MolNFT v1 · #146781 · protein
Crystal structure of CJ0485 dehydrogenase in complex with NADP+
6DS1 · Putative oxidoreductase: “Crystal structure of CJ0485 dehydrogenase in complex with NADP+”. X-ray diffraction, 2 ligands (NAP, MG), 6 pockets (best druggability 0.87). MolNFT v1 #146781 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DS1
- Type
- protein
- Length
- 1,037 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase
- UniProt
- Q0PB28
- Ligands
- NAP, MG
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative oxidoreductase | protein | 258 | 48% helix, 13% strand | Q0PB28 |
| B, C | Putative oxidoreductase | protein | 260 | 49% helix, 13% strand | Q0PB28 |
| D | Putative oxidoreductase | protein | 259 | 49% helix, 14% strand | Q0PB28 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.87 | 0.88 | 66 | empty |
| 2 | 629 | 0.77 | 0.83 | 67 | NAP |
| 3 | 725 | 0.76 | 0.81 | 69 | NAP |
| 4 | 578 | 0.75 | 0.82 | 58 | NAP |
| 5 | 74 | 0.73 | 0.96 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1768 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1732 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1711 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1673 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 665 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6DS1 · Crystal structure of Cj0485 dehydrogenase in complex with NADP+ · 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 Q0PB28
- Elsewhere: RCSB PDB 6DS1 · PDBe 6DS1 · UniProt Q0PB28
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