MolNFT v1 · #4127 · protein
Crystal structure of a mixture of arachidonic acid and prostaglandin bound to the cyclooxygenase active site of COX-2: prostaglandin structure
1DDX · Protein (prostaglandin H2 synthase-2): “Crystal structure of a mixture of arachidonic acid and prostaglandin bound to the cyclooxygenase active site…”. X-ray diffraction, 2 ligands (PGX, NAG), 20 pockets (best druggability 0.88).…
- PDB
- 1DDX
- Type
- protein
- Length
- 2,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (prostaglandin H2 synthase-2)
- EC
- 1.14.99.1
- UniProt
- Q05769
- Ligands
- PGX, NAG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (prostaglandin H2 synthase-2) (EC 1.14.99.1) | protein | 552 | 45% helix, 6% strand | Q05769 |
Ligands and binding sites
- PGX · 7-[6-(3-hydroperoxy-oct-1-enyl)-2,3-dioxa-bicyclo[2.2.1]hept-5-yl]-hept-5-enoic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.88 | 0.89 | 146 | empty |
| 2 | 867 | 0.86 | 0.88 | 114 | PGX |
| 3 | 967 | 0.85 | 0.86 | 130 | PGX |
| 4 | 468 | 0.85 | 0.91 | 70 | PGX |
| 5 | 1007 | 0.85 | 0.85 | 112 | PGX |
Interfaces
3 interfaces between chains.
- A–B · 2544 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 2535 Ų buried · 61 hydrogen bonds · protein-protein
- A–D · 409 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 1DDX · Crystal structure of a mixture of arachidonic acid and prostaglandin bound to the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05769 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (Q05769) · 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 Q05769
- Elsewhere: RCSB PDB 1DDX · PDBe 1DDX · UniProt Q05769
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