Research workbench
MDH3 wild type, apo-form
Analyse MDH3 wild type, apo-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZI3
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- A0A250W9L1
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 339 | 53% helix, 17% strand | A0A250W9L1 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.74 | 0.85 | 55 | GOL |
| 2 | 484 | 0.73 | 0.82 | 65 | empty |
| 3 | 464 | 0.68 | 0.79 | 46 | empty |
| 4 | 134 | 0.40 | 0.74 | 20 | empty |
| 5 | 87 | 0.33 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1641 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5ZI3 · MDH3 wild type, apo-form · 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 A0A250W9L1
- Elsewhere: RCSB PDB 5ZI3 · PDBe 5ZI3 · UniProt A0A250W9L1
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