MolNFT v1 · #11447 · protein
Crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida with inhibitor
1JMZ: “Crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida with inhibitor”. X-ray diffraction, 3 ligands (HEC, PND, NI), 8 pockets (best druggability 0.87). MolNFT v1 #11447 on GenesisL1: 3D structure…
- PDB
- 1JMZ
- 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, PND, 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
- HEC · Heme C · ligand · 2 copies · chains A, G, B
- PND · P-nitrophenylhydrazine · ligand · chains B, G
- NI · Nickel (II) ion · metal · chains A
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 | 530 | 0.87 | 0.93 | 66 | HEC |
| 2 | 848 | 0.79 | 0.82 | 69 | empty |
| 3 | 335 | 0.70 | 0.83 | 37 | empty |
| 4 | 247 | 0.60 | 0.80 | 30 | empty |
| 5 | 173 | 0.56 | 0.81 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–G · 2290 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1113 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 1104 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 covalent, 1 disulfide, 1 modified (heme c attachment, covalent ligand, disulfide, cofactor).
Compared structures
- 1JMZ · crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida with… · 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 1JMZ · PDBe 1JMZ · UniProt Q8VW85 · UniProt Q8VW82 · UniProt P0A182
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