Research workbench
Crystal structure of eicosapentanoic acid bound in the cyclooxygenase channel of prostaglandin endoperoxide H synthase-1.
Analyse Crystal structure of eicosapentanoic acid bound in the cyclooxygenase channel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IGX
- Type
- protein
- Length
- 553 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin endoperoxide H synthase-1
- EC
- 1.14.99.1
- Ligands
- COH, EPA, NAG, BMA, NDG, MAN, BGC
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin endoperoxide H synthase-1 (EC 1.14.99.1) | protein | 553 | 42% helix, 9% strand | — |
Ligands and binding sites
- COH · Protoporphyrin IX containing co · ligand · chains A
- EPA · 5,8,11,14,17-eicosapentaenoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar
- BGC · beta-D-glucopyranose · sugar · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.77 | 0.96 | 26 | EPA |
| 2 | 680 | 0.71 | 0.78 | 72 | BGC |
| 3 | 441 | 0.68 | 0.79 | 38 | COH |
| 4 | 114 | 0.37 | 0.74 | 24 | empty |
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1IGX · Crystal Structure of Eicosapentanoic Acid Bound in the Cyclooxygenase Channel of… · 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
- Elsewhere: RCSB PDB 1IGX · PDBe 1IGX
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