Research workbench
Malate dehydrogenase from geobacillus stearothermophilus (gs-mdh) G218Y mutant
Analyse Malate dehydrogenase from geobacillus stearothermophilus (gs-mdh) G218Y mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F8D
- Type
- protein
- Length
- 1,250 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- A0A143T1U9
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Malate dehydrogenase (EC 1.1.1.37) | protein | 313 | 51% helix, 20% strand | A0A143T1U9 |
| B, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 312 | 51% helix, 20% strand | A0A143T1U9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.82 | 0.90 | 59 | empty |
| 2 | 416 | 0.81 | 0.89 | 49 | empty |
| 3 | 658 | 0.75 | 0.81 | 83 | NAD |
| 4 | 435 | 0.75 | 0.84 | 72 | NAD |
| 5 | 153 | 0.73 | 0.91 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2093 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2089 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1101 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1058 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 964 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7F8D · Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) G218Y mutant · the same entry in another collection · 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 A0A143T1U9
- Elsewhere: RCSB PDB 7F8D · PDBe 7F8D · UniProt A0A143T1U9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.