1I5K	Blood Clotting	date	Feb 27, 2001
title	Structure And Binding Determinants Of The Recombinant Kringl Of Human Plasminogen To An Internal Peptide From A Group A Streptococcal Surface Protein
authors	J.L.Rios-Steiner, M.Schenone, I.Mochalkin, A.Tulinsky, F.J.Caste
compound		source
Molecule: Plasminogen Chain: A, B Fragment: Modified Recombinant Kringle-2 Domain Ec: 3.4.21.7 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Pichia Pastoris Expression_system_taxid: 4922
Molecule: M Protein Chain: C, D Fragment: Vek-30 (30 Residue Internal Peptide) Engineered: Yes		Synthetic: Yes Other_details: Vek-30 Was Synthesized By Automated Solid Ph Peptide Synthesis
symmetry	Space Group: P 61 2 2	R_factor 0.195 R_Free 0.262
crystal cell	length a length b length c angle alpha angle beta angle gamma 91.980 91.980 151.779 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand		enzyme	Hydrolase E.C.3.4.21.7 BRENDA
note	1I5K is a representative structure
related structures	by homologous chain: 1B2I, 1KI0
Gene Ontology	Chain Function Process Component A, B 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	Structure and binding determinants of the recombinant kringle-2 domain of human plasminogen to an internal peptide from a group A Streptococcal surface protein., Rios-Steiner JL, Schenone M, Mochalkin I, Tulinsky A, Castellino FJ, J Mol Biol 2001 May 11;308(4):705-19. PMID:11350170

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk] Biological Unit Coordinates (1i5k.pdb1.gz) 39 Kb CSU: Contacts of Structural Units for 1I5K Likely Quarternary Molecular Structure file(s) for 1I5K Retrieve 1I5K in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1I5K from S2C, [Save to disk]

View 1I5K 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 1I5K

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 1I5K, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1i5ka_, region A [Jmol] [rasmolscript] [script source]     - Domain d1i5kb_, region B [Jmol] [rasmolscript] [script source] Fold representative 1i5k 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: [1i5k_A] [1i5k_B] [1i5k_C] [1i5k_D] SWISS-PROT database: [P49054] [P00747] Domain organization of [PAM_STRPY] [PLMN_HUMAN] by SWISSPFAM Domain found in 1I5K: [KR ] by SMART Alignments of the sequence of 1I5K with the sequences similar proteins can be viewed for 1I5K's classification [PAM_STRPY] [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 [PAM_STRPY] [PLMN_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1I5K

Community annotation for 1I5K at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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