Research workbench
Structure of cyanase with the di-anion oxalate bound at the enzyme active site
Analyse Structure of cyanase with the di-anion oxalate bound at the enzyme active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DWK
- Type
- protein
- Length
- 1,560 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyanate hydratase
- EC
- 4.2.1.104
- UniProt
- P00816
- Ligands
- OXL, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cyanate hydratase (EC 4.2.1.104) | protein | 156 | 47% helix, 20% strand | P00816 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 5 copies · chains A, B, D, F, C, H, I, J, E, G
- SO4 · Sulfate ion · ion · 23 copies · chains A, C, I, J, B, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.77 | 0.89 | 57 | empty |
| 2 | 535 | 0.77 | 0.84 | 54 | SO4 |
| 3 | 188 | 0.73 | 0.90 | 36 | empty |
| 4 | 147 | 0.72 | 0.91 | 35 | empty |
| 5 | 153 | 0.71 | 0.90 | 36 | empty |
Interfaces
25 interfaces between chains.
- B–F · 3464 Ų buried · 54 hydrogen bonds · protein-protein
- I–J · 3457 Ų buried · 53 hydrogen bonds · protein-protein
- C–H · 3451 Ų buried · 53 hydrogen bonds · protein-protein
- E–G · 3449 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 3441 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 1DWK · Structure of cyanase with the di-anion oxalate bound at the enzyme active site · the same entry in another collection · chain J against J, TM-score 1.00
- P00816 · AlphaFold monomer V2.0 prediction for cyanate hydratase (P00816) · a predicted model of the same protein · chain F 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 P00816
- Elsewhere: RCSB PDB 1DWK · PDBe 1DWK · UniProt P00816
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