Research workbench
Structure of the native full-length HIV-1 capsid protein in helical assembly (-13,8)
Analyse Structure of the native full-length HIV-1 capsid protein in helical assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SKK
- Type
- protein
- Length
- 1,320 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q71B32
- Pockets
- 19 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Capsid protein | protein | 220 | 59% helix, 3% strand | Q71B32 |
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.75 | 0.79 | 108 | empty |
| 2 | 841 | 0.75 | 0.79 | 86 | empty |
| 3 | 1045 | 0.73 | 0.76 | 100 | empty |
| 4 | 514 | 0.68 | 0.79 | 64 | empty |
| 5 | 593 | 0.68 | 0.77 | 58 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1160 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 1154 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1092 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1079 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1077 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6SKK · Structure of the native full-length HIV-1 capsid protein in helical assembly (-13,8) · 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
- Every structure of UniProt Q71B32
- Elsewhere: RCSB PDB 6SKK · PDBe 6SKK · UniProt Q71B32
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