Research workbench
WOR5 from Pyrococcus furiosus, as crystallized
Analyse WOR5 from Pyrococcus furiosus, as crystallized in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X1O
- Type
- protein
- Length
- 1,579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.094
- Source
- Pyrococcus furiosus COM1
- Molecule
- Formaldehyde:ferredoxin oxidoreductase wor5; Oxidoreductase, Fe-S subunit
- UniProt
- I6V2C3, I6U881
- Ligands
- SF4, UKM, PTE, MG, PO4, CL
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.094 · 3 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formaldehyde:ferredoxin oxidoreductase wor5 | protein | 623 | 44% helix, 13% strand | I6V2C3 |
| B, D | Oxidoreductase, Fe-S subunit | protein | 166 | 36% helix, 17% strand | I6U881 |
| C | Formaldehyde:ferredoxin oxidoreductase wor5 | protein | 624 | 46% helix, 13% strand | I6V2C3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 10 copies · chains A, B, C, D
- UKM · (1R)-1-hydroxybutane-1-sulfonic acid · ligand · 2 copies · chains A, C
- PTE · Tungstopterin cofactor · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, D, C
- CL · Chloride ion · ion · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.86 | 0.92 | 53 | empty |
| 2 | 861 | 0.80 | 0.82 | 76 | UKM, PTE, SF4, MG |
| 3 | 945 | 0.80 | 0.81 | 87 | UKM, PTE, SF4, MG |
| 4 | 90 | 0.62 | 0.89 | 15 | empty |
| 5 | 366 | 0.59 | 0.76 | 38 | PO4 |
Interfaces
6 interfaces between chains.
- B–C · 2157 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 2124 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1103 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1070 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6X1O · WOR5 from pyrococcus furiosus, as crystallized · 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 I6V2C3
- Every structure of UniProt I6U881
- Elsewhere: RCSB PDB 6X1O · PDBe 6X1O · UniProt I6V2C3 · UniProt I6U881
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