Research workbench
Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface.
Analyse Large improvement in the thermal stability of a tetrameric malate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UXG
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P80040
- Ligands
- NAD, FUM
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 308 | 49% helix, 22% strand | P80040 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- FUM · Fumaric acid · ligand · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.80 | 0.84 | 100 | NAD, FUM |
| 2 | 95 | 0.42 | 0.78 | 18 | empty |
| 3 | 108 | 0.41 | 0.76 | 23 | empty |
| 4 | 64 | 0.33 | 0.76 | 13 | empty |
| 5 | 56 | 0.28 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2233 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1UXG · Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single… · the same entry in another collection · chain A against A, TM-score 1.00
- P80040 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P80040) · 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 P80040
- Elsewhere: RCSB PDB 1UXG · PDBe 1UXG · UniProt P80040
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