Research workbench
Crystal structure of malate dehydrogenase from haloarcula marismortui with potassium and chloride ions
Analyse Crystal structure of malate dehydrogenase from haloarcula marismortui with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q3X
- Type
- protein
- Length
- 1,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q07841
- Ligands
- K, CL
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 50% helix, 20% strand | Q07841 |
Ligands and binding sites
- K · Potassium ion · metal · 21 copies · chains A, C, D, B
- CL · Chloride ion · ion · 28 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.80 | 0.84 | 67 | CL |
| 2 | 811 | 0.80 | 0.83 | 71 | K, CL |
| 3 | 510 | 0.66 | 0.78 | 49 | CL |
| 4 | 489 | 0.65 | 0.77 | 49 | CL |
| 5 | 508 | 0.65 | 0.77 | 52 | CL |
Interfaces
6 interfaces between chains.
- C–D · 2288 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2204 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 713 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 711 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 178 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7Q3X · Crystal structure of Malate dehydrogenase from Haloarcula marismortui with Potassium and… · 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 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 Q07841
- Elsewhere: RCSB PDB 7Q3X · PDBe 7Q3X · UniProt Q07841
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