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- PDB-4k23: Structure of anti-uPAR Fab ATN-658 -

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Basic information

Entry
Database: PDB / ID: 4k23
TitleStructure of anti-uPAR Fab ATN-658
Components
  • anti-uPAR antibody, heavy chain
  • anti-uPAR antibody, light chain
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYuan, C. / Huang, M. / Chen, L.
CitationJournal: Plos One / Year: 2014
Title: Identification of a New Epitope in uPAR as a Target for the Cancer Therapeutic Monoclonal Antibody ATN-658, a Structural Homolog of the uPAR Binding Integrin CD11b ( alpha M)
Authors: Xu, X. / Cai, Y. / Wei, Y. / Donate, F. / Juarez, J. / Parry, G. / Chen, L. / Meehan, E.J. / Ahn, R.W. / Ugolkov, A. / Dubrovskyi, O. / O'halloran, T.V. / Huang, M. / Mazar, A.P.
History
DepositionApr 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 8, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: anti-uPAR antibody, heavy chain
L: anti-uPAR antibody, light chain


Theoretical massNumber of molelcules
Total (without water)48,6392
Polymers48,6392
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-25 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.313, 132.296, 46.831
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody anti-uPAR antibody, heavy chain


Mass: 24482.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody anti-uPAR antibody, light chain


Mass: 24156.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.
Source detailsTHE ANTIBODY ATN658 IS A MONOCLONAL ANTIBODY RAISED AGAINST UROKINASE RECEPTOR IN MOUSE.

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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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 295 K / pH: 8.25
Details: 20-22% PEG3350, 0.1M Tris(PH 8.0-8.5), vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.04
DetectorDetector: CCD / Date: Jul 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.6→66.08 Å / Num. obs: 49312 / % possible obs: 85.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.29 / % possible all: 70

