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
- 4CGG
- Type
- protein
- Length
- 299 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
- K5Q, SO4, CL
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.7) | protein | 150 | 55% helix, 21% strand | Q76353 |
| B | Integrase (EC 2.7.7.7) | protein | 149 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- K5Q · (2S)-6-[(E)-[(2E)-2-hydroxyimino-3H-inden-1-ylidene]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.67 | 0.81 | 41 | SO4, K5Q |
| 2 | 123 | 0.50 | 0.80 | 26 | EDO |
| 3 | 113 | 0.48 | 0.80 | 25 | EDO |
| 4 | 170 | 0.46 | 0.75 | 37 | empty |
| 5 | 134 | 0.45 | 0.76 | 17 | K5Q |
Interfaces
1 interface between chains.
- A–B · 1464 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4CGG · 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 4CGG · PDBe 4CGG · UniProt Q76353
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