Research workbench
Crystal structure of nitrile hydratase from pseudonocardia thermophila bound to butaneboronic acid via crystal soaking
Analyse Crystal structure of nitrile hydratase from pseudonocardia thermophila bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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