5WY8 Hydrolase Protein Binding date Jan 11, 2017
title Crystal Structure Of Ptp Delta Ig1-Ig3 In Complex With Il1ra Ig3
authors H.M.Kim, S.Y.Won, D.Kim
compound source
Molecule: Receptor-Type Tyrosine-Protein Phosphatase Delta
Chain: A
Fragment: Unp Residues 21-318
Synonym: R-Ptp-Delta
Ec: 3.1.3.48
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ptprd
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Interleukin-1 Receptor Accessory Protein-Like 1
Chain: B
Fragment: Unp Residues 27-349
Synonym: Il1rapl-1,Oligophrenin-4,Three Immunoglobulin Doma Containing Il-1 Receptor-Related 2,Tigirr-2,X-Linked Interl Receptor Accessory Protein-Like 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il1rapl1, Ophn4
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 32 1 2
R_factor 0.233 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.416 110.416 210.536 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.07 Å
ligand BMA, FUC, MAN, NAG, ZN enzyme Hydrolase E.C.3.1.3.48 BRENDA
Primary referenceLAR-RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate., Won SY, Kim CY, Kim D, Ko J, Um JW, Lee SB, Buck M, Kim E, Heo WD, Lee JO, Kim HM, Front Mol Neurosci. 2017 Oct 13;10:327. doi: 10.3389/fnmol.2017.00327., eCollection 2017. PMID:29081732
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (5wy8.pdb1.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 5WY8
  • CSU: Contacts of Structural Units for 5WY8
  • Structure Factors (713 Kb)
  • Retrieve 5WY8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5WY8 from S2C, [Save to disk]
  • View 5WY8 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 5WY8
  • 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 5wy8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5wy8_A] [5wy8_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5WY8
  • Community annotation for 5WY8 at PDBWiki (http://pdbwiki.org)

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