Research workbench
Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site
Analyse Structure of cyanase reveals that a novel dimeric and decameric arrangement of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DW9
- Type
- protein
- Length
- 1,560 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyanate lyase
- EC
- 4.3.99.1
- UniProt
- P00816
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cyanate lyase (EC 4.3.99.1) | protein | 156 | 45% helix, 20% strand | P00816 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 23 copies · chains A, B, D, E, F, C, J, G, H, I
- CL · Chloride ion · ion · 10 copies · chains A, D, I, J, B, F, C, H, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.78 | 0.89 | 56 | empty |
| 2 | 302 | 0.77 | 0.89 | 60 | empty |
| 3 | 532 | 0.76 | 0.84 | 55 | SO4 |
| 4 | 191 | 0.73 | 0.90 | 36 | empty |
| 5 | 158 | 0.72 | 0.90 | 35 | empty |
Interfaces
25 interfaces between chains.
- B–F · 3469 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 3462 Ų buried · 53 hydrogen bonds · protein-protein
- E–G · 3457 Ų buried · 53 hydrogen bonds · protein-protein
- C–H · 3453 Ų buried · 51 hydrogen bonds · protein-protein
- I–J · 3442 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 1DW9 · Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits… · 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 1DW9 · PDBe 1DW9 · UniProt P00816
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