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- PDB-6ztr: Crystal Structure of the anti-human P-Cadherin Fab CQY684 in comp... -

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Basic information

Entry
Database: PDB / ID: 6ztr
TitleCrystal Structure of the anti-human P-Cadherin Fab CQY684 in complex with human P-Cadherin(108-324)
Components
  • CQY684 Fab heavy-chain
  • CQY684 Fab light-chain
  • Cadherin-3
KeywordsIMMUNE SYSTEM / Immunoglobulin Cell Adhesion
Function / homology
Function and homology information


negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / cell-cell adhesion mediated by cadherin / catenin complex / adherens junction organization ...negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / cell-cell adhesion mediated by cadherin / catenin complex / adherens junction organization / cell-cell junction assembly / Adherens junctions interactions / retina homeostasis / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell adhesion via plasma membrane adhesion molecules / visual perception / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / cell morphogenesis / beta-catenin binding / cell junction / positive regulation of canonical Wnt signaling pathway / cell migration / cell adhesion / cadherin binding / response to xenobiotic stimulus / calcium ion binding / positive regulation of gene expression / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRondeau, J.M. / Lehmann, S.
CitationJournal: Mol.Cancer Ther. / Year: 2021
Title: PCA062, a P-cadherin Targeting Antibody-Drug Conjugate, Displays Potent Antitumor Activity Against P-cadherin-expressing Malignancies.
Authors: Sheng, Q. / D'Alessio, J.A. / Menezes, D.L. / Karim, C. / Tang, Y. / Tam, A. / Clark, S. / Ying, C. / Connor, A. / Mansfield, K.G. / Rondeau, J.M. / Ghoddusi, M. / Geyer, F.C. / Gu, J. / ...Authors: Sheng, Q. / D'Alessio, J.A. / Menezes, D.L. / Karim, C. / Tang, Y. / Tam, A. / Clark, S. / Ying, C. / Connor, A. / Mansfield, K.G. / Rondeau, J.M. / Ghoddusi, M. / Geyer, F.C. / Gu, J. / McLaughlin, M.E. / Newcombe, R. / Elliot, G. / Tschantz, W.R. / Lehmann, S. / Fanton, C.P. / Miller, K. / Huber, T. / Rendahl, K.G. / Jeffry, U. / Pryer, N.K. / Lees, E. / Kwon, P. / Abraham, J.A. / Damiano, J.S. / Abrams, T.J.
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CQY684 Fab heavy-chain
B: CQY684 Fab light-chain
H: CQY684 Fab heavy-chain
I: Cadherin-3
J: Cadherin-3
L: CQY684 Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,35712
Polymers147,1176
Non-polymers2406
Water11,205622
1
A: CQY684 Fab heavy-chain
B: CQY684 Fab light-chain
J: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6796
Polymers73,5583
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: CQY684 Fab heavy-chain
I: Cadherin-3
L: CQY684 Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6796
Polymers73,5583
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.691, 77.795, 133.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody CQY684 Fab heavy-chain


Mass: 26420.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1F-
#2: Antibody CQY684 Fab light-chain


Mass: 23278.812 Da / Num. of mol.: 2 / Fragment: Fab heavy-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1F-
#3: Protein Cadherin-3 / Placental cadherin / P-cadherin


Mass: 23859.352 Da / Num. of mol.: 2 / Fragment: Fab light-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3, CDHP / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P22223
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M calcium acetate, 10% (w/v) PEG 8,000, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.1→72.49 Å / Num. obs: 105445 / % possible obs: 100 % / Redundancy: 6.714 % / Biso Wilson estimate: 40.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.216 / Χ2: 0.993 / Net I/σ(I): 7.97 / Num. measured all: 707980 / Scaling rejects: 114
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.9672.3920.8853822772877250.3962.585100
2.15-2.216.9192.0191.0751945751075080.5352.183100
2.21-2.286.8331.6561.3149881730573000.6511.79299.9
2.28-2.356.7411.4951.4648041713071270.6541.621100
2.35-2.426.4481.1731.844516690869040.7531.27799.9
2.42-2.516.4380.9762.1542845665866550.8061.063100
2.51-2.66.8940.7882.7744550646364620.8790.852100
2.6-2.716.9350.6243.4942929619061900.9020.675100
2.71-2.836.9130.4834.4741290597459730.9310.522100
2.83-2.976.8520.365.8239351574357430.9580.39100
2.97-3.136.4860.2647.5335165542254220.9750.287100
3.13-3.326.5060.1810.6333617516851670.9860.196100
3.32-3.557.0220.13114.3534084485548540.9920.142100
3.55-3.836.8870.10317.4931303454545450.9950.112100
3.83-4.26.6820.08420.6228010419441920.9960.091100
4.2-4.76.1390.06723.9923287379537930.9970.07399.9
4.7-5.426.5210.06325.1122072338633850.9970.068100
5.42-6.646.7090.06823.5619469290429020.9970.07399.9
6.64-9.396.0520.05326.2513683226622610.9980.05899.8
9.39-72.496.0730.03933.368120134613370.9950.04399.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å72.49 Å
Translation2.5 Å72.49 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.3.0phasing
BUSTERrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZTF,6ZTB

