Research workbench
Crystal structure of the wild-type full-length HIV-1 capsid protein
Analyse Crystal structure of the wild-type full-length HIV-1 capsid protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NTE
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 capsid protein
- UniProt
- Q77YG1
- Ligands
- I3M, FE, NA, IOD
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 capsid protein | protein | 221 | 60% helix, 3% strand | Q77YG1 |
| B | HIV-1 capsid protein | protein | 216 | 62% helix, 3% strand | Q77YG1 |
Ligands and binding sites
- I3M · Tri-iodode Anion · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 23 copies · chains A, B
- NA · Sodium ion · metal · chains B
- IOD · Iodide ion · ion · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.74 | 0.96 | 16 | I3M |
| 2 | 61 | 0.69 | 0.96 | 17 | I3M |
| 3 | 303 | 0.57 | 0.76 | 36 | empty |
| 4 | 84 | 0.43 | 0.80 | 23 | empty |
| 5 | 65 | 0.31 | 0.75 | 15 | IOD, FE |
Interfaces
1 interface between chains.
- A–B · 1322 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3NTE · Crystal Structure of the Wild-type Full-Length HIV-1 Capsid Protein · 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 Q77YG1
- Elsewhere: RCSB PDB 3NTE · PDBe 3NTE · UniProt Q77YG1
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