MolNFT v1 · #102076 · protein
Crystal structure of nitrile hydratase from pseudonocardia thermophila : a reference structure to boronic acid inhibition of nitrile hydratase
4OB3 · Cobalt-containing nitrile hydratase subunit alpha: “Crystal structure of nitrile hydratase from pseudonocardia thermophila : a reference structure to boronic…”. X-ray diffraction, 1 ligand (CO), 7 pockets (best druggability 0.73).…
- PDB
- 4OB3
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cobalt-containing nitrile hydratase subunit alpha; Cobalt-containing nitrile hydratase…
- EC
- 4.2.1.84
- UniProt
- Q7SID2, Q7SID3
- Ligands
- CO
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cobalt-containing nitrile hydratase subunit alpha (EC 4.2.1.84) | protein | 204 | 48% helix, 11% strand | Q7SID2 |
| B | Cobalt-containing nitrile hydratase subunit beta (EC 4.2.1.84) | protein | 229 | 38% helix, 17% strand | Q7SID3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.73 | 0.89 | 53 | empty |
| 2 | 226 | 0.52 | 0.77 | 27 | empty |
| 3 | 132 | 0.45 | 0.77 | 16 | empty |
| 4 | 64 | 0.32 | 0.75 | 17 | empty |
| 5 | 60 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4320 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4OB3 · Crystal Structure of Nitrile Hydratase from Pseudonocardia thermophila : A Reference… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7SID2 · AlphaFold monomer V2.0 prediction for cobalt-containing nitrile hydratase subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 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 Q7SID2
- Every structure of UniProt Q7SID3
- Elsewhere: RCSB PDB 4OB3 · PDBe 4OB3 · UniProt Q7SID2 · UniProt Q7SID3
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