MolNFT v1 · #24512 · protein
Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface
1UXI: “Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at…”. X-ray diffraction, 3 ligands (NAD, FUM, NA), 5 pockets (best druggability 0.73). MolNFT v1 #24512 on GenesisL1: 3D…
- PDB
- 1UXI
- 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, NA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 308 | 49% helix, 23% 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
- NA · Sodium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.73 | 0.85 | 60 | NAD, FUM |
| 2 | 315 | 0.71 | 0.84 | 53 | NAD, FUM |
| 3 | 100 | 0.44 | 0.79 | 18 | empty |
| 4 | 92 | 0.40 | 0.77 | 20 | empty |
| 5 | 71 | 0.35 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2261 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1UXI · Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single… · the same entry in another collection · chain B against B, 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 1UXI · PDBe 1UXI · UniProt P80040
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