Research workbench
Structure at 1.9 a resolution of a quinohemoprotein alcohol dehydrogenase from pseudomonas putida HK5
Analyse Structure at 1.9 a resolution of a quinohemoprotein alcohol dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KV9
- Type
- protein
- Length
- 664 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II quinohemoprotein alcohol dehydrogenase
- EC
- 1.1.99.-
- UniProt
- Q8GR64
- Ligands
- PQQ, HEC, ACN, CA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II quinohemoprotein alcohol dehydrogenase (EC 1.1.99.-) | protein | 664 | 17% helix, 32% strand | Q8GR64 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · chains A
- HEC · Heme C · ligand · chains A
- ACN · Acetone · ligand · chains A
- CA · Calcium ion · metal · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.78 | 0.97 | 34 | CA, PQQ, ACN |
| 2 | 260 | 0.69 | 0.84 | 42 | HEC |
| 3 | 91 | 0.57 | 0.86 | 28 | empty |
| 4 | 93 | 0.49 | 0.81 | 17 | empty |
| 5 | 104 | 0.42 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 2 cofactor, 1 disulfide (heme c attachment, disulfide).
Compared structures
- 1KV9 · Structure at 1.9 A Resolution of a Quinohemoprotein Alcohol Dehydrogenase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8GR64 · AlphaFold monomer V2.0 prediction for quinohemoprotein alcohol dehydrogenase adh iib… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8GR64
- Elsewhere: RCSB PDB 1KV9 · PDBe 1KV9 · UniProt Q8GR64
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