MolNFT v1 · #52721 · protein
Crystal structure of human zinc-binding alcohol dehydrogenase 1 (ZADH1) in ternary complex with NADP and phenylbutazone
2W98 · Prostaglandin reductase 2: “Crystal structure of human zinc-binding alcohol dehydrogenase 1 (ZADH1) in ternary complex with NADP and…”. X-ray diffraction, 6 ligands (P1Z, NAP, LMR), 4 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 2W98
- Type
- protein
- Length
- 703 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin reductase 2
- EC
- 1.3.1.48
- UniProt
- Q8N8N7
- Ligands
- P1Z, NAP, LMR, NA, PO4, CL
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin reductase 2 (EC 1.3.1.48) | protein | 348 | 33% helix, 29% strand | Q8N8N7 |
| B | Prostaglandin reductase 2 (EC 1.3.1.48) | protein | 355 | 33% helix, 28% strand | Q8N8N7 |
Ligands and binding sites
- P1Z · 4-butyl-1,2-diphenyl-pyrazolidine-3,5-dione · ligand · 7 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · chains B
- NA · Sodium ion · metal · chains B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.85 | 0.86 | 98 | NAP, P1Z, PO4 |
| 2 | 847 | 0.83 | 0.85 | 86 | NAP, P1Z, PO4 |
| 3 | 52 | 0.28 | 0.75 | 7 | P1Z |
| 4 | 54 | 0.24 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 145 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2W98 · Crystal structure of human zinc-binding alcohol dehydrogenase 1 (ZADH1) in ternary… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N8N7 · AlphaFold monomer V2.0 prediction for prostaglandin reductase 2 (Q8N8N7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8N8N7
- Elsewhere: RCSB PDB 2W98 · PDBe 2W98 · UniProt Q8N8N7
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