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
- 6VLH
- Type
- protein
- Length
- 273 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.49
- UniProt
- F2WR39
- Ligands
- R2A, SO4, IOD
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.49) | protein | 137 | 48% helix, 21% strand | F2WR39 |
| B | Integrase (EC 2.7.7.49) | protein | 136 | 48% helix, 24% strand | F2WR39 |
Ligands and binding sites
- R2A · (2-{[3-(4-{2-[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzene-1-carbonyl) amino]ethyl}piperazine-1-carbonyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 9 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.65 | 0.80 | 54 | R2A |
| 2 | 89 | 0.43 | 0.79 | 22 | empty |
| 3 | 104 | 0.40 | 0.76 | 20 | SO4 |
| 4 | 56 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1426 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6VLH · 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 6VLH · PDBe 6VLH · UniProt F2WR39
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