MolNFT v1 · #12114 · protein
Crystal structure of a two-domain fragment of HIV-1 integrase
1K6Y: “Crystal structure of a two-domain fragment of HIV-1 integrase”. X-ray diffraction, 3 ligands (ZN, K, PO4), 20 pockets (best druggability 0.57). MolNFT v1 #12114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K6Y
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.49
- UniProt
- Q72498
- Ligands
- ZN, K, PO4
- Pockets
- 20 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.49) | protein | 192 | 52% helix, 16% strand | Q72498 |
| B | Integrase (EC 2.7.7.49) | protein | 194 | 54% helix, 18% strand | Q72498 |
| C | Integrase (EC 2.7.7.49) | protein | 191 | 53% helix, 17% strand | Q72498 |
| D | Integrase (EC 2.7.7.49) | protein | 189 | 52% helix, 16% strand | Q72498 |
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
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.57 | 0.81 | 30 | empty |
| 2 | 116 | 0.55 | 0.83 | 22 | empty |
| 3 | 222 | 0.54 | 0.78 | 27 | empty |
| 4 | 219 | 0.54 | 0.78 | 32 | empty |
| 5 | 156 | 0.53 | 0.80 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2068 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2011 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1111 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 119 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 115 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1K6Y · Crystal Structure of a Two-Domain Fragment of HIV-1 Integrase · 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 Q72498
- Elsewhere: RCSB PDB 1K6Y · PDBe 1K6Y · UniProt Q72498
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