4PY0

Crystal structure of P2Y12 receptor in complex with 2MeSATP

Structural Biology Knowledgebase: 4PY0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.222

Literature

Macromolecules
Sequence Display for 4PY0

Classification: MEMBRANE PROTEIN

Total Structure Weight: 54515.82

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 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6AT
Query on 6AT

A 2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate)
2-methylthio-adenosine-5'-triphosphate (Synonym)
C11 H18 N5 O13 P3 S
XNOBOKJVOTYSJV-KQYNXXCUSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.222
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.65 α = 90.00
b = 65.11 β = 95.50
c = 100.74 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

  • 2014-09-03
    Type: Biological assembly | Details: --
  • 2014-05-28
    Type: Citation | Details: Citation update