5LU9 Hydrolase date Sep 08, 2016
title Crystal Structure Of Yvad-Cmk Bound Human Legumain (Aep) In With Compound 11
authors E.Dall, K.Ye, H.Brandstetter
compound source
Molecule: Ac-Tyr-Val-Ala-Asp-Chloromethylketone
Chain: C
Engineered: Yes
Other_details: Ac-Yvad-Chloromethyleketone Inhibitor
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Legumain
Chain: A
Fragment: Unp Residues 26-288
Synonym: Asparaginyl Endopeptidase,Protease,Cysteine 1
Ec: 3.4.22.34
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lgmn, Prsc1
Expression_system: Leishmania Tarentolae
Expression_system_taxid: 5689
symmetry Space Group: P 42
R_factor 0.244 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.390 64.390 79.330 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.27 Å
ligand 0QE, 3Y7, ACE, NAG, SNN, SO4 enzyme Hydrolase E.C.3.4.22.34 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer's disease., Zhang Z, Obianyo O, Dall E, Du Y, Fu H, Liu X, Kang SS, Song M, Yu SP, Cabrele C, Schubert M, Li X, Wang JZ, Brandstetter H, Ye K, Nat Commun. 2017 Mar 27;8:14740. doi: 10.1038/ncomms14740. PMID:28345579
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (5lu9.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 5LU9
  • CSU: Contacts of Structural Units for 5LU9
  • Structure Factors (982 Kb)
  • Retrieve 5LU9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LU9 from S2C, [Save to disk]
  • Re-refined 5lu9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LU9 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 5LU9
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5lu9_A] [5lu9] [5lu9_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5LU9
  • Community annotation for 5LU9 at PDBWiki (http://pdbwiki.org)

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