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Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases
Analyse Structural basis for thermophilic protein stability: structures of thermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GV1
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P80039
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Malate dehydrogenase (EC 1.1.1.37) | protein | 305 | 49% helix, 21% strand | P80039 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 290 | 49% helix, 22% strand | P80039 |
| D | Malate dehydrogenase (EC 1.1.1.37) | protein | 292 | 49% helix, 22% strand | P80039 |
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.86 | 0.94 | 73 | empty |
| 2 | 466 | 0.85 | 0.92 | 73 | empty |
| 3 | 689 | 0.83 | 0.87 | 95 | empty |
| 4 | 927 | 0.78 | 0.80 | 94 | empty |
| 5 | 703 | 0.72 | 0.79 | 62 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2208 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 2160 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1035 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1031 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 555 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1GV1 · Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and… · the same entry in another collection · chain A against A, TM-score 1.00
- P80039 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P80039) · a predicted model of the same protein · chain B 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 P80039
- Elsewhere: RCSB PDB 1GV1 · PDBe 1GV1 · UniProt P80039
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