5NDD Membrane Protein date Mar 08, 2017
title Crystal Structure Of A Thermostabilised Human Protease-Activ Receptor-2 (Par2) In Complex With Az8838 At 2.8 Angstrom Re
authors R.K.Y.Cheng, C.Fiez-Vandal, O.Schlenker, K.Edman, B.Aggeler, D.G. G.Brown, R.M.Cooke, C.E.Dumelin, A.S.Dore, S.Geschwindner, C.Gre O.Hermansson, A.Jazayeri, P.Johansson, L.Leong, R.Prihandoko, M. H.Soutter, A.Snijder, L.Sundstrom, B.Tehan, P.Thornton, D.Troast G.Wiggin, A.Zhukov, F.H.Marshall, N.Dekker
compound source
Molecule: Lysozyme,Proteinase-Activated Receptor 2,Soluble B562,Proteinase-Activated Receptor 2;
Chain: A
Synonym: Par-2,Coagulation Factor II Receptor-Like 1,G-Prot Coupled Receptor 11,Thrombin Receptor-Like 1,Cytochrome B-5 Coagulation Factor II Receptor-Like 1,G-Protein Coupled Rec Thrombin Receptor-Like 1;
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage T4, Homo Sapiens, Escherichia Coli;
Organism_common: Human
Organism_taxid: 10665, 9606, 562
Gene: E, T4tp126, F2rl1, Gpr11, Par2, Cybc
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 1
R_factor 0.222 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
37.109 62.264 87.341 104.88 90.88 96.89
method X-Ray Diffractionresolution 2.80 Å
ligand 8TZ, NA, PO4 enzyme Hydrolase E.C. BRENDA

Primary referenceStructural insight into allosteric modulation of protease-activated receptor 2., Cheng RKY, Fiez-Vandal C, Schlenker O, Edman K, Aggeler B, Brown DG, Brown GA, Cooke RM, Dumelin CE, Dore AS, Geschwindner S, Grebner C, Hermansson NO, Jazayeri A, Johansson P, Leong L, Prihandoko R, Rappas M, Soutter H, Snijder A, Sundstrom L, Tehan B, Thornton P, Troast D, Wiggin G, Zhukov A, Marshall FH, Dekker N, Nature. 2017 Apr 26. doi: 10.1038/nature22309. PMID:28445455
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (5ndd.pdb1.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 5NDD
  • CSU: Contacts of Structural Units for 5NDD
  • Structure Factors (179 Kb)
  • Retrieve 5NDD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NDD from S2C, [Save to disk]
  • Re-refined 5ndd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5NDD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5NDD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ndd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ndd_A] [5ndd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NDD
  • Community annotation for 5NDD at PDBWiki (http://pdbwiki.org)

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