Research workbench
Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1) in complex with substrate analog U51605
Analyse Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B99
- Type
- protein
- Length
- 860 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin I2 synthase
- EC
- 5.3.99.4
- UniProt
- A9LLA5
- Ligands
- U51, HEM
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin I2 synthase (EC 5.3.99.4) | protein | 445 | 48% helix, 14% strand | A9LLA5 |
| B | Prostaglandin I2 synthase (EC 5.3.99.4) | protein | 415 | 50% helix, 15% strand | A9LLA5 |
Ligands and binding sites
- U51 · (5Z)-7-{(1R,4S,5R,6R)-6-[(1E)-oct-1-en-1-yl]-2,3-diazabicyclo[2.2.1]hept-2-en-5-yl}hept-5-enoic acid · ligand · 6 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.85 | 0.85 | 87 | HEM, U51 |
| 2 | 1183 | 0.84 | 0.84 | 81 | HEM, U51 |
| 3 | 918 | 0.80 | 0.82 | 81 | empty |
| 4 | 270 | 0.62 | 0.80 | 30 | empty |
| 5 | 285 | 0.58 | 0.78 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 437 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3B99 · Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1) in complex… · 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
- Every structure of UniProt A9LLA5
- Elsewhere: RCSB PDB 3B99 · PDBe 3B99 · UniProt A9LLA5
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