4A5T Hydrolase date Oct 28, 2011
title Structural Basis For The Conformational Modulation
authors Y.Xue, C.Bodin, K.Olsson
compound source
Molecule: Plasminogen
Chain: S
Synonym: Plasmin Heavy Chain A, Activation Peptide, Angiost Plasmin Heavy Chain A\,Short Form, Plasmin Light Chain B;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 43 21 2
R_factor 0.2085 R_Free 0.2501
length a length b length c angle alpha angle beta angle gamma
118.460 118.460 179.250 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.49 Å
ligand CL, GAL, NGA, SIA enzyme Hydrolase E.C. BRENDA

Primary referenceCrystal structure of the native plasminogen reveals an activation-resistant compact conformation., Xue Y, Bodin C, Olsson K, J Thromb Haemost. 2012 Apr 28. doi: 10.1111/j.1538-7836.2012.04765.x. PMID:22540246
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (269 Kb) [Save to disk]
  • Biological Unit Coordinates (4a5t.pdb1.gz) 261 Kb
  • LPC: Ligand-Protein Contacts for 4A5T
  • CSU: Contacts of Structural Units for 4A5T
  • Structure Factors (321 Kb)
  • Retrieve 4A5T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4A5T from S2C, [Save to disk]
  • Re-refined 4a5t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4A5T 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 4A5T
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4A5T, from MSDmotif at EBI
  • Fold representative 4a5t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4a5t_S] [4a5t]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4A5T: [KR] [PAN_AP] [Tryp_SPc ] by SMART
  • Alignments of the sequence of 4A5T with the sequences similar proteins can be viewed for 4A5T'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 4A5T
  • Community annotation for 4A5T at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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