Research workbench
Structural basis for alteration of cofactor specificity of malate dehydrogenase from thermus flavus
Analyse Structural basis for alteration of cofactor specificity 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
- 1WZE
- Type
- protein
- Length
- 654 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
- NAD
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 327 | 45% helix, 19% strand | P10584 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.61 | 0.75 | 62 | NAD |
| 2 | 348 | 0.58 | 0.76 | 45 | NAD |
| 3 | 197 | 0.52 | 0.78 | 34 | empty |
| 4 | 234 | 0.52 | 0.76 | 40 | empty |
| 5 | 103 | 0.44 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1662 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 1WZE · Structural basis for alteration of cofactor specificity of Malate dehydrogenase from… · 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 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 P10584
- Elsewhere: RCSB PDB 1WZE · PDBe 1WZE · UniProt P10584
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