Research workbench
1.8 a resolution structure of the malate dehydrogenase from picrophilus torridus in its apo form
Analyse 1.8 a resolution structure of the malate dehydrogenase from picrophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BGV
- Type
- protein
- Length
- 1,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q6L0C3
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 323 | 51% helix, 22% strand | Q6L0C3 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B, C, D
- CIT · Citric acid · additive · chains B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.88 | 0.92 | 123 | PEG |
| 2 | 1104 | 0.80 | 0.81 | 144 | PEG |
| 3 | 753 | 0.74 | 0.79 | 71 | empty |
| 4 | 865 | 0.73 | 0.77 | 100 | PEG |
| 5 | 118 | 0.65 | 0.89 | 29 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2197 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2193 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1178 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1130 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 476 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4BGV · 1.8 A resolution structure of the malate dehydrogenase from Picrophilus torridus in its… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6L0C3 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q6L0C3) · 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 Q6L0C3
- Elsewhere: RCSB PDB 4BGV · PDBe 4BGV · UniProt Q6L0C3
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