Research workbench
Crystal structure of co-type nitrile hydratase beta-Y215F from pseudomonas putida.
Analyse Crystal structure of co-type nitrile hydratase beta-Y215F from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QZ9
- Type
- protein
- Length
- 1,678 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Co-type nitrile hydratase alpha subunit; Co-type nitrile hydratase beta subunit
- Ligands
- 3CO
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Co-type nitrile hydratase alpha subunit | protein | 201 | 45% helix, 11% strand | — |
| B, D, F, H | Co-type nitrile hydratase beta subunit | protein | 219 | 35% helix, 16% strand | — |
| E, G | Co-type nitrile hydratase alpha subunit | protein | 200 | 43% helix, 11% strand | — |
Ligands and binding sites
- 3CO · Cobalt (III) ion · metal · 4 copies · chains A, C, E, G
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.85 | 0.89 | 94 | GOL |
| 2 | 598 | 0.82 | 0.87 | 72 | empty |
| 3 | 942 | 0.79 | 0.81 | 96 | GOL |
| 4 | 376 | 0.76 | 0.86 | 58 | GOL |
| 5 | 315 | 0.71 | 0.84 | 48 | empty |
Interfaces
9 interfaces between chains.
- C–D · 3971 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 3963 Ų buried · 66 hydrogen bonds · protein-protein
- E–F · 3923 Ų buried · 60 hydrogen bonds · protein-protein
- G–H · 3921 Ų buried · 60 hydrogen bonds · protein-protein
- B–F · 604 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 3QZ9 · Crystal structure of Co-type nitrile hydratase beta-Y215F from Pseudomonas putida. · 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
- Elsewhere: RCSB PDB 3QZ9 · PDBe 3QZ9
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