MolNFT v1 · #40530 · protein
Site directed mutagenesis of key residues involved in the catalytic mechanism of cyanase
2IVG · Cyanate lyase: “Site directed mutagenesis of key residues involved in the catalytic mechanism of cyanase”. X-ray diffraction, 3 ligands (SO4, CL, AZI), 20 pockets (best druggability 0.81). MolNFT v1 #40530 on GenesisL1: 3D…
- 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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