Research workbench
A structural basis for substrate and stereo selectivity in octopine dehydrogenase (odh-NADH)
Analyse A structural basis for substrate and stereo selectivity in octopine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C7A
- Type
- protein
- Length
- 403 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Octopine dehydrogenase
- EC
- 1.5.1.11
- UniProt
- Q9BHM6
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Octopine dehydrogenase (EC 1.5.1.11) | protein | 403 | 40% helix, 20% strand | Q9BHM6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.70 | 0.77 | 57 | NAD, EDO |
| 2 | 105 | 0.37 | 0.74 | 19 | empty |
| 3 | 78 | 0.36 | 0.76 | 17 | empty |
| 4 | 64 | 0.29 | 0.74 | 16 | empty |
| 5 | 58 | 0.27 | 0.73 | 13 | empty |
Compared structures
- 3C7A · A structural basis for substrate and stereo selectivity in octopine dehydrogenase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BHM6 · AlphaFold monomer V2.0 prediction for octopine dehydrogenase (Q9BHM6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9BHM6
- Elsewhere: RCSB PDB 3C7A · PDBe 3C7A · UniProt Q9BHM6
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