3K9M	Hydrolase Hydrolase Inhibitor	date	Oct 16, 2009
title	Cathepsin B In Complex With Stefin A
authors	M.Renko, D.Turk
compound		source
Molecule: Cathepsin B Chain: A, B Synonym: Cathepsin B1, App Secretase, Apps, Cathepsin B Lig Cathepsin B Heavy Chain; Ec: 3.4.22.1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ctsb, Cpsb Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21de3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet3a
Molecule: Cystatin-A Chain: C, D Synonym: Cystatin-As, Stefin-A Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Csta, Stf1, Stfa Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21de3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet3a
symmetry	Space Group: P 1	R_factor 0.198 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 62.122 31.078 70.937 89.95 104.45 89.90
method	X-Ray Diffraction	resolution	2.61 Å
ligand		enzyme	Hydrolase E.C.3.4.22.1 BRENDA
Gene Ontology	Chain Function Process Component A, B D, C endopeptidase inhibitor acti... cysteine-type endopeptidase ...
Primary reference	Stefin A displaces the occluding loop of cathepsin B only by as much as required to bind to the active site cleft., Renko M, Pozgan U, Majera D, Turk D, FEBS J. 2010 Oct;277(20):4338-45. doi: 10.1111/j.1742-4658.2010.07824.x., Epub 2010 Sep 22. PMID:20860624

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk] Biological Unit Coordinates (3k9m.pdb1.gz) 56 Kb Biological Unit Coordinates (3k9m.pdb2.gz) 57 Kb CSU: Contacts of Structural Units for 3K9M Structure Factors (192 Kb) Retrieve 3K9M in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3K9M from S2C, [Save to disk] Re-refined 3k9m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3K9M 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.

Visual 3D analysis of 3K9M

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3K9M, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3k9m_C] [3k9m_D] [3k9m_B] [3k9m] [3k9m_A] SWISS-PROT database: [P07858] [P01040] Domain organization of [CATB_HUMAN] [CYTA_HUMAN] by SWISSPFAM Domains found in 3K9M: [CY] [Pept_C1 ] by SMART

Other resources with information on 3K9M

Community annotation for 3K9M at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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