MolNFT v1 · #141839 · protein
Crystal structure of the human platelet-activating factor receptor in complex with sr 27417
5ZKP · Platelet-activating factor RECEPTOR,FLAVODOXIN,PLATELET…: “Crystal structure of the human platelet-activating factor receptor in complex with sr 27417”. X-ray diffraction, 2 ligands (9ER, FMN), 6 pockets (best druggability 0.83).…
- PDB
- 5ZKP
- Type
- protein
- Length
- 436 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-activating factor RECEPTOR,FLAVODOXIN,PLATELET- activating factor receptor
- UniProt
- P25105, P00323
- Ligands
- 9ER, FMN
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-activating factor RECEPTOR,FLAVODOXIN,PLATELET- activating factor receptor | protein | 436 | 62% helix, 11% strand | P25105, P00323 |
Ligands and binding sites
- 9ER · N1,N1-dimethyl-N2-[(pyridin-3-yl)methyl]-N2-{4-[2,4,6-tri(propan-2-yl)phenyl]-1,3-thiazol-2-yl}ethane-1,2-diamine · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.83 | 0.85 | 80 | 9ER |
| 2 | 267 | 0.65 | 0.82 | 22 | empty |
| 3 | 325 | 0.60 | 0.77 | 29 | empty |
| 4 | 112 | 0.47 | 0.79 | 24 | FMN |
| 5 | 94 | 0.43 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ZKP · Crystal structure of the human platelet-activating factor receptor in complex with SR… · the same entry in another collection · chain A against A, TM-score 1.00
- P25105 · AlphaFold monomer V2.0 prediction for platelet-activating factor receptor (P25105) · a predicted model of the same protein · chain A against A, TM-score 0.59
- P00323 · AlphaFold monomer V2.0 prediction for flavodoxin (P00323) · a predicted model of the same protein · chain A against A, TM-score 0.34
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 P25105
- Every structure of UniProt P00323
- Elsewhere: RCSB PDB 5ZKP · PDBe 5ZKP · UniProt P25105 · UniProt P00323
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