5JBT Hydrolase Hydrolase Inhibitor date Apr 13, 2016
title Mesotrypsin In Complex With Cleaved Amyloid Precursor Like P Inhibitor (Aplp2)
authors O.Kayode, R.Wang, D.Pendlebury, A.Soares, E.S.Radisky
compound source
Molecule: Prss3 Protein
Chain: A
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Pancreas
Gene: Prss3
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Ptrap-T7-Wthu3

Molecule: Amyloid-Like Protein 2
Chain: X
Synonym: Aplp-2,Apph,Amyloid Protein Homolog,Cdei Box-Bindi Protein,Cdebp;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aplp2, Appl2
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_plasmid: Ppicza

Molecule: Amyloid-Like Protein 2
Chain: Y
Synonym: Aplp-2,Apph,Amyloid Protein Homolog,Cdei Box-Bindi Protein,Cdebp;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aplp2, Appl2
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_plasmid: Ppicza
symmetry Space Group: P 21 21 2
R_factor 0.163 R_Free 0.199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.956 54.539 56.632 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.40 Å
ligand CA, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Y


Primary referenceAn Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis., Kayode O, Wang R, Pendlebury DF, Cohen I, Henin RD, Hockla A, Soares AS, Papo N, Caulfield TR, Radisky ES, J Biol Chem. 2016 Nov 3. pii: jbc.M116.758417. PMID:27810896
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (5jbt.pdb1.gz) 99 Kb
  • LPC: Ligand-Protein Contacts for 5JBT
  • CSU: Contacts of Structural Units for 5JBT
  • Structure Factors (1304 Kb)
  • Retrieve 5JBT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JBT from S2C, [Save to disk]
  • Re-refined 5jbt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JBT 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 5JBT
  • 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 5jbt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jbt_Y] [5jbt_A] [5jbt_X] [5jbt]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JBT: [KU] [Tryp_SPc ] by SMART
  • Other resources with information on 5JBT
  • Community annotation for 5JBT at PDBWiki (http://pdbwiki.org)

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