1YM2

Crystal structure of human beta secretase complexed with NVP-AUR200

Structural Biology Knowledgebase: 1YM2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YM2

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 136337.23

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A, B, C 402 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: UNP residues 48-447
Gene Name(s): BACE1 Gene View BACE KIAA1149
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NVP-AUR200 INHIBITOR X, Y, Z 6 synthetic

Small Molecules
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000291 (24O,ACE,VAL,LYT,MET,LEU) X, Y, Z BETA-SECRETASE INHIBITOR NVP-AUR200 Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.212
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.26 α = 90.00
b = 103.26 β = 104.12
c = 100.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-20
  • Released Date: 2006-01-17
  • Deposition author(s): Hanessian, S., Yun, H., Hou, Y., Yang, G., Bayrakdarian, M., Therrien, E., Moitessier, N., Roggo, S., Veenstra, S.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature