MolNFT v1 · #96144 · protein
Crystal structure of antibody VRC06 in complex with HIV-1 GP120 core
4JB9 · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of antibody VRC06 in complex with HIV-1 GP120 core”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.73). MolNFT v1 #96144 on GenesisL1: 3D structure, binding…
- PDB
- 4JB9
- Type
- protein
- Length
- 778 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; Antibody VRC06 heavy chain; Antibody VRC06 light chain
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 344 | 17% helix, 35% strand | — |
| H | Antibody VRC06 heavy chain | protein | 225 | 3% helix, 48% strand | — |
| L | Antibody VRC06 light chain | protein | 209 | 5% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.73 | 0.81 | 46 | empty |
| 2 | 604 | 0.62 | 0.74 | 63 | empty |
| 3 | 242 | 0.53 | 0.76 | 35 | empty |
| 4 | 61 | 0.53 | 0.87 | 17 | NAG |
| 5 | 68 | 0.50 | 0.85 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1870 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1152 Ų buried · 20 hydrogen bonds · protein-protein
- G–L · 294 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4JB9 · Crystal structure of antibody VRC06 in complex with HIV-1 gp120 core · the same entry in another collection · chain G against G, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4JB9 · PDBe 4JB9
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