Research workbench
Crystal structure of P2Y12 receptor in complex with 2MESADP
Analyse Crystal structure of P2Y12 receptor in complex with 2MESADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PXZ
- Type
- protein
- Length
- 392 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2Y purinoceptor 12, soluble cytochrome B562
- UniProt
- Q9H244, P0ABE7
- Ligands
- 6AD, CLR
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P2Y purinoceptor 12, soluble cytochrome B562 | protein | 392 | 79% helix, 0% strand | Q9H244, P0ABE7 |
Ligands and binding sites
- 6AD · 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate) · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.83 | 0.96 | 43 | 6AD |
| 2 | 121 | 0.57 | 0.83 | 23 | empty |
| 3 | 140 | 0.49 | 0.79 | 22 | empty |
| 4 | 52 | 0.36 | 0.80 | 18 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4PXZ · Crystal structure of P2Y12 receptor in complex with 2MeSADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H244 · AlphaFold monomer V2.0 prediction for P2Y purinoceptor 12 (Q9H244) · a predicted model of the same protein · chain A against A, TM-score 0.70
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.27
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 Q9H244
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 4PXZ · PDBe 4PXZ · UniProt Q9H244 · UniProt P0ABE7
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