4DUR Hydrolase date Feb 22, 2012
title The X-Ray Crystal Structure Of Full-Length Type II Human Pla
authors R.H.P.Law, T.Caradoc-Davies, J.C.Whisstock
compound source
Molecule: Plasminogen
Chain: A, B
Synonym: Serine Protease
Ec: 3.4.21.7
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Plasma
symmetry Space Group: P 32 2 1
R_factor 0.190 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.620 144.620 233.670 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.45 Å
ligand ACT, BCT, CL, GAL, K, NAG, SIA enzyme Hydrolase E.C.3.4.21.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe X-ray crystal structure of full-length human plasminogen., Law RH, Caradoc-Davies T, Cowieson N, Horvath AJ, Quek AJ, Encarnacao JA, Steer D, Cowan A, Zhang Q, Lu BG, Pike RN, Smith AI, Coughlin PB, Whisstock JC, Cell Rep. 2012 Mar 29;1(3):185-90. doi: 10.1016/j.celrep.2012.02.012. Epub 2012, Mar 8. PMID:22832192
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (547 Kb) [Save to disk]
  • Biological Unit Coordinates (4dur.pdb1.gz) 275 Kb
  • Biological Unit Coordinates (4dur.pdb2.gz) 269 Kb
  • LPC: Ligand-Protein Contacts for 4DUR
  • CSU: Contacts of Structural Units for 4DUR
  • Structure Factors (2057 Kb)
  • Retrieve 4DUR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DUR from S2C, [Save to disk]
  • Re-refined 4dur structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DUR 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 4DUR
  • 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 4DUR, from MSDmotif at EBI
  • Fold representative 4dur from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dur_A] [4dur_B] [4dur]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4DUR with the sequences similar proteins can be viewed for 4DUR'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 4DUR
  • Community annotation for 4DUR at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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