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
- 4OVL
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.1
- UniProt
- Q76353
- Ligands
- 1TD, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase (EC 2.7.7.1) | protein | 149 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- 1TD · 3-[(E)-(2-oxidanylidene-1H-indol-3-ylidene)methyl]benzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- ACY · Acetic acid · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains 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 | 243 | 0.65 | 0.83 | 29 | ACY, SO4 |
| 2 | 111 | 0.49 | 0.81 | 24 | ACY |
| 3 | 172 | 0.47 | 0.76 | 31 | empty |
| 4 | 109 | 0.47 | 0.80 | 25 | ACY |
| 5 | 130 | 0.46 | 0.77 | 19 | 1TD |
Interfaces
1 interface between chains.
- A–B · 1505 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4OVL · 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 4OVL · PDBe 4OVL · UniProt Q76353
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