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Crystal structure of arachidonic acid bound to a mutant of prostagladin H synthase-1 that forms predominantly 11-hpete.
Analyse Crystal structure of arachidonic acid bound to a mutant of prostagladin H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U67
- Type
- protein
- Length
- 553 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin G/H synthase 1 precursor
- EC
- 1.14.99.1
- UniProt
- P05979
- Ligands
- COH, ACD, NAG, NDG, BMA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin G/H synthase 1 precursor (EC 1.14.99.1) | protein | 553 | 42% helix, 8% strand | P05979 |
Ligands and binding sites
- COH · Protoporphyrin IX containing co · ligand · chains A
- ACD · Arachidonic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.81 | 0.96 | 32 | ACD |
| 2 | 664 | 0.70 | 0.78 | 69 | BOG |
| 3 | 481 | 0.68 | 0.79 | 39 | COH |
| 4 | 133 | 0.40 | 0.74 | 27 | empty |
| 5 | 52 | 0.37 | 0.80 | 13 | empty |
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1U67 · Crystal Structure of Arachidonic Acid Bound to a Mutant of Prostagladin H Synthase-1 that… · the same entry in another collection · chain A against A, TM-score 1.00
- P05979 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 1 (P05979) · a predicted model of the same protein · 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 P05979
- Elsewhere: RCSB PDB 1U67 · PDBe 1U67 · UniProt P05979
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