Research workbench
Crystal structure of co-type nitrile hydratase complexed with N-butyric acid
Analyse Crystal structure of co-type nitrile hydratase complexed with N-butyric acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UGP
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrile hydratase alpha subunit; Nitrile hydratase beta subunit
- EC
- 4.2.1.84
- UniProt
- Q7SID2, Q7SID3
- Ligands
- BUA, CO
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrile hydratase alpha subunit (EC 4.2.1.84) | protein | 203 | 48% helix, 12% strand | Q7SID2 |
| B | Nitrile hydratase beta subunit (EC 4.2.1.84) | protein | 226 | 39% helix, 16% 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 24 | BUA |
| 2 | 99 | 0.54 | 0.84 | 26 | empty |
| 3 | 204 | 0.51 | 0.77 | 29 | empty |
| 4 | 120 | 0.44 | 0.77 | 16 | empty |
| 5 | 56 | 0.36 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4394 Ų buried · 72 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1UGP · Crystal structure of Co-type nitrile hydratase complexed with n-butyric acid · 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 1UGP · PDBe 1UGP · UniProt Q7SID2 · UniProt Q7SID3
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