MolNFT v1 · #24514 · protein
Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface
1UXK: “Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at…”. X-ray diffraction, 4 ligands (NAD, CD, NA), 4 pockets (best druggability 0.66). MolNFT v1 #24514 on GenesisL1: 3D…
- PDB
- 1UXK
- Type
- protein
- Length
- 595 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, CD, NA, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 295 | 51% helix, 22% strand | P80040 |
| C | Malate dehydrogenase (EC 1.1.1.37) | protein | 300 | 52% helix, 21% strand | P80040 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- CD · Cadmium ion · metal · 10 copies · chains A, C
- NA · Sodium ion · metal · 6 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.66 | 0.78 | 73 | CD |
| 2 | 366 | 0.61 | 0.77 | 59 | NAD, CD |
| 3 | 199 | 0.53 | 0.78 | 31 | NAD |
| 4 | 56 | 0.29 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 1157 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 1UXK · 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 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 P80040
- Elsewhere: RCSB PDB 1UXK · PDBe 1UXK · UniProt P80040
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