4DCB	Hydrolase	date	Jan 17, 2012
title	Y. Pestis Plasminogen Activator Pla In Complex With Human Pl Activation Loop Peptide Alp11
authors	E.Eren, B.Van Den Berg
compound		source
Molecule: Coagulasefibrinolysin Chain: A Synonym: Plasminogen Activator Ec: 3.4.23.48 Engineered: Yes Mutation: Yes		Organism_scientific: Yersinia Pestis Organism_taxid: 632 Gene: Pla, Yppcp1.07, Yp_ppcp08 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)T1 Expression_system_plasmid: Pb22
Molecule: Plasminogen Chain: F Synonym: Plasmin Heavy Chain A, Activation Peptide, Angiost Plasmin Heavy Chain A, Short Form, Plasmin Light Chain B; Ec: 3.4.21.7 Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Other_details: This Seqeunce Naturally Exists In Human Plas Activation Domain
symmetry	Space Group: I 2 2 2	R_factor 0.180 R_Free 0.232
crystal cell	length a length b length c angle alpha angle beta angle gamma 52.377 63.105 201.225 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.03 Å
ligand	C8E, MPD, MRD, PO4	enzyme	Hydrolase E.C.3.4.23.48 BRENDA
Gene	YP
Gene Ontology	Chain Function Process Component A aspartic-type endopeptidase ... peptidase activity hydrolase activity proteolysis blood coagulation hemostasis fibrinolysis plasma membrane cell outer membrane membrane integral to membrane F 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	Structural basis for activation of an integral membrane protease by lipopolysaccharide., Eren E, van den Berg B, J Biol Chem. 2012 Jul 6;287(28):23971-6. Epub 2012 May 29. PMID:22645135

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk] Biological Unit Coordinates (4dcb.pdb1.gz) 98 Kb LPC: Ligand-Protein Contacts for 4DCB CSU: Contacts of Structural Units for 4DCB Structure Factors (241 Kb) Retrieve 4DCB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 4DCB from S2C, [Save to disk] Re-refined 4dcb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4DCB in 3D

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Visual 3D analysis of 4DCB

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Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 4DCB, from MSDmotif at EBI Fold representative 4dcb from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4dcb_A] [4dcb_F] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 4DCB with the sequences similar proteins can be viewed for 4DCB'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 4DCB

Community annotation for 4DCB at PDBWiki (http://pdbwiki.org)

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