Research workbench
Crystal structure of co-type nitrile hydratase mutant from pseudomonas thermophila - A129R
Analyse Crystal structure of co-type nitrile hydratase mutant from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W8M
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrile hydratase; Cobalt-containing nitrile hydratase subunit beta
- EC
- 4.2.1.84
- UniProt
- A0A1M6Q338, Q7SID3
- Ligands
- CO
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrile hydratase (EC 4.2.1.84) | protein | 203 | 49% helix, 11% strand | A0A1M6Q338 |
| B | Cobalt-containing nitrile hydratase subunit beta (EC 4.2.1.84) | protein | 228 | 39% helix, 17% strand | Q7SID3 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.76 | 0.97 | 25 | empty |
| 2 | 329 | 0.58 | 0.77 | 36 | empty |
| 3 | 86 | 0.55 | 0.85 | 28 | empty |
| 4 | 80 | 0.44 | 0.81 | 24 | empty |
| 5 | 81 | 0.34 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4432 Ų buried · 72 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7W8M · Crystal structure of Co-type nitrile hydratase mutant from Pseudomonas thermophila - A129R · the same entry in another collection · chain A against A, TM-score 1.00
- Q7SID3 · AlphaFold monomer V2.0 prediction for cobalt-containing nitrile hydratase subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A0A1M6Q338
- Every structure of UniProt Q7SID3
- Elsewhere: RCSB PDB 7W8M · PDBe 7W8M · UniProt A0A1M6Q338 · UniProt Q7SID3
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