Research workbench
The human P2Y1 receptor in complex with MRS2500
Analyse The human P2Y1 receptor in complex with MRS2500 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XNW
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2Y purinoceptor 1,RUBREDOXIN,P2Y purinoceptor 1
- UniProt
- P47900, P00268
- Ligands
- 2ID, ZN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P2Y purinoceptor 1,RUBREDOXIN,P2Y purinoceptor 1 | protein | 346 | 68% helix, 6% strand | P47900, P00268 |
| C | P2Y purinoceptor 1,RUBREDOXIN,P2Y purinoceptor 1 | protein | 350 | 67% helix, 6% strand | P47900, P00268 |
Ligands and binding sites
- 2ID · [(1R,2S,4S,5S)-4-[2-iodo-6-(methylamino)-9H-purin-9-yl]-2-(phosphonooxy)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.77 | 0.81 | 62 | empty |
| 2 | 731 | 0.71 | 0.77 | 67 | 2ID |
| 3 | 362 | 0.70 | 0.83 | 34 | 2ID |
| 4 | 128 | 0.40 | 0.74 | 18 | empty |
| 5 | 108 | 0.36 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–C · 1209 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4XNW · The human P2Y1 receptor in complex with MRS2500 · the same entry in another collection · chain A against A, TM-score 1.00
- P47900 · AlphaFold monomer V2.0 prediction for P2Y purinoceptor 1 (P47900) · a predicted model of the same protein · chain A against A, TM-score 0.83
- P00268 · AlphaFold monomer V2.0 prediction for rubredoxin (P00268) · a predicted model of the same protein · chain A against A, TM-score 0.16
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 P47900
- Every structure of UniProt P00268
- Elsewhere: RCSB PDB 4XNW · PDBe 4XNW · UniProt P47900 · UniProt P00268
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