MolNFT v1 · #58625 · protein
Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1) in complex with substrate analog U51605
3B99 · Prostaglandin I2 synthase: “Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1) in complex with substrate analog…”. X-ray diffraction, 2 ligands (U51, HEM), 12 pockets (best druggability 0.85). MolNFT v1…
- 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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