4DV9	Hydrolase Hydrolase Inhibitor	date	Feb 23, 2012
title	Crystal Structure Of Bace1 With Its Inhibitor
authors	Y.C.Xu, W.Y.Chen, L.Li, T.T.Chen
compound		source
Molecule: Beta-Secretase 1 Chain: A Fragment: Unp Residues 43-454 Synonym: Bace1, Aspartyl Protease 2, Asp2, Asp 2, Beta-Site Precursor Protein Cleaving Enzyme 1, Beta-Site App Cleaving Memapsin-2, Membrane-Associated Aspartic Protease 2; Ec: 3.4.23.46 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Bace1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: Methyl (2s)-1-[(2r,5s,8s,12s,13s,16s,19s,22s)-16- 3-Oxopropyl)-2,13-Dibenzyl-12,22-Dihydroxy-3,5,17-Trimethyl Methylpropyl)-4,7,10,15,18,21-Hexaoxo-19-(Propan-2-Yl)-3,6, 20-Hexaazatricosan-1-Oyl]Pyrrolidine-2-Carboxylate (Non-Pre Name); Chain: B Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630 Other_details: Synthetic Peptide Inhibitor
symmetry	Space Group: C 2 2 21	R_factor 0.172 R_Free 0.209
crystal cell	length a length b length c angle alpha angle beta angle gamma 105.528 128.846 76.766 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.08 Å
ligand	2OP, GNC, PLJ, PSA, SO4, ZAE	enzyme	Hydrolase E.C.3.4.23.46 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Cyanobacterial Peptides as a Prototype for the Design of Potent beta-Secretase Inhibitors and the Development of Selective Chemical Probes for Other Aspartic Proteases., Liu Y, Zhang W, Li L, Salvador LA, Chen T, Chen W, Felsenstein KM, Ladd TB, Price AR, Golde TE, He J, Xu Y, Li Y, Luesch H, J Med Chem. 2012 Dec 13;55(23):10749-65. doi: 10.1021/jm301630s. Epub 2012 Nov, 26. PMID:23181502

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk] Biological Unit Coordinates (4dv9.pdb1.gz) 67 Kb LPC: Ligand-Protein Contacts for 4DV9 CSU: Contacts of Structural Units for 4DV9 Structure Factors (1279 Kb) Retrieve 4DV9 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 4DV9 from S2C, [Save to disk] Re-refined 4dv9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4DV9 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 4DV9

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 4DV9, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4dv9_B] [4dv9_A] [4dv9] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 4DV9

Community annotation for 4DV9 at PDBWiki (http://pdbwiki.org)

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