Research workbench
Prostaglandin H2 synthase-1 complexed with 1-(4-iodobenzoyl)-5- methoxy-2-methylindole-3-acetic acid (iodoindomethacin), cis model
Analyse Prostaglandin H2 synthase-1 complexed with 1-(4-iodobenzoyl)-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PGF
- Type
- protein
- Length
- 1,102 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin H2 synthase-1
- EC
- 1.14.99.1
- Ligands
- HEM, IMM, NAG
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin H2 synthase-1 (EC 1.14.99.1) | protein | 551 | 46% helix, 9% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- IMM · 1-(4-iodobenzoyl)-5-methoxy-2-methyl indole-3-acetic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.85 | 0.85 | 115 | IMM |
| 2 | 1063 | 0.84 | 0.85 | 110 | IMM |
| 3 | 665 | 0.76 | 0.82 | 67 | empty |
| 4 | 457 | 0.68 | 0.79 | 38 | HEM |
| 5 | 450 | 0.67 | 0.78 | 38 | HEM |
Interfaces
1 interface between chains.
- A–B · 2551 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1PGF · Prostaglandin H2 synthase-1 complexed with 1-(4-iodobenzoyl)-5-methoxy-2-methylindole-3-ac… · 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 1PGF · PDBe 1PGF
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