1YM4

Crystal structure of human beta secretase complexed with NVP-AMK640

Structural Biology Knowledgebase: 1YM4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.240

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YM4

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 138234.53

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A, B, C 408 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: UNP residues 48-453
Gene Name(s): BACE1 Gene View BACE KIAA1149
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NVP-AMK640 INHIBITOR X, Y, Z 5 synthetic

Small Molecules
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000292 (VAL,ALA,24M,GLU,ASN) X, Y, Z BETA-SECRETASE INHIBITOR NVP-AMK640 Peptide-like /
Inhibitor
Ligand Explorer 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: 2.25 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.240
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 223.68 α = 90.00
b = 107.75 β = 100.32
c = 61.47 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: Atom nomenclature | Details: Atom nomenclature
  • 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