Research workbench
Crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida
Analyse Crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JMX
- Type
- protein
- Length
- 909 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine dehydrogenase
- UniProt
- Q8VW85, Q8VW82, P0A182
- Ligands
- HEC, NI
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amine dehydrogenase | protein | 493 | 23% helix, 41% strand | Q8VW85 |
| B | Amine dehydrogenase | protein | 339 | 2% helix, 51% strand | Q8VW82 |
| G | Amine dehydrogenase | protein | 77 | 21% helix, 0% strand | P0A182 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.87 | 0.93 | 66 | HEC |
| 2 | 819 | 0.79 | 0.82 | 72 | empty |
| 3 | 341 | 0.69 | 0.82 | 40 | empty |
| 4 | 242 | 0.62 | 0.81 | 36 | empty |
| 5 | 176 | 0.55 | 0.80 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–G · 2292 Ų buried · 45 hydrogen bonds · protein-protein
- B–G · 1105 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1100 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 disulfide, 1 modified (heme c attachment, disulfide, cofactor).
Compared structures
- 1JMX · crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida · the same entry in another collection · chain A against A, TM-score 1.00
- P0A182 · AlphaFold monomer V2.0 prediction for quinohemoprotein amine dehydrogenase subunit gamma… · a predicted model of the same protein · chain G against A, TM-score 0.96
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 Q8VW85
- Every structure of UniProt Q8VW82
- Every structure of UniProt P0A182
- Elsewhere: RCSB PDB 1JMX · PDBe 1JMX · UniProt Q8VW85 · UniProt Q8VW82 · UniProt P0A182
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