MolNFT v1 · #102075 · protein
Crystal structure of nitrile hydratase from pseudonocardia thermophila bound to butaneboronic acid via crystal soaking
4OB2 · Cobalt-containing nitrile hydratase subunit alpha: “Crystal structure of nitrile hydratase from pseudonocardia thermophila bound to butaneboronic acid via…”. X-ray diffraction, 2 ligands (BUB, CO), 7 pockets (best druggability…
- PDB
- 4OB2
- Type
- protein
- Length
- 431 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
- BUB, CO
- Pockets
- 7 · best druggability 0.72
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 | 203 | 48% helix, 12% strand | Q7SID2 |
| B | Cobalt-containing nitrile hydratase subunit beta (EC 4.2.1.84) | protein | 228 | 38% helix, 15% strand | Q7SID3 |
Ligands and binding sites
- BUB · 1-butane boronic acid · ligand · chains A, B
- CO · Cobalt (II) ion · metal · chains A
- MOH · Methanol · additive · 24 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.72 | 0.89 | 47 | BUB, GOL |
| 2 | 183 | 0.49 | 0.77 | 26 | MOH |
| 3 | 143 | 0.46 | 0.77 | 17 | empty |
| 4 | 88 | 0.45 | 0.81 | 23 | GOL |
| 5 | 60 | 0.32 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4313 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, oxidation).
Compared structures
- 4OB2 · Crystal Structure of Nitrile Hydratase from Pseudonocardia thermophila bound to… · 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 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 0.99
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 4OB2 · PDBe 4OB2 · UniProt Q7SID2 · UniProt Q7SID3
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