Research workbench
Crystal structure of 5-formly-3-hydroxy-2-methylpyridine 4-carboxylic acid (fhmpc) 5-dehydrogenase, an NAD+ dependent dismutase.
Analyse Crystal structure of 5-formly-3-hydroxy-2-methylpyridine 4-carboxylic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OM8
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxybutyryl-CoA dehydrogenase
- UniProt
- Q988C8
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-hydroxybutyryl-CoA dehydrogenase | protein | 309 | 52% helix, 13% strand | Q988C8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.72 | 0.76 | 119 | GOL |
| 2 | 438 | 0.57 | 0.73 | 59 | empty |
| 3 | 172 | 0.42 | 0.73 | 27 | empty |
| 4 | 111 | 0.40 | 0.75 | 19 | empty |
| 5 | 120 | 0.39 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 415 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4OM8 · Crystal structure of 5-formly-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q988C8 · AlphaFold monomer V2.0 prediction for 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylate… · a predicted model of the same protein · chain B 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 Q988C8
- Elsewhere: RCSB PDB 4OM8 · PDBe 4OM8 · UniProt Q988C8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.