6ztf

6ztb


Resolution: 2.1→72.49 Å / Cor.coef. Fo:Fc: 0.9338 / Cor.coef. Fo:Fc free: 0.9221 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 5273 5 %RANDOM
Rwork0.1921 ---
obs0.1936 105437 99.95 %-
Displacement parametersBiso max: 212.54 Å2 / Biso mean: 52.86 Å2 / Biso min: 20.69 Å2
Baniso -1Baniso -2Baniso -3
1-9.1882 Å20 Å20 Å2
2--4.0883 Å20 Å2
3----13.2766 Å2
Refine analyzeLuzzati coordinate error obs: 0.333 Å
Refinement stepCycle: final / Resolution: 2.1→72.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9990 0 6 622 10618
Biso mean--33.42 46.44 -
Num. residues----1305
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3407SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes247HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1473HARMONIC5
X-RAY DIFFRACTIONt_it10226HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1381SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11175SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10226HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13935HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion17.32
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2662 386 5.01 %
Rwork0.2427 7323 -
all0.2439 7709 -
obs--99.95 %
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)
12.886-1.26661.03381.17440.00882.02020.10180.42030.451-0.121-0.2002-0.2739-0.09680.07110.0983-0.0880.01420.0723-0.11230.09170.0499-19.034328.2822-63.7356
23.2568-1.2136-0.03460.76490.02941.76940.01670.20760.1351-0.11460.0556-0.17810.06470.1865-0.0723-0.066-0.0006-0.0248-0.0781-0.02420.0574-54.979534.8676-73.0416
32.5644-0.7046-0.34721.4959-0.1791.1997-0.0967-0.22780.08940.15690.1113-0.0782-0.0774-0.2431-0.0146-0.03840.0514-0.0013-0.00010.0225-0.0543-31.931822.4458-45.7336
43.65930.27270.51121.7910.4771.8365-0.1048-0.0148-0.5442-0.09660.02490.13610.2047-0.16170.0799-0.1011-0.0041-0.0266-0.2004-0.01210.1156-59.991220.6283-68.0847
54.20280.9145-0.45361.77830.54931.79030.2896-0.452-0.54420.1882-0.052-0.49920.177-0.01-0.2376-0.1618-0.0458-0.1273-0.17520.10480.1544-24.436716.3806-0.7915
63.04611.54050.34320.9917-0.34921.76370.0717-0.17160.37750.159-0.1560.0957-0.11990.31620.0843-0.1442-0.03-0.0084-0.06160.05190.1114-57.217811.23946.4266
72.16061.10280.33381.61370.24112.8958-0.27510.5442-0.5442-0.38070.2688-0.2209-0.04290.09730.0063-0.1697-0.06080.0723-0.0881-0.1520.0803-6.877529.6065-19.3056
81.0297-0.67890.33561.5753-0.91822.7336-0.1096-0.5442-0.24450.53090.09270.0286-0.15230.39010.0169-0.11510.0475-0.0150.12450.1284-0.089516.645931.593921.7304
91.9516-0.035-0.81362.0511.38083.4054-0.0097-0.34980.35050.39730.10190.03530.3250.1575-0.0922-0.05530.0387-0.0155-0.0638-0.0419-0.0533-5.106110.3118-46.0102
102.0771-0.0178-2.08381.1850.13965.1861-0.06660.5019-0.0126-0.54420.2464-0.3049-0.21170.0424-0.17980.0228-0.1520.1520.0449-0.0652-0.173916.55342.1103-87.7674
114.52160.9690.71791.9351-0.13851.094-0.11190.3614-0.2387-0.27080.2662-0.00610.0284-0.1138-0.1543-0.0788-0.0588-0.0197-0.02930.0161-0.0625-35.842123.7511-19.204
122.64950.1258-0.45251.5372-0.04714.4967-0.18690.0390.54420.0697-0.13310.3757-0.44330.06760.32-0.2382-0.0175-0.0445-0.28620.07950.3036-65.598124.05042.0491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|122 }A1 - 122
2X-RAY DIFFRACTION2{ A|123 - A|229 }A123 - 229
3X-RAY DIFFRACTION3{ B|1 - B|108 }B1 - 108
4X-RAY DIFFRACTION4{ B|109 - B|210 }B109 - 210
5X-RAY DIFFRACTION5{ H|1 - H|122 }H1 - 122
6X-RAY DIFFRACTION6{ H|123 - H|229 }H123 - 229
7X-RAY DIFFRACTION7{ I|109 - I|208 }I109 - 208
8X-RAY DIFFRACTION8{ I|209 - I|321 }I209 - 321
9X-RAY DIFFRACTION9{ J|109 - J|208 }J109 - 208
10X-RAY DIFFRACTION10{ J|209 - J|321 }J209 - 321
11X-RAY DIFFRACTION11{ L|1 - L|108 }L1 - 108
12X-RAY DIFFRACTION12{ L|109 - L|210 }L109 - 210

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