MolNFT v1 · #53640 · protein
R207S, R292S mutant of malate dehydrogenase from the halophilic archeon haloarcula marismortui (holoform)
2X0R: “R207S, R292S mutant of malate dehydrogenase from the halophilic archeon haloarcula marismortui (holoform)”. X-ray diffraction, 3 ligands (NAD, NA, CL), 5 pockets (best druggability 0.66). MolNFT v1 #53640 on GenesisL1: 3D structure…
- PDB
- 2X0R
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q07841
- Ligands
- NAD, NA, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 47% helix, 21% strand | Q07841 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.66 | 0.77 | 53 | NAD |
| 2 | 461 | 0.61 | 0.75 | 49 | NAD |
| 3 | 89 | 0.35 | 0.75 | 22 | empty |
| 4 | 88 | 0.35 | 0.75 | 17 | empty |
| 5 | 83 | 0.33 | 0.74 | 18 | NA |
Interfaces
1 interface between chains.
- A–B · 2257 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 2X0R · R207S, R292S Mutant of Malate Dehydrogenase from the Halophilic Archeon Haloarcula… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07841 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q07841) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q07841
- Elsewhere: RCSB PDB 2X0R · PDBe 2X0R · UniProt Q07841
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