Research workbench
R207S, R292S mutant of malate dehydrogenase from the halophilic archeon haloarcula marismortui (holoform)
Analyse R207S, R292S mutant of malate dehydrogenase from the halophilic archeon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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