1M4H Hydrolase Hydrolase Inhibitor date Jul 02, 2002
title Crystal Structure Of Beta-Secretase Complexed With Inhibitor
authors L.Hong, R.T.Turner, G.Koelsch, A.K.Ghosh, J.Tang
compound source
Molecule: Beta-Secretase
Chain: A, B
Fragment: Protease Domain
Synonym: Memapsin-2
Ec: 3.4.23.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bace
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Inhibitor Om00-3
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.450 88.787 130.954 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 1OL enzyme Hydrolase E.C.3.4.23 BRENDA
note 1M4H (Molecule of the Month:pdb115)
related structures by homologous chain: 1W51, 1XN3
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of memapsin 2 (beta-secretase) in complex with an inhibitor OM00-3., Hong L, Turner RT 3rd, Koelsch G, Shin D, Ghosh AK, Tang J, Biochemistry 2002 Sep 10;41(36):10963-7. PMID:12206667
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (1m4h.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (1m4h.pdb2.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 1M4H
  • CSU: Contacts of Structural Units for 1M4H
  • Likely Quarternary Molecular Structure file(s) for 1M4H
  • Structure Factors (863 Kb)
  • Retrieve 1M4H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M4H from S2C, [Save to disk]
  • Re-refined 1m4h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1M4H 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 1M4H
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1M4H, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m4ha_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m4hb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1m4h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1m4h_D] [1m4h] [1m4h_A] [1m4h_C] [1m4h_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 1M4H
  • Community annotation for 1M4H at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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