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The structure at 1.8 ångströms resolution of a single site mutant (T189I) of malate dehydrogenase from thermus flavus with increased enzymatic activity
Analyse The structure at 1.8 ångströms resolution of a single site mutant (T189I) of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BDM
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P10584
- Ligands
- NAX
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 317 | 46% helix, 20% strand | P10584 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 327 | 46% helix, 19% strand | P10584 |
Ligands and binding sites
- NAX · Beta-6-hydroxy-1,4,5,6-tetrhydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.55 | 0.76 | 42 | NAX |
| 2 | 291 | 0.54 | 0.76 | 41 | NAX |
| 3 | 227 | 0.52 | 0.77 | 41 | empty |
| 4 | 242 | 0.52 | 0.76 | 38 | empty |
| 5 | 127 | 0.47 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1649 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 1BDM · The structure at 1.8 ångströms resolution of a single site mutant (T189I) of malate… · the same entry in another collection · chain A against A, TM-score 1.00
- P10584 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P10584) · 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 P10584
- Elsewhere: RCSB PDB 1BDM · PDBe 1BDM · UniProt P10584
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