MolNFT v1 · #8238 · protein
Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases
1GV0: “Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate…”. X-ray diffraction, 1 ligand (NAD), 7 pockets (best druggability 0.76). MolNFT v1 #8238 on GenesisL1: 3D structure, binding…
- PDB
- 1GV0
- Type
- protein
- Length
- 596 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P80039
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 301 | 48% helix, 24% strand | P80039 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 295 | 49% helix, 23% strand | P80039 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.76 | 0.80 | 99 | NAD |
| 2 | 326 | 0.59 | 0.77 | 43 | NAD |
| 3 | 162 | 0.49 | 0.78 | 30 | empty |
| 4 | 161 | 0.46 | 0.76 | 24 | empty |
| 5 | 69 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2164 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1GV0 · 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 1GV0 · PDBe 1GV0 · UniProt P80039
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