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Crystal structure of the stabilized inner domain of clade A/E HIV-1 GP120 in complex with the adcc mediating anti-HIV-1 antibody A32
Analyse Crystal structure of the stabilized inner domain of clade A/E HIV-1 GP120 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YBL
- Type
- protein
- Length
- 1,111 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stabilized inner domain of clade A/E GP120; A32 antibody Fab heavy chain; A32 antibody…
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Stabilized inner domain of clade A/E GP120 | protein | 126 | 25% helix, 30% strand | — |
| H | A32 antibody Fab heavy chain | protein | 214 | 4% helix, 55% strand | — |
| L, C | A32 antibody light chain | protein | 210 | 7% helix, 51% strand | — |
| A | Stabilized inner domain of clade A/E GP120 | protein | 129 | 26% helix, 23% strand | — |
| B | A32 antibody Fab heavy chain | protein | 222 | 7% helix, 51% strand | — |
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.78 | 0.82 | 90 | empty |
| 2 | 718 | 0.66 | 0.75 | 59 | empty |
| 3 | 80 | 0.65 | 0.91 | 19 | empty |
| 4 | 631 | 0.64 | 0.75 | 55 | empty |
| 5 | 134 | 0.63 | 0.86 | 19 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1917 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1910 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 623 Ų buried · 8 hydrogen bonds · protein-protein
- H–A · 387 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4YBL · Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with… · 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 4YBL · PDBe 4YBL
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