Research workbench
Crystal structure of co-type nitrile hydratase from pseudomonas putida.
Analyse Crystal structure of co-type nitrile hydratase from pseudomonas putida. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QXE
- 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
- 14 · best druggability 0.84
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 | 44% 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 | 44% helix, 11% strand | — |
Ligands and binding sites
- 3CO · Cobalt (III) ion · metal · 4 copies · chains A, C, E, G
- GOL · Glycerol · additive · 8 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
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.84 | 0.88 | 90 | GOL |
| 2 | 611 | 0.82 | 0.87 | 76 | empty |
| 3 | 822 | 0.76 | 0.80 | 80 | empty |
| 4 | 316 | 0.73 | 0.85 | 47 | empty |
| 5 | 330 | 0.73 | 0.85 | 49 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3939 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 3928 Ų buried · 63 hydrogen bonds · protein-protein
- G–H · 3924 Ų buried · 60 hydrogen bonds · protein-protein
- E–F · 3902 Ų buried · 59 hydrogen bonds · protein-protein
- B–F · 587 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 3QXE · Crystal Structure of Co-type Nitrile Hydratase 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 3QXE · PDBe 3QXE
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.