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- PDB-2ze1: X-ray structure of Bace-1 in complex with compound 6g -

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Basic information

Entry
Database: PDB / ID: 2ze1
TitleX-ray structure of Bace-1 in complex with compound 6g
ComponentsBeta-secretase 1
KeywordsHYDROLASE / BACE / Aspartyl Protease / Acylguanidine Inhibitor / Alternative splicing / Glycoprotein / Membrane / Transmembrane / Zymogen
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 / amyloid-beta metabolic process / cellular response to manganese ion / 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 / amyloid-beta metabolic process / cellular response to manganese ion / 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 / multivesicular body / hippocampal mossy fiber to CA3 synapse / 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 / early endosome / lysosome / 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
Chem-411 / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChopra, R. / Olland, A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Acylguanidine inhibitors of beta-secretase: optimization of the pyrrole ring substituents extending into the S1 and S3 substrate binding pockets.
Authors: Cole, D.C. / Stock, J.R. / Chopra, R. / Cowling, R. / Ellingboe, J.W. / Fan, K.Y. / Harrison, B.L. / Hu, Y. / Jacobsen, S. / Jennings, L.D. / Jin, G. / Lohse, P.A. / Malamas, M.S. / Manas, E. ...Authors: Cole, D.C. / Stock, J.R. / Chopra, R. / Cowling, R. / Ellingboe, J.W. / Fan, K.Y. / Harrison, B.L. / Hu, Y. / Jacobsen, S. / Jennings, L.D. / Jin, G. / Lohse, P.A. / Malamas, M.S. / Manas, E.S. / Moore, W.J. / O'Donnell, M.M. / Olland, A.M. / Robichaud, A.J. / Svenson, K. / Wu, J. / Wagner, E. / Bard, J.
History
DepositionDec 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9572
Polymers46,4411
Non-polymers5161
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.026, 104.321, 50.465
Angle α, β, γ (deg.)90.00, 94.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

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Components

#1: Protein Beta-secretase 1 / Beta-site APP cleaving enzyme 1 / Beta-site amyloid precursor protein cleaving enzyme 1 / Membrane- ...Beta-site APP cleaving enzyme 1 / Beta-site amyloid precursor protein cleaving enzyme 1 / Membrane-associated aspartic protease 2 / Memapsin-2 / Aspartyl protease 2 / Asp 2 / ASP2


Mass: 46440.980 Da / Num. of mol.: 1 / Fragment: UNP residues 46-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-411 / 3-bromo-N-[4-[1-(2-carbamimidamido-2-oxo-ethyl)-5-phenyl-pyrrol-2-yl]phenyl]benzamide


Mass: 516.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H22BrN5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→59.76 Å / Num. obs: 15940 / % possible obs: 0.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PROTEUM PLUSPLUSdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.877 / SU B: 19.455 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.495 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28981 863 5.1 %RANDOM
Rwork0.24833 ---
obs0.25047 11136 87.78 %-
all-11879 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.909 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-0.56 Å2
2---0.38 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 34 86 2966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222959
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9574020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35123.507134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3815462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4641517
X-RAY DIFFRACTIONr_chiral_restr0.1360.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022280
X-RAY DIFFRACTIONr_nbd_refined0.2080.21294
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.23
X-RAY DIFFRACTIONr_mcbond_it0.5141.51830
X-RAY DIFFRACTIONr_mcangle_it0.91822880
X-RAY DIFFRACTIONr_scbond_it0.91431318
X-RAY DIFFRACTIONr_scangle_it1.4484.51140
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 64 -
Rwork0.311 1051 -
obs--80.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77420.66720.18651.17050.080.05590.05520.04680.03310.0972-0.04050.05320.0099-0.0227-0.0147-0.02470.00860.0102-0.0285-0.0025-0.033516.1407-0.594610.0198
20.11840.10060.12160.08550.10330.1248-0.0278-0.00930.02420.06880.013-0.05490.0105-0.04860.0148-0.0124-0.00480.02970.03280.03660.024217.0516-4.50179.828
322.0486-6.3574-8.819723.5351-9.268321.338-0.5339-0.9705-1.0294-0.50610.63630.53490.8844-0.6644-0.10240.1115-0.1148-0.03090.101-0.10510.058112.9848-7.153816.2705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA61 - 44615 - 400
2X-RAY DIFFRACTION2AC462 - 5471 - 86
3X-RAY DIFFRACTION3AB11

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