4RCA Signaling Protein date Sep 15, 2014
title Crystal Structure Of Human Ptpdelta And Human Slitrk1 Comple
authors H.M.Kim, B.S.Park, D.Kim, S.G.Lee
compound source
Molecule: Receptor-Type Tyrosine-Protein Phosphatase Delta
Chain: A
Synonym: Protein-Tyrosine Phosphatase Delta, R-Ptp-Delta
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ptprd
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Slit And Ntrk-Like Protein 1
Chain: B
Synonym: Leucine-Rich Repeat-Containing Protein 12
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Slitrk1, Kiaa1910, Lrrc12, Unq233pro266
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 1 21 1
R_factor 0.263 R_Free 0.269
length a length b length c angle alpha angle beta angle gamma
76.981 60.195 83.679 90.00 102.19 90.00
method X-Ray Diffractionresolution 2.99 Å
ligand NAG, SO4 enzyme Hydrolase E.C. BRENDA

Primary referenceStructural basis for LAR-RPTP/Slitrk complex-mediated synaptic adhesion., Um JW, Kim KH, Park BS, Choi Y, Kim D, Kim CY, Kim SJ, Kim M, Ko JS, Lee SG, Choii G, Nam J, Heo WD, Kim E, Lee JO, Ko J, Kim HM, Nat Commun. 2014 Nov 14;5:5423. doi: 10.1038/ncomms6423. PMID:25394468
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (4rca.pdb1.gz) 86 Kb
  • LPC: Ligand-Protein Contacts for 4RCA
  • CSU: Contacts of Structural Units for 4RCA
  • Structure Factors (268 Kb)
  • Retrieve 4RCA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4RCA from S2C, [Save to disk]
  • Re-refined 4rca structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RCA 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 4RCA
  • 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
  • 3D motif for 4RCA, from MSDmotif at EBI
  • Fold representative 4rca from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rca] [4rca_A] [4rca_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4RCA: [IGc2] [LRR] [LRRCT] [LRR_TYP ] by SMART
  • Other resources with information on 4RCA
  • Community annotation for 4RCA at PDBWiki (http://pdbwiki.org)

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