MolNFT v1 · #2111 · protein
Determinants of protein thermostability observed in the 1.9 ångströms crystal structure of malate dehydrogenase from the thermophilic bacterium thermus flavus
1BMD: “Determinants of protein thermostability observed in the 1.9 ångströms crystal structure of malate…”. X-ray diffraction, 1 ligand (NAD), 7 pockets (best druggability 0.59). MolNFT v1 #2111 on GenesisL1: 3D structure, binding sites…
- 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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