2PK4	Hydrolase(Serine Protease)	date	Jul 18, 1991
title	The Refined Structure Of The Epsilon-Aminocaproic Acid Complex Of Human Plasminogen Kringle
authors	A.Tulinsky, T.P.Wu
compound		source
Molecule: Human Plasminogen Kringle 4 Chain: A Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: P 1 21 1	R_factor R_Free NULL
crystal cell	length a length b length c angle alpha angle beta angle gamma 42.210 35.460 25.430 90.00 102.94 90.00
method	X-Ray Diffraction	resolution	2.25 Å
ligand	ACA	enzyme
related structures	by homologous chain: 1PMK, 4KIV
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 refined structure of the epsilon-aminocaproic acid complex of human plasminogen kringle 4., Wu TP, Padmanabhan K, Tulinsky A, Mulichak AM, Biochemistry 1991 Oct 29;30(43):10589-94. PMID:1657149

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (20 Kb) [Save to disk] Biological Unit Coordinates (2pk4.pdb1.gz) 16 Kb LPC: Ligand-Protein Contacts for 2PK4 CSU: Contacts of Structural Units for 2PK4 Likely Quarternary Molecular Structure file(s) for 2PK4 Retrieve 2PK4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2PK4 from S2C, [Save to disk]

View 2PK4 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 2PK4

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 2PK4, from MSDmotif at EBI Genome occurence of 2PK4's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d2pk4__, region [Jmol] [rasmolscript] [script source] Fold representative 2pk4 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: [2pk4_A] SWISS-PROT database: [P00747] Domain organization of [PLMN_HUMAN] by SWISSPFAM Domain found in 2PK4: [KR ] by SMART Alignments of the sequence of 2PK4 with the sequences similar proteins can be viewed for 2PK4'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 2PK4

Community annotation for 2PK4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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