4DCB Hydrolase date Jan 17, 2012
title Y. Pestis Plasminogen Activator Pla In Complex With Human Pl Activation Loop Peptide Alp11
authors E.Eren, B.Van Den Berg
compound source
Molecule: Coagulasefibrinolysin
Chain: A
Synonym: Plasminogen Activator
Ec: 3.4.23.48
Engineered: Yes
Mutation: Yes
Organism_scientific: Yersinia Pestis
Organism_taxid: 632
Gene: Pla, Yppcp1.07, Yp_ppcp08
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)T1
Expression_system_plasmid: Pb22

Molecule: Plasminogen
Chain: F
Synonym: Plasmin Heavy Chain A, Activation Peptide, Angiost Plasmin Heavy Chain A, Short Form, Plasmin Light Chain B;
Ec: 3.4.21.7
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: This Seqeunce Naturally Exists In Human Plas Activation Domain
symmetry Space Group: I 2 2 2
R_factor 0.180 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.377 63.105 201.225 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.03 Å
ligand C8E, MPD, MRD, PO4 enzyme Hydrolase E.C.3.4.23.48 BRENDA
Gene YP
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for activation of an integral membrane protease by lipopolysaccharide., Eren E, van den Berg B, J Biol Chem. 2012 Jul 6;287(28):23971-6. Epub 2012 May 29. PMID:22645135
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (4dcb.pdb1.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 4DCB
  • CSU: Contacts of Structural Units for 4DCB
  • Structure Factors (241 Kb)
  • Retrieve 4DCB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DCB from S2C, [Save to disk]
  • Re-refined 4dcb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DCB 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 4DCB
  • 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 4DCB, from MSDmotif at EBI
  • Fold representative 4dcb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dcb_F] [4dcb_A] [4dcb]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4DCB
  • Community annotation for 4DCB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
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