MolNFT v1 · #14811 · protein
Refined structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for dicarboxylic acid oxidoreductases
1MLD: “Refined structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for…”. X-ray diffraction, 17 pockets (best druggability 0.72). MolNFT v1 #14811 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1MLD
- Type
- protein
- Length
- 1,252 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P00346
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 313 | 48% helix, 18% strand | P00346 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.72 | 0.83 | 61 | CIT |
| 2 | 378 | 0.72 | 0.84 | 51 | CIT |
| 3 | 279 | 0.71 | 0.85 | 49 | CIT |
| 4 | 268 | 0.69 | 0.84 | 44 | CIT |
| 5 | 142 | 0.51 | 0.80 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1571 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1554 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 424 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1MLD · Refined structure of mitochondrial malate dehydrogenase from porcine heart and the… · the same entry in another collection · chain A against A, TM-score 1.00
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 P00346
- Elsewhere: RCSB PDB 1MLD · PDBe 1MLD · UniProt P00346
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