- PDB-2xfk: Human BACE-1 in complex with N-((1S,2R)-3-(((1S)-2-(cyclohexylami... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2xfk
Title
Human BACE-1 in complex with N-((1S,2R)-3-(((1S)-2-(cyclohexylamino)- 1-methyl-2-oxoethyl)amino)-2-hydroxy-1-(phenylmethyl)propyl)-3-(ethylamino)-5-((methylsulfonyl)(phenyl)amino)benzamide
Components
BETA-SECRETASE 1
Keywords
HYDROLASE / ZYMOGEN / PROTEASE
Function / homology
Function and homology information
memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / lysosome / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane Similarity search - Function
Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta Similarity search - Domain/homology
SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.
Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 223 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 354 TO GLN
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.2 Å3/Da / Density % sol: 43.97 % / Description: NONE
Crystal grow
Temperature: 293 K / Method: vapor diffusion Details: CRYSTALS GROWN BY VAPOUR DIFFUSION AT 20C USING STREAK SEEDING, WITH 10% PEG8000 AND 0.1M GLYCINE PH 3.2
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9393 Å / Relative weight: 1
Reflection
Resolution: 1.8→25 Å / Num. obs: 36639 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.5
Reflection shell
Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.8 / % possible all: 94.8
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Processing
Software
Name
Version
Classification
REFMAC
5.5
refinement
DENZO
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.8→61.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.177 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19515
1465
4 %
RANDOM
Rwork
0.16329
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obs
0.16456
35116
99.59 %
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Displacement parameters
Biso mean: 16.947 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.87 Å2
0 Å2
0 Å2
2-
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-0.54 Å2
0 Å2
3-
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-1.33 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→61.9 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2928
0
46
361
3335
LS refinement shell
Resolution: 1.796→1.843 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.247
107
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Rwork
0.189
2498
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obs
-
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97.06 %
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