MolNFT v1 · #18936 · protein
2.0 ångström crystal structure of ovine prostaglandin H2 synthase-1, in complex with alpha-methyl-4-biphenylacetic acid
1Q4G · Prostaglandin G/H synthase 1: “2.0 ångström crystal structure of ovine prostaglandin H2 synthase-1, in complex with…”. X-ray diffraction, 6 ligands (BFL, HEM, NAG), 9 pockets (best druggability 0.83). MolNFT v1 #18936 on GenesisL1…
- PDB
- 1Q4G
- Type
- protein
- Length
- 1,106 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin G/H synthase 1
- EC
- 1.14.99.1
- Ligands
- BFL, HEM, NAG, BMA, NDG, MAN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin G/H synthase 1 (EC 1.14.99.1) | protein | 553 | 45% helix, 9% strand | — |
Ligands and binding sites
- BFL · 2-(1,1'-biphenyl-4-yl)propanoic acid · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- BOG · octyl beta-D-glucopyranoside · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.83 | 0.84 | 116 | BOG, BFL |
| 2 | 719 | 0.81 | 0.85 | 74 | empty |
| 3 | 607 | 0.78 | 0.84 | 82 | GOL |
| 4 | 287 | 0.78 | 0.89 | 44 | BOG, BFL |
| 5 | 432 | 0.69 | 0.80 | 41 | HEM, GOL |
Interfaces
1 interface between chains.
- A–B · 2647 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1Q4G · 2.0 Angstrom Crystal Structure of Ovine Prostaglandin H2 Synthase-1, in complex with… · 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 1Q4G · PDBe 1Q4G
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