Research workbench
Crystal structure of malate dehydrogenase from metallosphaera sedula
Analyse Crystal structure of malate dehydrogenase from metallosphaera sedula in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IHE
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase (NAD)
- EC
- 1.1.1.37
- UniProt
- A0A088E2H7
- Ligands
- NAD, MLT
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (NAD) (EC 1.1.1.37) | protein | 303 | 50% helix, 20% strand | A0A088E2H7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MLT · D-malate · ligand · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.75 | 0.87 | 43 | NAD, MLT |
| 2 | 293 | 0.73 | 0.86 | 44 | NAD, MLT |
| 3 | 101 | 0.57 | 0.85 | 18 | PGE |
| 4 | 100 | 0.57 | 0.85 | 18 | EDO |
| 5 | 122 | 0.48 | 0.79 | 23 | PG4, PGE |
Interfaces
1 interface between chains.
- A–B · 1012 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6IHE · Crystal structure of Malate dehydrogenase from Metallosphaera sedula · 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 A0A088E2H7
- Elsewhere: RCSB PDB 6IHE · PDBe 6IHE · UniProt A0A088E2H7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.