3ZKM	Hydrolase Immune System	date	Jan 23, 2013
title	Bace2 Fab Complex
authors	D.W.Banner, A.Kuglstatter, J.Benz, M.Stihle, A.Ruf
compound		source
Molecule: Beta-Secretase 2 Chain: A, B Fragment: Extracellular, Residues 75-460 Synonym: Aspartic-Like Protease 56 Kda, Aspartyl Protease 1 Asp 1, Beta-Site Amyloid Precursor Protein Cleaving Enzyme Site App Cleaving Enzyme 2, Down Region Aspartic Protease, Memapsin-1, Membrane-Associated Aspartic Protease 1, Theta- Bace2; Ec: 3.4.23.45 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)
Molecule: Fab Heavy Chain Chain: C, H Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_cell_line: Hybridoma Cell
Molecule: Fab Light Chain Chain: D, L Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Human Organism_taxid: 10090 Expression_system: Mus Musculus Expression_system_taxid: 10090 Expression_system_strain: House Mouse Expression_system_cell_line: Hybridoma Cell
symmetry	Space Group: P 21 21 21	R_factor 0.211 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 67.944 161.101 163.233 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.85 Å
ligand	DMS, GOL, PCA, SO4	enzyme	Hydrolase E.C.3.4.23.45 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Mapping the conformational space accessible to BACE2 using surface mutants and cocrystals with Fab fragments, Fynomers and Xaperones., Banner DW, Gsell B, Benz J, Bertschinger J, Burger D, Brack S, Cuppuleri S, Debulpaep M, Gast A, Grabulovski D, Hennig M, Hilpert H, Huber W, Kuglstatter A, Kusznir E, Laeremans T, Matile H, Miscenic C, Rufer AC, Schlatter D, Steyaert J, Stihle M, Thoma R, Weber M, Ruf A, Acta Crystallogr D Biol Crystallogr. 2013 Jun;69(Pt 6):1124-37. doi:, 10.1107/S0907444913006574. Epub 2013 May 15. PMID:23695257

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (276 Kb) [Save to disk] Biological Unit Coordinates (3zkm.pdb1.gz) 139 Kb Biological Unit Coordinates (3zkm.pdb2.gz) 137 Kb LPC: Ligand-Protein Contacts for 3ZKM CSU: Contacts of Structural Units for 3ZKM Structure Factors (2908 Kb) Retrieve 3ZKM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3ZKM from S2C, [Save to disk] Re-refined 3zkm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3ZKM 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 3ZKM

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3ZKM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3zkm_A] [3zkm_D] [3zkm_L] [3zkm_B] [3zkm_C] [3zkm_H] [3zkm] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3ZKM: [IG_like] [IGv ] by SMART

Other resources with information on 3ZKM

Community annotation for 3ZKM at PDBWiki (http://pdbwiki.org)

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