Research workbench
Refined structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for dicarboxylic acid oxidoreductases
Analyse Refined structure of mitochondrial malate dehydrogenase from porcine heart and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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