MolNFT v1 · #95245 · protein + DNA
Pfv intasome with inhibitor mb-76
4IKF · Integrase: “Pfv intasome with inhibitor mb-76”. X-ray diffraction, 5 ligands (M76, MG, ZN), 11 pockets (best druggability 0.68). MolNFT v1 #95245 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4IKF
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP *a)-3'…
- EC
- 2.7.7.-
- UniProt
- P14350
- Ligands
- M76, MG, ZN, SO4, NH4
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.-) | protein | 368 | 32% helix, 19% strand | P14350 |
| B | Integrase (EC 2.7.7.-) | protein | 184 | 33% helix, 16% strand | P14350 |
| C | 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP *a)-3' | dna | 19 | — | — |
| D | 5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)- 3' | dna | 17 | — | — |
Ligands and binding sites
- M76 · N-(4-fluorobenzyl)-2,3-dihydroxy-1-oxo-1,2-dihydroisoquinoline-4-carboxamide · ligand · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, B
- HEZ · Hexane-1,6-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.68 | 0.81 | 48 | empty |
| 2 | 552 | 0.67 | 0.77 | 40 | HEZ |
| 3 | 71 | 0.63 | 0.92 | 19 | empty |
| 4 | 76 | 0.49 | 0.84 | 18 | empty |
| 5 | 175 | 0.49 | 0.76 | 24 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1454 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1088 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–D · 713 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–D · 326 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 4IKF · PFV intasome with inhibitor MB-76 · 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 P14350
- Elsewhere: RCSB PDB 4IKF · PDBe 4IKF · UniProt P14350
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