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- PDB-5mxd: BACE-1 IN COMPLEX WITH LIGAND 32397778 -

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Basic information

Entry
Database: PDB / ID: 5mxd
TitleBACE-1 IN COMPLEX WITH LIGAND 32397778
ComponentsBeta-secretase 1
KeywordsHYDROLASE / BACE 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 / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / cellular response to manganese ion ...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 / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / cellular response to manganese ion / prepulse inhibition / 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 / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / 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
Chem-III / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsAlexander, R.
CitationJournal: to be published
Title: Human Beta Secretase 1 In Complex With Ligand 32397778
Authors: Alexander, R.
History
DepositionJan 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
B: Beta-secretase 1
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,1679
Polymers144,3333
Non-polymers8336
Water00
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3893
Polymers48,1111
Non-polymers2782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3893
Polymers48,1111
Non-polymers2782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3893
Polymers48,1111
Non-polymers2782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)232.913, 100.737, 59.045
Angle α, β, γ (deg.)90.00, 102.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 48111.129 Da / Num. of mol.: 3 / Fragment: PROTEASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-III / ~{N},~{N}-dimethyl-2-pyrrolidin-1-yl-quinazolin-4-amine


Mass: 242.320 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H18N4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
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: 2.57 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2014
Details: LN2 cooled fixed-exit Si(111) monochromator, Dynamically bendable mirror, KB mirror pair
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.52→113.9 Å / Num. obs: 43635 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.64
Reflection shellResolution: 2.52→2.77 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.556 / % possible all: 97.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→113.9 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU B: 34.555 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.683 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28085 991 2.3 %RANDOM
Rwork0.22695 ---
obs0.22822 42644 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.783 Å2
Baniso -1Baniso -2Baniso -3
1--3.7 Å20 Å2-0.84 Å2
2---2.28 Å2-0 Å2
3---5.81 Å2
Refinement stepCycle: LAST / Resolution: 2.52→113.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8960 0 57 0 9017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199256
X-RAY DIFFRACTIONr_bond_other_d0.0020.028558
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.95312589
X-RAY DIFFRACTIONr_angle_other_deg0.899319677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78851134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14523.863422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.515151462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3581551
X-RAY DIFFRACTIONr_chiral_restr0.0710.21361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022201
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5164.3824554
X-RAY DIFFRACTIONr_mcbond_other3.5164.3824553
X-RAY DIFFRACTIONr_mcangle_it5.3017.3845682
X-RAY DIFFRACTIONr_mcangle_other5.3017.3845683
X-RAY DIFFRACTIONr_scbond_it3.5694.6994702
X-RAY DIFFRACTIONr_scbond_other3.5694.7014703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2697.7936908
X-RAY DIFFRACTIONr_long_range_B_refined7.2219.7959834
X-RAY DIFFRACTIONr_long_range_B_other7.21919.7989835
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 68 -
Rwork0.388 3231 -
obs--97.86 %
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)
10.7339-2.806-1.3720.57260.60795.00640.11170.06590.0952-1.1338-0.1109-0.61060.09180.0376-0.00090.0971-0.006-0.02180.22170.00360.1615-27.871-57.67211.411
24.83291.78450.9032.6908-0.34622.298-0.02760.30410.1475-0.04990.0549-0.12910.0266-0.1225-0.02720.0092-0.0199-0.00180.13210.02520.0311-44.319-56.79314.325
32.15884.9395-0.683611.7764-0.8984.9030.461-0.13130.23331.0901-0.16520.1191-0.55370.3434-0.29580.19460.0593-0.03120.33-0.08290.4602-51.351-46.41219.163
44.47980.880.13693.338-0.39691.2981-0.01480.01190.60150.1223-0.0245-0.0163-0.1506-0.02010.03930.05860.014-0.07410.1263-0.01610.199-21.487-46.53225.285
55.12523.3665-3.10432.4593-0.67969.6004-0.24310.0296-0.3493-0.22150.1466-0.2194-0.29831.01620.09650.3345-0.150.09730.5127-0.14880.3311-18.187-88.469-7.62
63.89071.89080.03035.1292.3913.7553-0.18260.20270.0581-0.37340.3756-0.6943-0.18010.7596-0.19310.1028-0.03630.00630.3146-0.07580.2186-15.631-79.4166.441
71.3201-2.29220.335617.3781.65090.7753-0.1657-0.178-0.260.40710.3595-0.13750.21830.0926-0.19380.26170.02820.00040.31070.01120.285-11.916-84.00319.006
81.97470.20350.45974.64131.06671.55290.0828-0.0025-0.14670.24640.1041-0.32140.18280.2218-0.1870.09360.0489-0.06750.2306-0.02490.0588-26.787-104.5881.695
911.7535-9.24342.143312.2567-0.3790.7459-0.1431-0.9453-0.61340.5230.24250.69660.0844-0.3202-0.09930.0531-0.0320.02370.28290.00860.2364-71.653-27.02140.177
103.12341.61850.29682.51660.7072.3239-0.14260.1664-0.1841-0.22250.10360.08130.3335-0.17270.03890.25740.056-0.02760.3418-0.06490.0607-71.539-37.91227.417
117.5348-0.36835.59322.52590.176.60830.1023-0.04540.06230.2432-0.0030.00650.23340.2601-0.09920.2885-0.01730.05360.2593-0.00910.2584-62.87-47.89725.476
121.9905-0.29931.12942.80980.47743.01520.09730.2077-0.1954-0.03870.0046-0.36730.26140.1816-0.10190.05130.0591-0.00310.1709-0.04640.0845-51.1-25.36640.967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 63
3X-RAY DIFFRACTION2A81 - 146
4X-RAY DIFFRACTION3A64 - 80
5X-RAY DIFFRACTION4A147 - 385
6X-RAY DIFFRACTION5B1 - 11
7X-RAY DIFFRACTION6B12 - 63
8X-RAY DIFFRACTION6B81 - 146
9X-RAY DIFFRACTION7B64 - 80
10X-RAY DIFFRACTION8B147 - 385
11X-RAY DIFFRACTION9C1 - 11
12X-RAY DIFFRACTION10C12 - 63
13X-RAY DIFFRACTION10C81 - 146
14X-RAY DIFFRACTION11C64 - 80
15X-RAY DIFFRACTION12C147 - 385

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