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1.95 a resolution structure of (R207S,R292S) mutant of malate dehydrogenase from the halophilic archaeon haloarcula marismortui (holo form)
Analyse 1.95 a resolution structure of (R207S,R292S) mutant of malate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O6Z
- Type
- protein
- Length
- 1,202 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
- NAD, CL
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 50% helix, 20% strand | Q07841 |
| B, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 298 | 50% helix, 20% strand | Q07841 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.82 | 0.84 | 132 | empty |
| 2 | 772 | 0.80 | 0.84 | 72 | CL |
| 3 | 537 | 0.65 | 0.76 | 54 | NAD |
| 4 | 505 | 0.64 | 0.76 | 48 | NAD |
| 5 | 467 | 0.62 | 0.76 | 55 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 2241 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2190 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 570 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 168 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1O6Z · 1.95 A resolution structure of (R207S,R292S) mutant of malate dehydrogenase from the… · 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 1O6Z · PDBe 1O6Z · UniProt Q07841
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