Research workbench
Interrogating HIV integrase for compounds that bind- a sampl challenge
Analyse Interrogating HIV integrase for compounds that bind- a sampl challenge in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CFB
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.7
- UniProt
- Q76353
- Ligands
- OM3, SO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase (EC 2.7.7.7) | protein | 149 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- OM3 · (R)-(4-carboxy-1,3-benzodioxol-5-yl)methyl-[[2-(cyclohexylmethylcarbamoyl)phenyl]methyl]-methyl-azanium · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.64 | 0.82 | 30 | ACT |
| 2 | 88 | 0.48 | 0.82 | 21 | ACT |
| 3 | 188 | 0.47 | 0.75 | 33 | empty |
| 4 | 122 | 0.47 | 0.78 | 17 | OM3 |
| 5 | 136 | 0.45 | 0.76 | 17 | OM3 |
Interfaces
1 interface between chains.
- A–B · 1503 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4CFB · Interrogating HIV integrase for compounds that bind- a SAMPL challenge · 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 Q76353
- Elsewhere: RCSB PDB 4CFB · PDBe 4CFB · UniProt Q76353
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