4AY1 Hydrolase date Jun 17, 2012
title Human Ykl-39 Is A Pseudo-Chitinase With Retained Chitooligos Binding Properties
authors M.Schimpl, C.L.Rush, M.Betou, I.M.Eggleston, G.A.Penman, A.D.Reck D.M.F.Van Aalten
compound source
Molecule: Chitinase-3-Like Protein 2
Chain: A, B, C, D, E, F, G, H, I, J, K, L
Synonym: Chondrocyte Protein 39, Ykl-39
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Komagataella Pastoris
Expression_system_taxid: 644223
Expression_system_strain: Gs115
symmetry Space Group: C 1 2 1
R_factor 0.191 R_Free 0.239
length a length b length c angle alpha angle beta angle gamma
255.686 152.543 138.186 90.00 94.62 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand NAG enzyme
F, A, J, K, E, B, H, C, D, I, G, L

Primary referenceHuman YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties., Schimpl M, Rush CL, Betou M, Eggleston IM, Recklies AD, van Aalten DM, Biochem J. 2012 Aug 15;446(1):149-57. PMID:22742450
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1458 Kb) [Save to disk]
  • Biological Unit Coordinates (4ay1.pdb1.gz) 130 Kb
  • Biological Unit Coordinates (4ay1.pdb2.gz) 129 Kb
  • Biological Unit Coordinates (4ay1.pdb3.gz) 130 Kb
  • Biological Unit Coordinates (4ay1.pdb4.gz) 130 Kb
  • Biological Unit Coordinates (4ay1.pdb5.gz) 130 Kb
  • Biological Unit Coordinates (4ay1.pdb6.gz) 129 Kb
  • Biological Unit Coordinates (4ay1.pdb7.gz) 129 Kb
  • Biological Unit Coordinates (4ay1.pdb8.gz) 128 Kb
  • Biological Unit Coordinates (4ay1.pdb9.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 4AY1
  • CSU: Contacts of Structural Units for 4AY1
  • Structure Factors (5806 Kb)
  • Retrieve 4AY1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AY1 from S2C, [Save to disk]
  • Re-refined 4ay1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AY1 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 4AY1
  • 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 4AY1, from MSDmotif at EBI
  • Fold representative 4ay1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ay1_I] [4ay1_D] [4ay1_C] [4ay1_J] [4ay1] [4ay1_E] [4ay1_F] [4ay1_K] [4ay1_B] [4ay1_A] [4ay1_G] [4ay1_L] [4ay1_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4AY1: [Glyco_18 ] by SMART
  • Other resources with information on 4AY1
  • Community annotation for 4AY1 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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