Research workbench
Determinants of protein thermostability observed in the 1.9 ångströms crystal structure of malate dehydrogenase from the thermophilic bacterium thermus flavus
Analyse Determinants of protein thermostability observed in the 1.9 ångströms crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BMD
- 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 0.59
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 327 | 46% 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 | 411 | 0.59 | 0.75 | 51 | NAD |
| 2 | 386 | 0.59 | 0.76 | 52 | NAD |
| 3 | 256 | 0.54 | 0.77 | 39 | empty |
| 4 | 229 | 0.54 | 0.78 | 39 | empty |
| 5 | 119 | 0.46 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1649 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 1BMD · Determinants of protein thermostability observed in the 1.9 ångströms crystal structure… · 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 1BMD · PDBe 1BMD · UniProt P10584
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