Research workbench
Crystal structure of anti-HIV-1 antibody DH822 bound to GP120 V2 peptide
Analyse Crystal structure of anti-HIV-1 antibody DH822 bound to GP120 V2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VBQ
- Type
- protein
- Length
- 1,780 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH822 heavy chain; DH822 light chain; Envelope glycoprotein GP160
- UniProt
- I2E6B7
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, C | DH822 heavy chain | protein | 223 | 7% helix, 52% strand | — |
| L, B, F, D | DH822 light chain | protein | 208 | 8% helix, 50% strand | — |
| A, E | DH822 heavy chain | protein | 222 | 9% helix, 53% strand | — |
| J, P, I | Envelope glycoprotein GP160 | protein | 15 | 40% helix, 7% strand | I2E6B7 |
| K | Envelope glycoprotein GP160 | protein | 13 | 46% helix, 8% strand | I2E6B7 |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.74 | 0.77 | 85 | empty |
| 2 | 280 | 0.57 | 0.77 | 36 | empty |
| 3 | 266 | 0.54 | 0.76 | 29 | empty |
| 4 | 278 | 0.51 | 0.74 | 30 | empty |
| 5 | 268 | 0.51 | 0.74 | 51 | empty |
Interfaces
22 interfaces between chains.
- B–A · 1700 Ų buried · 15 hydrogen bonds · protein-protein
- F–E · 1693 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 1679 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1642 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 608 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6VBQ · Crystal structure of anti-HIV-1 antibody DH822 bound to gp120 V2 peptide · the same entry in another collection · chain H against H, 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 6VBQ · PDBe 6VBQ · UniProt I2E6B7
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