Research workbench
Malate dehydrogenase from geobacillus stearothermophilus (gs-mdh) complexed with oxaloacetic acid (oaa) and nicotinamide adenine dinucleotide (NAD)
Analyse Malate dehydrogenase from geobacillus stearothermophilus (gs-mdh) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BY9
- Type
- protein
- Length
- 1,231 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, OAA
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 311 | 50% helix, 20% strand | A0A143T1U9 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 307 | 51% helix, 21% strand | A0A143T1U9 |
| C | Malate dehydrogenase (EC 1.1.1.37) | protein | 302 | 48% helix, 21% strand | A0A143T1U9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- OAA · Oxaloacetate ion · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.87 | 0.89 | 137 | empty |
| 2 | 148 | 0.76 | 0.94 | 22 | empty |
| 3 | 820 | 0.75 | 0.79 | 92 | NAD, OAA |
| 4 | 146 | 0.75 | 0.93 | 25 | empty |
| 5 | 798 | 0.73 | 0.78 | 85 | NAD, OAA |
Interfaces
6 interfaces between chains.
- C–D · 2074 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2049 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1075 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1060 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 794 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7BY9 · Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with… · 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 7BY9 · PDBe 7BY9 · UniProt A0A143T1U9
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