MolNFT v1 · #12244 · protein
Crystal structure of quinohemoprotein alcohol dehydrogenase from comamonas testosteroni
1KB0: “Crystal structure of quinohemoprotein alcohol dehydrogenase from comamonas testosteroni”. X-ray diffraction, 4 ligands (HEC, TFB, PQQ), 4 pockets (best druggability 0.75). MolNFT v1 #12244 on GenesisL1: 3D structure, binding sites…
- PDB
- 1KB0
- Type
- protein
- Length
- 670 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quinohemoprotein alcohol dehydrogenase
- EC
- 1.1.99.-
- UniProt
- Q46444
- Ligands
- HEC, TFB, PQQ, CA
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quinohemoprotein alcohol dehydrogenase (EC 1.1.99.-) | protein | 670 | 17% helix, 31% strand | Q46444 |
Ligands and binding sites
- HEC · Heme C · ligand · chains A
- TFB · Tetrahydrofuran-2-carboxylic acid · ligand · chains A
- PQQ · Pyrroloquinoline quinone · ligand · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.75 | 0.84 | 67 | CA, TFB, PQQ, GOL |
| 2 | 404 | 0.70 | 0.82 | 71 | HEC, GOL |
| 3 | 177 | 0.50 | 0.77 | 19 | empty |
| 4 | 84 | 0.39 | 0.77 | 23 | empty |
Modifications
Observed in the structure: 2 cofactor, 1 disulfide, 1 modified (heme c attachment, disulfide, nonstandard).
Compared structures
- 1KB0 · Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroni · the same entry in another collection · chain A against A, TM-score 1.00
- Q46444 · AlphaFold monomer V2.0 prediction for quinohemoprotein alcohol dehydrogenase (Q46444) · a predicted model of the same protein · 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 Q46444
- Elsewhere: RCSB PDB 1KB0 · PDBe 1KB0 · UniProt Q46444
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