- PDB-4xnw: The human P2Y1 receptor in complex with MRS2500 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4xnw
Title
The human P2Y1 receptor in complex with MRS2500
Components
P2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1
Keywords
TRANSPORT PROTEIN / human P2Y1 receptor / G protein coupled receptor / platelet activation / membrane protein / PSI-Biology / Structural Genomics / GPCR Network / GPCR
Function / homology
Function and homology information
G protein-coupled ATP receptor activity / relaxation of muscle / G protein-coupled ADP receptor activity / P2Y receptors / cellular response to purine-containing compound / G protein-coupled purinergic nucleotide receptor activity / positive regulation of inositol trisphosphate biosynthetic process / positive regulation of monoatomic ion transport / positive regulation of penile erection / negative regulation of norepinephrine secretion ...G protein-coupled ATP receptor activity / relaxation of muscle / G protein-coupled ADP receptor activity / P2Y receptors / cellular response to purine-containing compound / G protein-coupled purinergic nucleotide receptor activity / positive regulation of inositol trisphosphate biosynthetic process / positive regulation of monoatomic ion transport / positive regulation of penile erection / negative regulation of norepinephrine secretion / A1 adenosine receptor binding / glial cell migration / alkane catabolic process / regulation of presynaptic cytosolic calcium ion concentration / G protein-coupled adenosine receptor signaling pathway / positive regulation of hormone secretion / signal transduction involved in regulation of gene expression / response to growth factor / cellular response to ATP / eating behavior / regulation of synaptic vesicle exocytosis / monoatomic ion transport / presynaptic active zone membrane / response to mechanical stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / blood vessel diameter maintenance / establishment of localization in cell / protein localization to plasma membrane / platelet activation / ADP binding / cilium / ADP signalling through P2Y purinoceptor 1 / phospholipase C-activating G protein-coupled receptor signaling pathway / signaling receptor activity / regulation of cell shape / cell body / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / G alpha (q) signalling events / basolateral plasma membrane / postsynaptic membrane / electron transfer activity / postsynaptic density / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / iron ion binding / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / apical plasma membrane / protein heterodimerization activity / glutamatergic synapse / dendrite / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane Similarity search - Function
Mass: 47468.289 Da / Num. of mol.: 2 / Mutation: D320N Source method: isolated from a genetically manipulated source Details: Chimera protein of P2Y purinoceptor 1 (P2RY1_HUMA) with Rubredoxin (RUBR_CLOPA) inserted into ICL3 domain between residues 247LYS and 253PRO, and replaced residues 248ASN to 252SER. Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria) Gene: P2RY1 / Production host: Spodoptera (butterflies/moths) / References: UniProt: P47900, UniProt: P00268
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2013
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.7→50 Å / Num. obs: 20471 / % possible obs: 98.2 % / Redundancy: 4.9 % / Net I/σ(I): 18.9
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Processing
Software
Name
Version
Classification
REFMAC
5.7.0029
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
PHASER
phasing
Refinement
Resolution: 2.7→29.31 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.27 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26714
1027
5.1 %
RANDOM
Rwork
0.21834
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obs
0.22094
19283
98.1 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK