 | Kappa | engineered outer domain of gp120 | SAbDab (2026-03-20) |
