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Structural and kinetic properties of a beta-hydroxyacid dehydrogenase involved in nicotinate fermentation
Analyse Structural and kinetic properties of a beta-hydroxyacid dehydrogenase involved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CKY
- Type
- protein
- Length
- 1,129 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxymethyl glutarate dehydrogenase
- EC
- 1.1.1.291
- UniProt
- Q0QLF5
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-hydroxymethyl glutarate dehydrogenase (EC 1.1.1.291) | protein | 297 | 56% helix, 14% strand | Q0QLF5 |
| B | 2-hydroxymethyl glutarate dehydrogenase (EC 1.1.1.291) | protein | 296 | 56% helix, 15% strand | Q0QLF5 |
| C | 2-hydroxymethyl glutarate dehydrogenase (EC 1.1.1.291) | protein | 296 | 56% helix, 15% strand | Q0QLF5 |
| D | 2-hydroxymethyl glutarate dehydrogenase (EC 1.1.1.291) | protein | 240 | 59% helix, 13% strand | Q0QLF5 |
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.76 | 0.99 | 20 | empty |
| 2 | 59 | 0.75 | 0.99 | 18 | empty |
| 3 | 463 | 0.66 | 0.78 | 57 | empty |
| 4 | 446 | 0.65 | 0.78 | 41 | empty |
| 5 | 507 | 0.64 | 0.76 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2501 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2477 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 731 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 689 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 333 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3CKY · Structural and Kinetic Properties of a beta-hydroxyacid dehydrogenase involved in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q0QLF5 · AlphaFold monomer V2.0 prediction for 2-(HYDROXYMETHYL)GLUTARATE dehydrogenase (Q0QLF5) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q0QLF5
- Elsewhere: RCSB PDB 3CKY · PDBe 3CKY · UniProt Q0QLF5
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