2KNF	Blood Clotting	date	Aug 21, 2009
title	Solution Structure And Functional Characterization Of Human Plasminogen Kringle 5
authors	M.D.Battistel, A.Grishaev, S.A.An, F.J.Castellino, M.Llinas
compound		source
Molecule: Plasminogen Chain: A Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Plg Expression_system: Pichia Pastoris Expression_system_taxid: 4922 Expression_system_strain: Gs115 Expression_system_variant: (Met+)
method	Solution NMR
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	Solution Structure and Functional Characterization of Human Plasminogen Kringle 5 (,)., Battistel MD, Grishaev A, An SS, Castellino FJ, Llinas M, Biochemistry. 2009 Nov 3;48(43):10208-10219. PMID:19821587

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (433 Kb) [Save to disk] CSU: Contacts of Structural Units for 2KNF Original NMR restraints for 2KNF from PDB Retrieve 2KNF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2KNF from S2C, [Save to disk]

View 2KNF 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 2KNF

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 2KNF, from MSDmotif at EBI Fold representative 2knf from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2knf_A] SWISS-PROT database: [P00747] Domain organization of [PLMN_HUMAN] by SWISSPFAM Domain found in 2KNF: [KR ] by SMART Alignments of the sequence of 2KNF with the sequences similar proteins can be viewed for 2KNF'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 2KNF

Community annotation for 2KNF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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