Research workbench
HIV integrase core domain (in) in complex with dimer-spanning ligand
Analyse HIV integrase core domain (in) in complex with dimer-spanning ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VKA
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.-
- UniProt
- F2WR39
- Ligands
- QZV, SO4, IOD
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.-) | protein | 141 | 48% helix, 22% strand | F2WR39 |
| B | Integrase (EC 2.7.7.-) | protein | 143 | 48% helix, 22% strand | F2WR39 |
Ligands and binding sites
- QZV · 2,2'-{ethane-1,2-diylbis[oxyethane-2,1-diylcarbamoyl-4, 1-phenyleneethyne-2,1-diyl(5-methyl-1-benzofuran-2,3-diyl)]}diacetic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- IOD · Iodide ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.62 | 0.83 | 33 | SO4 |
| 2 | 116 | 0.47 | 0.79 | 18 | empty |
| 3 | 95 | 0.45 | 0.79 | 17 | empty |
| 4 | 113 | 0.44 | 0.77 | 21 | empty |
| 5 | 90 | 0.40 | 0.77 | 22 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1511 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6VKA · HIV Integrase Core domain (IN) in complex with dimer-spanning ligand · 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 6VKA · PDBe 6VKA · UniProt F2WR39
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