MolNFT v1 · #3379 · protein
Prostaglandin H2 synthase-1 complex with flurbiprofen
1CQE · Protein (prostaglandin H2 synthase-1): “Prostaglandin H2 synthase-1 complex with flurbiprofen”. X-ray diffraction, 3 ligands (HEM, FLP, NAG), 12 pockets (best druggability 0.85). MolNFT v1 #3379 on GenesisL1: 3D structure, binding…
- PDB
- 1CQE
- Type
- protein
- Length
- 1,105 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (prostaglandin H2 synthase-1)
- EC
- 1.14.99.1
- UniProt
- P05979
- Ligands
- HEM, FLP, NAG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (prostaglandin H2 synthase-1) (EC 1.14.99.1) | protein | 552 | 45% helix, 10% strand | P05979 |
| B | Protein (prostaglandin H2 synthase-1) (EC 1.14.99.1) | protein | 553 | 45% helix, 10% strand | P05979 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- FLP · Flurbiprofen · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.85 | 0.86 | 123 | empty |
| 2 | 640 | 0.76 | 0.82 | 64 | empty |
| 3 | 116 | 0.76 | 0.95 | 22 | FLP |
| 4 | 255 | 0.75 | 0.88 | 39 | BOG, FLP |
| 5 | 52 | 0.69 | 0.97 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2539 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 1CQE · PDBe 1CQE · UniProt P05979
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