Research workbench
Crystal structure of wild type human lipocalin pgds in complex with substrate analog U44069
Analyse Crystal structure of wild type human lipocalin pgds in complex with substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IMO
- Type
- protein
- Length
- 155 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipocalin-type prostaglandin-D synthase
- EC
- 5.3.99.2
- UniProt
- P41222
- Ligands
- PWZ, SCN
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipocalin-type prostaglandin-D synthase (EC 5.3.99.2) | protein | 155 | 16% helix, 47% strand | P41222 |
Ligands and binding sites
- PWZ · (5E)-7-{(1R,4S,5S,6R)-5-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-6-yl}hept-5-enoic acid · ligand · 2 copies · chains A
- SCN · Thiocyanate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.71 | 0.78 | 37 | PWZ |
Compared structures
- 4IMO · Crystal structure of wild type human Lipocalin PGDS in complex with substrate analog… · the same entry in another collection · chain A against A, TM-score 1.00
- P41222 · AlphaFold monomer V2.0 prediction for prostaglandin-H2 D-isomerase (P41222) · 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 P41222
- Elsewhere: RCSB PDB 4IMO · PDBe 4IMO · UniProt P41222
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