MolNFT v1 · #9496 · protein
Crystal structure of MJ0490 gene product, the family of LACTATE/MALATE dehydrogenase
1HYG · L-LACTATE/MALATE dehydrogenase: “Crystal structure of MJ0490 gene product, the family of LACTATE/MALATE dehydrogenase”. X-ray diffraction, 1 ligand (NAP), 6 pockets (best druggability 0.75). MolNFT v1 #9496 on GenesisL1: 3D…
- PDB
- 1HYG
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-LACTATE/MALATE dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q60176
- Ligands
- NAP
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-LACTATE/MALATE dehydrogenase (EC 1.1.1.27) | protein | 313 | 47% helix, 19% strand | Q60176 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.75 | 0.82 | 62 | NAP |
| 2 | 599 | 0.74 | 0.81 | 58 | NAP |
| 3 | 501 | 0.66 | 0.78 | 73 | empty |
| 4 | 267 | 0.58 | 0.78 | 28 | empty |
| 5 | 281 | 0.56 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1661 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1HYG · Crystal structure of MJ0490 gene product, the family of lactate/malate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- Q60176 · AlphaFold monomer V2.0 prediction for L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))… · a predicted model of the same protein · chain A 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 Q60176
- Elsewhere: RCSB PDB 1HYG · PDBe 1HYG · UniProt Q60176
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