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
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;
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
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. BRENDA
Gene YP

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
  • Alignments of the sequence of 4DCB with the sequences similar proteins can be viewed for 4DCB's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4DCB
  • Community annotation for 4DCB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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