MolNFT v1 · #126793 · protein
Crystal structure of ternary complex of porcine cytoplasmic malate dehydrogenase alpha-ketomalonate and tnad at 2.4 ångströms resolution
5MDH: “Crystal structure of ternary complex of porcine cytoplasmic malate dehydrogenase alpha-ketomalonate and tnad…”. X-ray diffraction, 2 ligands (NAD, MAK), 7 pockets (best druggability 0.68). MolNFT v1 #126793 on GenesisL1: 3D…
- PDB
- 5MDH
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P11708
- Ligands
- NAD, MAK
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 333 | 44% helix, 19% strand | P11708 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MAK · Alpha-ketomalonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.68 | 0.82 | 43 | NAD, MAK |
| 2 | 331 | 0.66 | 0.81 | 45 | NAD, MAK |
| 3 | 56 | 0.64 | 0.94 | 17 | empty |
| 4 | 411 | 0.58 | 0.75 | 54 | empty |
| 5 | 105 | 0.52 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1717 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 5MDH · Crystal structure of ternary complex of porcine cytoplasmic malate dehydrogenase… · the same entry in another collection · chain A against A, TM-score 1.00
- P11708 · AlphaFold monomer V2.0 prediction for malate dehydrogenase, cytoplasmic (P11708) · 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 P11708
- Elsewhere: RCSB PDB 5MDH · PDBe 5MDH · UniProt P11708
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