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Structure of malate dehydrogenase from pyrococcus horikoshii OT3
Analyse Structure of malate dehydrogenase from pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V9N
- Type
- protein
- Length
- 348 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- O59028
- Ligands
- NDP
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 348 | 40% helix, 17% strand | O59028 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.70 | 0.81 | 65 | NDP |
| 2 | 89 | 0.40 | 0.78 | 16 | empty |
| 3 | 54 | 0.27 | 0.74 | 13 | empty |
| 4 | 58 | 0.26 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
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 O59028
- Elsewhere: RCSB PDB 1V9N · PDBe 1V9N · UniProt O59028
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