MolNFT v1 · #69888 · protein
Structure of HIV-1 integrase core domain in complex with sucrose
3L3V · Pol polyprotein: “Structure of HIV-1 integrase core domain in complex with sucrose”. X-ray diffraction, 4 ligands (GLC, FRU, CD), 5 pockets (best druggability 0.57). MolNFT v1 #69888 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3L3V
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- Q72498
- Ligands
- GLC, FRU, CD, SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 144 | 47% helix, 24% strand | Q72498 |
| B | Pol polyprotein | protein | 140 | 50% helix, 22% strand | Q72498 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 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 | 266 | 0.57 | 0.77 | 31 | GLC, FRU |
| 2 | 113 | 0.45 | 0.78 | 23 | empty |
| 3 | 65 | 0.39 | 0.79 | 21 | empty |
| 4 | 75 | 0.38 | 0.77 | 17 | empty |
| 5 | 55 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1513 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3L3V · Structure of HIV-1 integrase core domain in complex with sucrose · 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 Q72498
- Elsewhere: RCSB PDB 3L3V · PDBe 3L3V · UniProt Q72498
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