MolNFT v1 · #167133 · protein
Crystal structure of anti-HIV-1 antibody DH813 bound to GP120 V2 peptide
6VBO · DH813 light chain: “Crystal structure of anti-HIV-1 antibody DH813 bound to GP120 V2 peptide”. X-ray diffraction, 6 pockets (best druggability 0.71). MolNFT v1 #167133 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VBO
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH813 light chain; DH813 heavy chain; Envelope glycoprotein GP160
- UniProt
- I2E6B7
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | DH813 light chain | protein | 218 | 5% helix, 50% strand | — |
| H | DH813 heavy chain | protein | 210 | 9% helix, 52% strand | — |
| C | Envelope glycoprotein GP160 | protein | 16 | 31% helix, 0% strand | I2E6B7 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.98 | 25 | empty |
| 2 | 348 | 0.54 | 0.74 | 42 | empty |
| 3 | 51 | 0.49 | 0.87 | 21 | empty |
| 4 | 57 | 0.29 | 0.74 | 14 | empty |
| 5 | 52 | 0.29 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1577 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 700 Ų buried · 7 hydrogen bonds · protein-protein
- L–C · 294 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6VBO · Crystal structure of anti-HIV-1 antibody DH813 bound to gp120 V2 peptide · the same entry in another collection · chain L against L, 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
- Every structure of UniProt I2E6B7
- Elsewhere: RCSB PDB 6VBO · PDBe 6VBO · UniProt I2E6B7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.