MolNFT v1 · #152436 · protein
Crystal structure of malate dehydrogenase from metallosphaera sedula
6IHD: “Crystal structure of malate dehydrogenase from metallosphaera sedula”. X-ray diffraction, 2 ligands (NAD, ETX), 6 pockets (best druggability 0.76). MolNFT v1 #152436 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IHD
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- A0A088E2H7
- Ligands
- NAD, ETX
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 299 | 51% helix, 21% strand | A0A088E2H7 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 304 | 50% helix, 22% strand | A0A088E2H7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ETX · 2-ethoxyethanol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.76 | 0.83 | 60 | NAD |
| 2 | 607 | 0.70 | 0.78 | 56 | NAD |
| 3 | 174 | 0.55 | 0.80 | 27 | empty |
| 4 | 68 | 0.44 | 0.82 | 15 | empty |
| 5 | 58 | 0.44 | 0.83 | 15 | ETX |
Interfaces
1 interface between chains.
- A–B · 2213 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6IHD · 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 6IHD · PDBe 6IHD · UniProt A0A088E2H7
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