Research workbench
NADPH bound to the dehydrogenase domain of the bifunctional mannitol- 1-phosphate DEHYDROGENASE/PHOSPHATASE mtld-N374A from acinetobacter baumannii
Analyse NADPH bound to the dehydrogenase domain of the bifunctional mannitol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OCT
- Type
- protein
- Length
- 1,364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Had hydrolase, family ia, variant 3
- UniProt
- D0C7J2
- Ligands
- NDP, MG, K, SO4, CL
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Had hydrolase, family ia, variant 3 | protein | 686 | 55% helix, 14% strand | D0C7J2 |
| B | Had hydrolase, family ia, variant 3 | protein | 678 | 55% helix, 14% strand | D0C7J2 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.87 | 0.88 | 121 | EPE |
| 2 | 467 | 0.81 | 0.88 | 46 | NDP, SO4 |
| 3 | 1057 | 0.80 | 0.82 | 78 | EDO, NDP, SO4, EPE |
| 4 | 479 | 0.69 | 0.80 | 45 | MG |
| 5 | 143 | 0.64 | 0.86 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4473 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 7OCT · NADPH bound to the dehydrogenase domain of the bifunctional mannitol-1-phosphate… · 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 D0C7J2
- Elsewhere: RCSB PDB 7OCT · PDBe 7OCT · UniProt D0C7J2
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