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- PDB-5qd9: Crystal structure of BACE complex with BMC005 -

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Basic information

Entry
Database: PDB / ID: 5qd9
TitleCrystal structure of BACE complex with BMC005
ComponentsBeta-secretase 1
KeywordsHYDROLASE / Hydroloase / D3R / BACE / Ligand Docking
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 / 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 / synaptic vesicle / late endosome / 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-E6Y / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.602 Å
Model detailsStructures for D3R docking challenge
AuthorsRondeau, J.M. / Shao, C. / Yang, H. / Burley, S.K.
CitationJournal: J.Comput.Aided Mol.Des. / Year: 2020
Title: D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Authors: Parks, C.D. / Gaieb, Z. / Chiu, M. / Yang, H. / Shao, C. / Walters, W.P. / Jansen, J.M. / McGaughey, G. / Lewis, R.A. / Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Burley, S.K. / Amaro, R.E. / Gilson, M.K.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.2Feb 10, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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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)135,9216
Polymers134,3323
Non-polymers1,5893
Water1,09961
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3072
Polymers44,7771
Non-polymers5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3072
Polymers44,7771
Non-polymers5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3072
Polymers44,7771
Non-polymers5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.489, 103.490, 99.382
Angle α, β, γ (deg.)90.000, 104.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31(chain C and (resid -2 through 157 or resid 169 through 385))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA-2 - 385
211chain BB-2 - 385
311(chain C and (resid -2 through 157 or resid 169 through 385))C-2 - 157
321(chain C and (resid -2 through 157 or resid 169 through 385))C169 - 385

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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: 44777.336 Da / Num. of mol.: 3
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-E6Y / (5S,8S,10R)-8-[(1R)-2-{[1-(3-tert-butylphenyl)cyclopropyl]amino}-1-hydroxyethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione


Mass: 529.754 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H51N3O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 292 K / Method: hanging drop
Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE. PROTEIN STOCK WAS BACE MUT46B BATCH XIV 6.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 7-FOLD ...Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE. PROTEIN STOCK WAS BACE MUT46B BATCH XIV 6.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 7-FOLD EXCESS OF BMC005 ADDED FROM A 50MM STOCK SOLUTION IN DMSO (2.0% DMSO IN DROP). CRYO- PROTECTANT WAS 1.2M AMMONIUM SULFATE, 25%(V/V)GLYCEROL, 2.0% DMSO, 1MM BMC005.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97856
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.602→46.539 Å / Num. obs: 48870 / % possible obs: 99.44 % / Rmerge(I) obs: 0.083

