4PXZ

Crystal structure of P2Y12 receptor in complex with 2MeSADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 4PXZ

Classification: MEMBRANE PROTEIN

Total Structure Weight: 55284.57

Macromolecule Entities
Molecule Chains Length Organism Details
P2Y purinoceptor 12, Soluble cytochrome b562 A 466 Escherichia coli Homo sapiens Mutation: M1007W, H1102I, R1106L, D294N
Details: Chimera protein of N-terminal residues 2-223 from P2Y12R (P2Y12_HUMAN), Soluble cytochrome b562 (C562_ECOLX), and C-terminal residues 224-342 from P2Y12R (P2Y12_HUMAN).
Gene Name(s): cybC P2RY12 Gene View HORK3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: P2Y12 receptor in complex with an antithrombotic drug


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6AD
Query on 6AD

A 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)
2-methylthio-adenosine-5'-diphosphate (Synonym)
C11 H17 N5 O10 P2 S
WLMZTKAZJUWXCB-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CLR
Query on CLR

A CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLC
Query on OLC

A (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.200
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 65.11 α = 90.00
b = 104.17 β = 90.00
c = 169.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-03-25
  • Released Date: 2014-04-30
  • Deposition author(s): Zhang, J., Zhang, K., Gao, Z.G., Paoletta, S., Zhang, D., Han, G.W., Li, T., Ma, L., Zhang, W., Muller, C.E., Yang, H., Jiang, H., Cherezov, V., Katritch, V., Jacobson, K.A., Stevens, R.C., Wu, B., Zhao, Q., GPCR Network (GPCR)

Revision History

  • Version 1_0: 2014-04-30

    Type: Initial release

  • Version 1_1: 2014-05-28

    Type: Database references

  • Version 1_2: 2014-09-03

    Type: Derived calculations

  • Version 1_3: 2017-08-16

    Type: Refinement description, Source and taxonomy