MolNFT v1 · #26446 · protein
Crystal structure of pyrococcus furiosus hef helicase domain
1WP9 · ATP-dependent RNA helicase, putative: “Crystal structure of pyrococcus furiosus hef helicase domain”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.72). MolNFT v1 #26446 on GenesisL1: 3D structure, binding sites…
- PDB
- 1WP9
- Type
- protein
- Length
- 2,850 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase, putative
- EC
- 3.6.1.3
- UniProt
- Q8TZH8
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase, putative (EC 3.6.1.3) | protein | 479 | 54% helix, 13% strand | Q8TZH8 |
| B | ATP-dependent RNA helicase, putative (EC 3.6.1.3) | protein | 477 | 54% helix, 13% strand | Q8TZH8 |
| C, E, F | ATP-dependent RNA helicase, putative (EC 3.6.1.3) | protein | 475 | 55% helix, 13% strand | Q8TZH8 |
| D | ATP-dependent RNA helicase, putative (EC 3.6.1.3) | protein | 469 | 55% helix, 13% strand | Q8TZH8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.72 | 0.80 | 54 | PO4 |
| 2 | 202 | 0.70 | 0.87 | 31 | empty |
| 3 | 156 | 0.68 | 0.88 | 28 | empty |
| 4 | 175 | 0.68 | 0.87 | 31 | empty |
| 5 | 195 | 0.67 | 0.86 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1824 Ų buried · 32 hydrogen bonds · protein-protein
- C–F · 1824 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1813 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1531 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1525 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1WP9 · Crystal structure of Pyrococcus furiosus Hef helicase domain · the same entry in another collection · chain B against B, 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 Q8TZH8
- Elsewhere: RCSB PDB 1WP9 · PDBe 1WP9 · UniProt Q8TZH8
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