Research workbench
Site directed mutagenesis of key residues involved in the catalytic mechanism of cyanase
Analyse Site directed mutagenesis of key residues involved in the catalytic mechanism… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IVG
- Type
- protein
- Length
- 1,560 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyanate lyase
- EC
- 4.2.1.104
- UniProt
- P00816
- Ligands
- SO4, CL, AZI
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cyanate lyase (EC 4.2.1.104) | protein | 156 | 46% helix, 20% strand | P00816 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 29 copies · chains A, J, B, D, E, F, C, G, H, I
- CL · Chloride ion · ion · 20 copies · chains A, D, B, F, C, H, E, G, J, I
- AZI · Azide ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.81 | 0.89 | 84 | empty |
| 2 | 284 | 0.76 | 0.89 | 62 | empty |
| 3 | 270 | 0.76 | 0.89 | 59 | empty |
| 4 | 455 | 0.75 | 0.84 | 51 | SO4 |
| 5 | 139 | 0.67 | 0.88 | 29 | empty |
Interfaces
25 interfaces between chains.
- I–J · 3484 Ų buried · 54 hydrogen bonds · protein-protein
- E–G · 3477 Ų buried · 54 hydrogen bonds · protein-protein
- B–F · 3476 Ų buried · 57 hydrogen bonds · protein-protein
- A–D · 3474 Ų buried · 55 hydrogen bonds · protein-protein
- C–H · 3469 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 2IVG · Site directed mutagenesis of key residues involved in the catalytic mechanism of cyanase · 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 I 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 2IVG · PDBe 2IVG · UniProt P00816
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