Research workbench
Structure of the antibody 7B2 that captures HIV-1 virions
Analyse Structure of the antibody 7B2 that captures HIV-1 virions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YDV
- Type
- protein
- Length
- 874 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV GP41 peptide GP41(596-606); HIV antibody 7B2 light CHAIN,IG kappa chain C region; HIV…
- UniProt
- P01834, S6B291
- Ligands
- ACE, NH2
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, Q | HIV GP41 peptide GP41(596-606) | protein | 11 | 0% helix, 27% strand | — |
| L, A | HIV antibody 7B2 light CHAIN,IG kappa chain C region | protein | 206 | 6% helix, 51% strand | P01834 |
| H, B | HIV antibody 7B2 heavy CHAIN,IGG H chain | protein | 220 | 7% helix, 57% strand | S6B291 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains P, H, B, Q
- NH2 · Amino group · ion · 2 copies · chains P, Q, L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.59 | 0.76 | 48 | empty |
| 2 | 385 | 0.57 | 0.75 | 49 | empty |
| 3 | 75 | 0.32 | 0.74 | 16 | empty |
| 4 | 73 | 0.32 | 0.74 | 22 | empty |
| 5 | 85 | 0.30 | 0.72 | 19 | ACE |
Interfaces
10 interfaces between chains.
- L–H · 1730 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1729 Ų buried · 12 hydrogen bonds · protein-protein
- P–H · 513 Ų buried · 17 hydrogen bonds · protein-protein
- Q–B · 508 Ų buried · 16 hydrogen bonds · protein-protein
- P–Q · 334 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
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 P01834
- Every structure of UniProt S6B291
- Elsewhere: RCSB PDB 4YDV · PDBe 4YDV · UniProt P01834 · UniProt S6B291
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