1YM2	Hydrolase Hydrolase Inhibitor	date	Jan 20, 2005
title	Crystal Structure Of Human Beta Secretase Complexed With Nvp
authors	S.Hanessian, H.Yun, Y.Hou, G.Yang, M.Bayrakdarian, E.Therrien, N.Moitessier, S.Roggo, S.Veenstra
compound		source
Molecule: Beta-Secretase 1 Chain: A, B, C Fragment: Unp Residues 48-447 Synonym: Beta-Site App Cleaving Enzyme 1, Beta-Site Amyloid Protein Cleaving Enzyme 1, Aspartyl Protease 2, Asp 2, Asp2 Membrane-Associated Aspartic Protease 2, Memapsin-2; Ec: 3.4.23.46 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet24
Molecule: Nvp-Aur200 Inhibitor Chain: X, Y, Z Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.212 R_Free 0.237
crystal cell	length a length b length c angle alpha angle beta angle gamma 82.261 103.258 100.621 90.00 104.12 90.00
method	X-Ray Diffraction	resolution	2.05 Å
ligand	24O, ACE, LYT BindingDB	enzyme	Hydrolase E.C.3.4.23.46 BRENDA
Gene Ontology	Chain Function Process Component A, C, B
Primary reference	Structure-based design, synthesis, and memapsin 2 (BACE) inhibitory activity of carbocyclic and heterocyclic peptidomimetics., Hanessian S, Yun H, Hou Y, Yang G, Bayrakdarian M, Therrien E, Moitessier N, Roggo S, Veenstra S, Tintelnot-Blomley M, Rondeau JM, Ostermeier C, Strauss A, Ramage P, Paganetti P, Neumann U, Betschart C, J Med Chem. 2005 Aug 11;48(16):5175-90. PMID:16078837

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (198 Kb) [Save to disk] Biological Unit Coordinates (1ym2.pdb1.gz) 67 Kb Biological Unit Coordinates (1ym2.pdb2.gz) 67 Kb Biological Unit Coordinates (1ym2.pdb3.gz) 67 Kb LPC: Ligand-Protein Contacts for 1YM2 CSU: Contacts of Structural Units for 1YM2 Likely Quarternary Molecular Structure file(s) for 1YM2 Structure Factors (943 Kb) Retrieve 1YM2 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YM2 from S2C, [Save to disk] Re-refined 1ym2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YM2 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 1YM2

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 1YM2, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ym2] [1ym2_Y] [1ym2_Z] [1ym2_C] [1ym2_X] [1ym2_A] [1ym2_B] 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 1YM2

Community annotation for 1YM2 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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