Research workbench
Crystal structure of thermostable bacillus sp. RAPC8 nitrile hydratase
Analyse Crystal structure of thermostable bacillus sp. RAPC8 nitrile hydratase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DPP
- 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
- Q84FS5, Q84FS6
- Ligands
- CO
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrile hydratase alpha subunit (EC 4.2.1.84) | protein | 202 | 45% helix, 11% strand | Q84FS5 |
| B | Nitrile hydratase beta subunit (EC 4.2.1.84) | protein | 227 | 38% helix, 16% strand | Q84FS6 |
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
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.48 | 0.82 | 26 | empty |
| 2 | 111 | 0.41 | 0.76 | 25 | empty |
| 3 | 115 | 0.40 | 0.76 | 19 | empty |
| 4 | 88 | 0.34 | 0.74 | 19 | empty |
| 5 | 53 | 0.26 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4644 Ų buried · 74 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2DPP · Crystal structure of thermostable Bacillus sp. RAPc8 nitrile hydratase · the same entry in another collection · chain A against A, TM-score 1.00
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 Q84FS5
- Every structure of UniProt Q84FS6
- Elsewhere: RCSB PDB 2DPP · PDBe 2DPP · UniProt Q84FS5 · UniProt Q84FS6
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