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; Ec: 3.4.21.7		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
crystal cell	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 Diffraction	resolution	3.49 Å
ligand	CL, GAL, NGA, SIA	enzyme	Hydrolase E.C.3.4.21.7 BRENDA
Gene Ontology	Chain Function Process Component S serine-type endopeptidase ac... protein binding peptidase activity serine-type peptidase activi... hydrolase activity protein domain specific bind... apolipoprotein binding cell surface binding platelet degranulation proteolysis blood coagulation hemostasis negative regulation of cell ... negative regulation of cell-... extracellular matrix disasse... platelet activation extracellular matrix organiz... fibrinolysis cellular protein metabolic p... tissue remodeling negative regulation of fibri... positive regulation of fibri... negative regulation of cell-... extracellular region extracellular space plasma membrane platelet alpha granule lumen... extrinsic to external side o...
Primary reference	Crystal 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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] SWISS-PROT database: Domain organization of by SWISSPFAM 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)

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