MolNFT v1 · #126913 · protein
D-2-hydroxyacid dehydrogenases (D2-hdh) from haloferax mediterranei in complex with 2-keto-hexanoic acid and NADP+ (1.4 a resolution)
5MH5: “D-2-hydroxyacid dehydrogenases (D2-hdh) from haloferax mediterranei in complex with 2-keto-hexanoic acid and…”. X-ray diffraction, 4 ligands (7N5, NAP, MG), 5 pockets (best druggability 0.76). MolNFT v1 #126913 on GenesisL1: 3D…
- PDB
- 5MH5
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-2-hydroxyacid dehydrogenase
- EC
- 1.1.1.-
- UniProt
- Q2VEQ7
- Ligands
- 7N5, NAP, MG, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-2-hydroxyacid dehydrogenase (EC 1.1.1.-) | protein | 308 | 36% helix, 17% strand | Q2VEQ7 |
Ligands and binding sites
- 7N5 · 2-Ketohexanoic acid · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 21 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.76 | 0.82 | 61 | 7N5, NAP |
| 2 | 612 | 0.76 | 0.82 | 66 | 7N5, NAP |
| 3 | 52 | 0.72 | 0.99 | 20 | empty |
| 4 | 72 | 0.46 | 0.82 | 15 | empty |
| 5 | 77 | 0.39 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2598 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 5MH5 · D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2VEQ7 · AlphaFold monomer V2.0 prediction for D-2-hydroxyacid dehydrogenase (Q2VEQ7) · a predicted model of the same protein · chain B 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 Q2VEQ7
- Elsewhere: RCSB PDB 5MH5 · PDBe 5MH5 · UniProt Q2VEQ7
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