MolNFT v1 · #167657 · protein
Structure of HIV-1 integrase with native amino-terminal sequence
6VRG: “Structure of HIV-1 integrase with native amino-terminal sequence”. X-ray diffraction, 3 ligands (ZN, K, PO4), 17 pockets (best druggability 0.64). MolNFT v1 #167657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VRG
- Type
- protein
- Length
- 754 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- UniProt
- F2WR39
- Ligands
- ZN, K, PO4
- Pockets
- 17 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 191 | 52% helix, 16% strand | F2WR39 |
| B | Integrase | protein | 189 | 52% helix, 16% strand | F2WR39 |
| C | Integrase | protein | 186 | 53% helix, 18% strand | F2WR39 |
| D | Integrase | protein | 188 | 54% helix, 17% strand | F2WR39 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.64 | 0.77 | 53 | empty |
| 2 | 152 | 0.54 | 0.81 | 26 | empty |
| 3 | 165 | 0.53 | 0.79 | 26 | empty |
| 4 | 208 | 0.53 | 0.77 | 32 | empty |
| 5 | 161 | 0.53 | 0.79 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1744 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1719 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 546 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 97 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VRG · Structure of HIV-1 integrase with native amino-terminal sequence · 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 F2WR39
- Elsewhere: RCSB PDB 6VRG · PDBe 6VRG · UniProt F2WR39
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