2VKM	Hydrolase	date	Dec 04, 2007
title	Crystal Structure Of Grl-8234 Bound To Bace (Beta-Secretase)
authors	L.Hong, J.Tang, A.K.Ghosh
compound		source
Molecule: Beta-Secretase 1 Chain: A, B, C, D Fragment: Beta-Secretase Catalytic Domain, Residues 58-446 Synonym: Beta-Site App Cleaving Enzyme 1, Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1, Membrane-Associated Aspartic Protease 2, Memapsin-2, Aspartyl Protease 2, Asp 2, Asp2, Bace; Engineered: Yes Other_details: Beta Secretase Inhibitor		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21
symmetry	Space Group: P 1 21 1	R_factor 0.2016 R_Free 0.2418
crystal cell	length a length b length c angle alpha angle beta angle gamma 86.704 130.308 87.711 90.00 97.41 90.00
method	X-Ray Diffraction	resolution	2.05 Å
ligand	BSD BindingDB	enzyme
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Potent memapsin 2 (beta-secretase) inhibitors: design, synthesis, protein-ligand X-ray structure, and in vivo evaluation., Ghosh AK, Kumaragurubaran N, Hong L, Kulkarni S, Xu X, Miller HB, Reddy DS, Weerasena V, Turner R, Chang W, Koelsch G, Tang J, Bioorg Med Chem Lett. 2008 Feb 1;18(3):1031-6. Epub 2008 Jan 3. PMID:18180160

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (272 Kb) [Save to disk] Biological Unit Coordinates (2vkm.pdb1.gz) 70 Kb Biological Unit Coordinates (2vkm.pdb2.gz) 71 Kb Biological Unit Coordinates (2vkm.pdb3.gz) 71 Kb Biological Unit Coordinates (2vkm.pdb4.gz) 69 Kb LPC: Ligand-Protein Contacts for 2VKM CSU: Contacts of Structural Units for 2VKM Likely Quarternary Molecular Structure file(s) for 2VKM Structure Factors (1684 Kb) Retrieve 2VKM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VKM from S2C, [Save to disk] Re-refined 2vkm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VKM in 3D

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Visual 3D analysis of 2VKM

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 2VKM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vkm_C] [2vkm_B] [2vkm_D] [2vkm] [2vkm_A] SWISS-PROT database: [P56817] Belongs to the β-amyloid cleaving enzyme (bace1) family according to TCDB. Domain organization of [BACE1_HUMAN] by SWISSPFAM

Other resources with information on 2VKM

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

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