MolNFT v1 · #174529 · protein
Malate dehydrogenase from geobacillus stearothermophilus (gs-mdh) complexed with oxaloacetic acid (oaa) and adenosine 5'- diphosphoribose (apr)
7BYA: “Malate dehydrogenase from geobacillus stearothermophilus (gs-mdh) complexed with oxaloacetic acid (oaa) and…”. X-ray diffraction, 2 ligands (APR, OAA), 20 pockets (best druggability 0.83). MolNFT v1 #174529 on GenesisL1: 3D…
- PDB
- 7BYA
- Type
- protein
- Length
- 1,236 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
- APR, OAA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 311 | 51% helix, 21% strand | A0A143T1U9 |
| C | Malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 52% helix, 21% strand | A0A143T1U9 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 4 copies · chains A, B, C, D
- OAA · Oxaloacetate ion · ligand · chains 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.83 | 0.90 | 67 | empty |
| 2 | 482 | 0.82 | 0.89 | 59 | empty |
| 3 | 161 | 0.76 | 0.93 | 25 | empty |
| 4 | 162 | 0.75 | 0.92 | 26 | empty |
| 5 | 508 | 0.73 | 0.82 | 72 | APR, OAA |
Interfaces
6 interfaces between chains.
- B–C · 2064 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 2018 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1066 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1048 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 792 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7BYA · 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 7BYA · PDBe 7BYA · UniProt A0A143T1U9
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