Research workbench
Crystal structure of the stabilized inner domain of clade A/E HIV-1 GP120 from E. COLI in complex with the antibody A32.
Analyse Crystal structure of the stabilized inner domain of clade A/E HIV-1 GP120 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YC2
- Type
- protein
- Length
- 1,127 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The stabilized inner domain of clade A/E HIV-1 GP120 from E. COLI; The antibody A32 Fab…
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | The stabilized inner domain of clade A/E HIV-1 GP120 from E. COLI | protein | 133 | 23% helix, 30% strand | — |
| H | The antibody A32 Fab heavy chain. | protein | 220 | 7% helix, 52% strand | — |
| L, C | The antibody A32 Fab light chain. | protein | 210 | 7% helix, 50% strand | — |
| A | The stabilized inner domain of clade A/E HIV-1 GP120 from E. COLI | protein | 131 | 24% helix, 18% strand | — |
| B | The antibody A32 Fab heavy chain. | protein | 223 | 5% helix, 53% strand | — |
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.74 | 0.79 | 88 | empty |
| 2 | 506 | 0.66 | 0.78 | 72 | empty |
| 3 | 700 | 0.66 | 0.75 | 54 | empty |
| 4 | 168 | 0.64 | 0.85 | 22 | empty |
| 5 | 582 | 0.63 | 0.74 | 56 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1931 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1917 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 648 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 642 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 350 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4YC2 · Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 from E. coli in… · 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 4YC2 · PDBe 4YC2
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