MolNFT v1 · #126914 · protein
D-2-hydroxyacid dehydrogenases (D2-hdh) from haloferax mediterranei in complex with 2-ketohexanoic acid and NAD+ (1.35 a resolution)
5MH6: “D-2-hydroxyacid dehydrogenases (D2-hdh) from haloferax mediterranei in complex with 2-ketohexanoic acid and…”. X-ray diffraction, 5 ligands (NAD, 7N5, MG), 11 pockets (best druggability 0.78). MolNFT v1 #126914 on GenesisL1: 3D…
- PDB
- 5MH6
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-2-hydroxyacid dehydrogenase
- EC
- 1.1.1.-
- UniProt
- Q2VEQ7
- Ligands
- NAD, 7N5, MG, NA, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-2-hydroxyacid dehydrogenase (EC 1.1.1.-) | protein | 306 | 36% helix, 17% strand | Q2VEQ7 |
| C, D | D-2-hydroxyacid dehydrogenase (EC 1.1.1.-) | protein | 308 | 36% helix, 17% strand | Q2VEQ7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 7N5 · 2-Ketohexanoic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 24 copies · chains A, C, B, D
- NA · Sodium ion · metal · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.78 | 0.87 | 53 | SO4, MG, EDO |
| 2 | 359 | 0.76 | 0.87 | 43 | NAD, 7N5, EDO |
| 3 | 365 | 0.76 | 0.86 | 45 | EDO, NAD, 7N5 |
| 4 | 583 | 0.76 | 0.82 | 64 | EDO, NAD, 7N5 |
| 5 | 614 | 0.75 | 0.81 | 64 | SO4, NAD, 7N5 |
Interfaces
3 interfaces between chains.
- A–B · 2563 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 2547 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5MH6 · D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with… · the same entry in another collection · chain D against D, 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 0.97
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 5MH6 · PDBe 5MH6 · UniProt Q2VEQ7
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