MolNFT v1 · #71057 · protein
The crystal structure of dehydrogenase from chromobacterium violaceum
3M2T · Probable dehydrogenase: “The crystal structure of dehydrogenase from chromobacterium violaceum”. X-ray diffraction, 2 ligands (NAD, SO4), 7 pockets (best druggability 0.62). MolNFT v1 #71057 on GenesisL1: 3D structure, binding sites…
- PDB
- 3M2T
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable dehydrogenase
- UniProt
- Q7NY68
- Ligands
- NAD, SO4
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable dehydrogenase | protein | 342 | 40% helix, 25% strand | Q7NY68 |
| B | Probable dehydrogenase | protein | 342 | 39% helix, 25% strand | Q7NY68 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.62 | 0.76 | 59 | NAD |
| 2 | 127 | 0.55 | 0.82 | 23 | empty |
| 3 | 276 | 0.53 | 0.75 | 39 | NAD |
| 4 | 132 | 0.44 | 0.76 | 28 | empty |
| 5 | 98 | 0.33 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1512 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3M2T · The crystal structure of dehydrogenase from Chromobacterium violaceum · 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 Q7NY68
- Elsewhere: RCSB PDB 3M2T · PDBe 3M2T · UniProt Q7NY68
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