MolNFT v1 · #118419 · protein
The crystal structure of salicylate bound to human cyclooxygenase-2
5F1A · Prostaglandin G/H synthase 2: “The crystal structure of salicylate bound to human cyclooxygenase-2”. X-ray diffraction, 5 ligands (AKR, SAL, COH), 7 pockets (best druggability 0.85). MolNFT v1 #118419 on GenesisL1: 3D structure…
- PDB
- 5F1A
- Type
- protein
- Length
- 1,105 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin G/H synthase 2
- EC
- 1.14.99.1
- UniProt
- P35354
- Ligands
- AKR, SAL, COH, NAG, MAN
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 553 | 47% helix, 9% strand | P35354 |
| B | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 552 | 48% helix, 9% strand | P35354 |
Ligands and binding sites
- AKR · Acrylic acid · ligand · 3 copies · chains A, B
- SAL · 2-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- COH · Protoporphyrin IX containing co · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.85 | 0.86 | 114 | SAL, EDO |
| 2 | 796 | 0.80 | 0.83 | 85 | empty |
| 3 | 709 | 0.79 | 0.84 | 63 | empty |
| 4 | 407 | 0.78 | 0.87 | 65 | SAL, EDO |
| 5 | 490 | 0.73 | 0.81 | 46 | COH |
Interfaces
1 interface between chains.
- A–B · 2491 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 5F1A · The Crystal Structure of Salicylate Bound to Human Cyclooxygenase-2 · the same entry in another collection · chain A against A, TM-score 1.00
- P35354 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (P35354) · 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 P35354
- Elsewhere: RCSB PDB 5F1A · PDBe 5F1A · UniProt P35354
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