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
CNXrefinement
CNXphasing
SCALEPACKdata scaling
HKL-2000date reduction
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.602→46.539 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 2452 5.02 %
Rwork0.165 46418 -
obs0.1673 48870 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.29 Å2 / Biso mean: 62.8772 Å2 / Biso min: 28.44 Å2
Refinement stepCycle: final / Resolution: 2.602→46.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8906 0 114 61 9081
Biso mean--47.32 47.26 -
Num. residues----1132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089260
X-RAY DIFFRACTIONf_angle_d0.95512601
X-RAY DIFFRACTIONf_chiral_restr0.061369
X-RAY DIFFRACTIONf_plane_restr0.0061612
X-RAY DIFFRACTIONf_dihedral_angle_d14.5925409
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5439X-RAY DIFFRACTION8.203TORSIONAL
12B5439X-RAY DIFFRACTION8.203TORSIONAL
13C5439X-RAY DIFFRACTION8.203TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6025-2.65250.28111420.2192443258595
2.6525-2.70670.30371310.211325642695100
2.7067-2.76550.28681520.20632557270999
2.7655-2.82980.25881300.20552551268199
2.8298-2.90060.29591580.208325602718100
2.9006-2.9790.26521260.203125872713100
2.979-3.06670.28381390.197125792718100
3.0667-3.16560.25081350.183325732708100
3.1656-3.27870.21971250.183526072732100
3.2787-3.410.23291490.177825892738100
3.41-3.56510.20961150.167526242739100
3.5651-3.7530.20751370.158225812718100
3.753-3.9880.19331320.140926162748100
3.988-4.29570.15731130.14126102723100
4.2957-4.72770.16081410.126525822723100
4.7277-5.41090.17481490.142725922741100
5.4109-6.81370.22381400.173426312771100
6.8137-46.54630.20891380.17462572271097
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)
11.18090.0222-0.10031.988-0.07050.7894-0.01830.16050.1399-0.09830.0035-0.0141-0.17930.0071-00.43940.0132-0.00850.3930.01740.275439.83075.071216.983
20.72880.2527-0.10471.3306-1.15491.5396-0.03240.16360.03370.29980.23020.316-0.3285-0.13030.03650.42690.11370.05960.32810.00420.430418.6058-4.472427.8769
31.0847-0.7177-0.08251.6742-0.4290.623-0.04920.0690.013-0.03220.1350.0736-0.0532-0.0776-0.00020.48210.04630.02570.433-0.02980.364930.8007-9.228923.8939
40.8119-0.1976-0.25920.224-0.08270.20040.0493-0.6196-0.27720.33340.00880.22620.3872-0.51060.00090.5514-0.0505-0.03880.63330.09660.553118.772611.5448-1.1295
51.3688-0.20310.42140.9423-0.06421.30110.0525-0.3318-0.40620.02440.04310.38690.2686-0.71130.00030.4161-0.0419-0.01540.72280.08780.56055.94311.1903-8.2278
60.81160.7014-0.34520.79220.14371.33410.1297-0.12370.01240.14-0.15540.2401-0.1519-0.368400.44350.0186-0.04870.37430.03690.385118.831719.9117-10.0719
71.70330.2040.70171.7511-0.6551.73490.00390.2572-0.4476-0.42550.0604-0.06680.2009-0.0231-0.00030.4411-0.02260.0470.3237-0.08470.438330.60167.0322-26.7016
80.97260.22530.63170.6482-0.34270.88450.10850.0697-0.5778-0.25870.0268-0.05290.17140.17990.0150.39360.04690.03660.25990.02510.729635.73070.6173-18.1289
91.5619-0.2388-0.54810.20630.10930.90130.0738-0.0378-0.4616-0.34290.1096-0.4371-0.1305-0.2210.00040.4145-0.0526-0.05620.31920.03680.493227.57838.4759-18.2418
100.92740.63320.38490.48770.16970.27910.0610.3289-0.75590.00190.11610.03280.04110.25850.00540.44350.0345-0.03410.4250.06280.55437.08214.5083-20.5853
111.13880.3867-0.7671.7762-0.12622.33760.0372-0.0522-0.13860.02220.01020.19430.2877-0.364200.3667-0.0211-0.06290.46670.06520.49913.8123-52.91441.5258
121.204-0.0655-0.71631.6811-0.49420.91540.1555-0.1508-0.02540.09250.0165-0.2593-0.03260.0815-00.33490.00090.00510.4123-0.00510.382121.1989-32.334739.8384
130.39440.19730.2581.3513-0.94461.2110.02380.01950.01990.32930.1940.3006-0.0858-0.33180.02250.40270.0980.10720.46940.05280.46069.1792-24.815640.6591
140.41330.2399-0.28690.5981-0.23370.93790.0271-0.0071-0.1063-0.0201-0.0239-0.0906-0.17640.10030.00050.44620.0597-0.01060.45360.01630.468818.6092-35.086730.2654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 233 )A-2 - 233
2X-RAY DIFFRACTION2chain 'A' and (resid 234 through 317 )A234 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 385 )A318 - 385
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 24 )B-2 - 24
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 116 )B25 - 116
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 183 )B117 - 183
7X-RAY DIFFRACTION7chain 'B' and (resid 184 through 267 )B184 - 267
8X-RAY DIFFRACTION8chain 'B' and (resid 268 through 317 )B268 - 317
9X-RAY DIFFRACTION9chain 'B' and (resid 318 through 349 )B318 - 349
10X-RAY DIFFRACTION10chain 'B' and (resid 350 through 385 )B350 - 385
11X-RAY DIFFRACTION11chain 'C' and (resid -2 through 183 )C-2 - 183
12X-RAY DIFFRACTION12chain 'C' and (resid 184 through 252 )C184 - 252
13X-RAY DIFFRACTION13chain 'C' and (resid 253 through 340 )C253 - 340
14X-RAY DIFFRACTION14chain 'C' and (resid 341 through 385 )C341 - 385

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