Research workbench
Fab structure of anti-HIV GP120 V2 mab 2158
Analyse Fab structure of anti-HIV GP120 V2 mab 2158 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OAW
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab fragment of anti-HIV1 GP120 V2 mab 2158; Heavy chain of Fab fragment…
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Light chain of Fab fragment of anti-HIV1 GP120 V2 mab 2158 | protein | 214 | 5% helix, 49% strand | — |
| B, D | Heavy chain of Fab fragment of anti-HIV1 GP120 V2 mab 2158 | protein | 236 | 6% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.55 | 0.79 | 31 | empty |
| 2 | 125 | 0.45 | 0.77 | 25 | GOL |
| 3 | 104 | 0.45 | 0.79 | 18 | empty |
| 4 | 109 | 0.43 | 0.77 | 19 | empty |
| 5 | 176 | 0.42 | 0.74 | 30 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2140 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2137 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 585 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4OAW · Fab structure of anti-HIV gp120 V2 mAb 2158 · the same entry in another collection · chain A against A, 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 4OAW · PDBe 4OAW
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