Research workbench
Crystal structure of dihomo-gamma-linoleic acid bound in the cyclooxygenase channel of prostaglandin endoperoxide H synthase-1.
Analyse Crystal structure of dihomo-gamma-linoleic acid bound in the cyclooxygenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FE2
- 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, LAX, NAG, BMA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin endoperoxide H synthase-1 (EC 1.14.99.1) | protein | 553 | 43% helix, 9% strand | — |
Ligands and binding sites
- COH · Protoporphyrin IX containing co · ligand · chains A
- LAX · Eicosa-8,11,14-trienoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.80 | 0.96 | 39 | LAX |
| 2 | 459 | 0.67 | 0.79 | 40 | COH |
| 3 | 438 | 0.66 | 0.79 | 58 | empty |
| 4 | 214 | 0.53 | 0.77 | 21 | BOG |
| 5 | 130 | 0.39 | 0.74 | 29 | empty |
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1FE2 · Crystal structure of dihomo-gamma-linoleic 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 1FE2 · PDBe 1FE2
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