1PKR	Plasminogen	date	Aug 03, 1993
title	The Structure Of Recombinant Plasminogen Kringle 1 And The Fibrin Binding Site
authors	T.P.Wu, A.Tulinsky
compound		source
Molecule: Plasminogen Chain: A Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: P 43 21 2	R_factor R_Free NULL
crystal cell	length a length b length c angle alpha angle beta angle gamma 58.930 58.930 54.640 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.48 Å
ligand	CL	enzyme
related structures	by homologous chain: 1CEB, 1HPJ
Gene Ontology	Chain Function Process Component A 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	The structure of recombinant plasminogen kringle 1 and the fibrin binding site., Wu TP, Padmanabhan KP, Tulinsky A, Blood Coagul Fibrinolysis 1994 Apr;5(2):157-66. PMID:8054447

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (19 Kb) [Save to disk] Biological Unit Coordinates (1pkr.pdb1.gz) 15 Kb LPC: Ligand-Protein Contacts for 1PKR CSU: Contacts of Structural Units for 1PKR Likely Quarternary Molecular Structure file(s) for 1PKR Retrieve 1PKR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1PKR from S2C, [Save to disk]

View 1PKR 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 1PKR

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 1PKR, from MSDmotif at EBI Genome occurence of 1PKR's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1pkr__, region [Jmol] [rasmolscript] [script source] Fold representative 1pkr from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1pkr_A] SWISS-PROT database: [P00747] Domain organization of [PLMN_HUMAN] by SWISSPFAM Domain found in 1PKR: [KR ] by SMART Alignments of the sequence of 1PKR with the sequences similar proteins can be viewed for 1PKR's classification [PLMN_HUMAN] 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 [PLMN_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1PKR

Community annotation for 1PKR at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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