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DDQ
Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.713 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2511 5.1 %RANDOM
Rwork0.198 ---
obs0.201 49278 85.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å22.44 Å2
2---1.51 Å20 Å2
3---3.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 0 324 3627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9494699
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67524.341129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61515556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9121511
X-RAY DIFFRACTIONr_chiral_restr0.10.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022580
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21480
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22371
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9271.52228
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48123565
X-RAY DIFFRACTIONr_scbond_it2.18631399
X-RAY DIFFRACTIONr_scangle_it3.0834.51134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 131 -
Rwork0.195 2800 -
obs--68.93 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.61723.205-1.94156.1615-1.2781.1009-0.0128-0.125-0.30120.1125-0.0208-0.42110.11140.16860.0336-0.00260.0239-0.02530.0753-0.02850.074414.39280.4273.183
229.4787-6.95691.85527.2427-0.8360.7091-0.2439-0.3594-0.40140.61070.35820.4868-0.039-0.0265-0.11430.05230.00090.04960.00280.01420.0717-4.69170.09477.572
39.35623.8178-2.14653.7728-1.86820.937-0.0065-0.1217-0.08820.10420.0984-0.0302-0.04630.0792-0.09190.0272-0.01250.01470.0406-0.06190.04137.40684.45575.111
41.24132.12130.03523.68060.28330.89640.021-0.10820.091-0.0612-0.03390.13330.01880.06560.01280.0136-0.0030.00130.0354-0.03850.10036.46185.96466.316
514.2339-0.20140.117922.5049-9.21136.75680.21380.1305-1.2019-0.624-0.34880.65710.6511-0.01540.1350.096-0.0164-0.00340.0029-0.06160.12721.59171.12360.489
61.6382-0.37520.39520.67250.92871.86630.01220.01650.1865-0.04040.05560.1064-0.1376-0.042-0.06780.03280.00160.01560.0104-0.02210.12930.86290.81666.628
70.79350.1696-0.01032.2525-2.23084.5699-0.0447-0.0305-0.1758-0.0864-0.0601-0.01730.1702-0.09770.1048-0.01260.0045-0.01010.0358-0.00050.1505-9.63682.47764.792
814.21852.72055.70553.6459-0.28992.90020.0363-0.46890.460.3368-0.09560.1805-0.0796-0.2140.05930.0178-0.00990.01670.0624-0.09530.04493.989.92876.54
914.60747.91141.08376.37671.86520.86140.1516-0.21270.00820.22410.00950.19160.02490.0353-0.16110.0361-0.0059-0.00560.01740.01430.0529-0.62582.49874.918
104.22983.351-1.60314.8591-1.16650.6124-0.0873-0.0114-0.0241-0.08390.05190.17130.0490.03320.03550.0254-0.0155-0.00840.0268-0.03730.07941.55876.25967.118
118.0104-1.2957.45098.804-4.67589.515-0.3770.08870.49160.02450.10840.0735-0.68820.05560.26870.0547-0.00910.01090.034-0.04250.096111.66289.53760.827
121.93930.9879-0.0491.5831-0.65030.36340.1807-0.1752-0.15840.14530.05570.1089-0.06570.0771-0.23640.03550.0049-0.00210.04330.01660.10921.30270.48772.72
139.5079-6.5033-2.25925.08241.55651.5181-0.18730.0214-0.29570.30760.00380.07780.03760.04160.18350.020.0004-0.00270.02910.00840.05549.34949.26779.252
1424.6087-7.4757-6.18136.09590.48352.0609-0.30050.3619-0.35940.0955-0.1431-0.2326-0.0204-0.09150.4436-0.01250.0048-0.01950.05460.01740.077118.91946.13473.09
154.2571-2.9361-0.61433.88481.24530.68550.18050.145-0.1242-0.0127-0.08560.0674-0.1522-0.0504-0.09490.060.0232-0.01640.0328-0.01220.02782.66957.90976.221
163.5140.76791.5661.2316-0.13461.0130.14010.1459-0.00210.1114-0.1314-0.151-0.24780.0873-0.00880.032-0.0215-0.01530.06650.02060.010519.91556.48874.789
177.5956-1.9817-1.25661.2110.50650.63480.14470.3032-0.303-0.0223-0.13060.1008-0.0903-0.081-0.01410.01080.0289-0.02650.0785-0.01640.03074.6553.82570.961
184.242-1.917-1.95784.52261.13940.9213-0.1274-0.13-0.08780.2976-0.0745-0.7050.11290.2310.202-0.05120.0264-0.04630.08240.11030.228227.4745.31377.478
1914.9378-7.7579-1.32994.8649-0.04960.7740.1175-0.34430.24520.0649-0.0617-0.08780.01230.0014-0.05570.0738-0.02490.00090.0585-0.0643-0.018710.42459.06782.967
205.2188-7.7721-4.111318.66621.12756.7575-0.123-0.4125-0.62830.508-0.2227-0.19190.00870.01310.34570.0236-0.0127-0.05580.05070.07810.061717.94545.56483.257
216.7452-4.4131-2.33524.01241.29720.85570.09760.4195-0.1078-0.1855-0.16880.06620.006-0.13860.07110.0320.0037-0.05130.1016-0.0738-0.049611.52670.1446.181
225.39843.2519-1.46828.31760.38661.76840.46611.26980.82520.0273-0.2077-0.0095-0.2298-0.3733-0.25850.07570.13530.03980.10240.20610.04523.99387.98344.899
232.3413-3.98180.7287.9158-3.46794.5727-0.12280.07490.30380.34120.0648-0.18920.0150.2350.0580.03940.0006-0.02350.03040.00750.029812.98278.63455.526
242.7793-1.2107-2.91682.91-0.40134.23430.2049-0.17110.4119-0.09870.1679-0.1523-0.0770.3052-0.37280.0195-0.04270.00130.0452-0.04580.046917.67183.12754.156
256.1593-1.4055-0.16411.16110.60931.34910.26740.50090.2243-0.1707-0.0646-0.2329-0.15790.0255-0.20280.05390.00120.01840.05760.0317-0.001717.37178.63445.451
269.9294-1.6203-5.74413.4511-3.493825.8262-0.1391-0.46120.56710.2380.2602-0.3505-0.19341.0579-0.1210.0391-0.0285-0.0460.0787-0.09240.025425.37768.68951.183
273.8843-4.0621-0.65486.1971-0.12990.616-0.060.05380.10.08440.1870.04840.0130.0093-0.1270.0430.0017-0.03040.0483-0.01210.00119.45177.47353.22
287.0207-6.4857-2.37337.66122.08731.0638-0.0760.0974-0.0876-0.04490.07560.18050.0737-0.08860.00040.0265-0.0076-0.03260.0511-0.01730.00065.60275.27353.736
291.14871.1862-1.84252.3662-1.92752.9559-0.0603-0.0678-0.2172-0.0962-0.0843-0.17530.0750.14650.14460-0.02590.02190.0266-0.03440.083516.52545.7764.078
302.41230.009-3.5112.4626-1.342412.4491-0.03520.1546-0.11280.2277-0.04250.32120.1214-0.30350.07770.0353-0.02620.0544-0.0084-0.03340.14864.49740.98578.981
312.37911.193-3.33132.6635-3.33567.4119-0.18770.0843-0.2473-0.21620.1872-0.03460.09480.02780.00050.0639-0.02540.00970.04-0.05730.011915.87148.94658.883
324.08337.0986-2.96912.4942-4.98312.3653-0.42960.4748-0.2822-0.52120.4583-0.01560.2139-0.3011-0.02870.0268-0.0720.0240.0658-0.04550.10075.67736.72260.94
335.37259.777-0.205724.58872.33922.8662-0.45660.08090.6997-0.57450.10572.2045-0.0563-0.53160.3509-0.05880.0093-0.03030.12030.02090.17760.56342.79864.129
3418.821810.23-11.564219.7177-13.566910.85020.29430.12450.3120.70640.52730.3194-0.5768-0.1466-0.82170.14240.01510.05140.0299-0.0223-0.08514.5556.91659.622
355.46511.1996-6.24053.6521-3.21328.1288-0.1685-0.27780.1343-0.04980.0429-0.0003-0.06850.31180.12560.0691-0.0182-0.01390.0473-0.03160.001718.78954.59759.007
365.05627.4901-6.696417.1038-10.8849.02330.33420.08370.18290.2758-0.29951.2572-0.21380.3653-0.0347-0.0243-0.02290.05130.0281-0.0480.18862.59541.20371.96
370.448-0.6543-0.897211.59861.65181.8080.2528-0.17370.17490.3708-0.08540.15230.1843-0.2008-0.16740.0144-0.03650.04250.0236-0.02970.16270.28631.43575.825
385.86787.1667-9.1599.1324-12.659420.017-0.14680.1448-0.4527-0.28620.0287-0.43070.0704-0.05990.11810.0238-0.03760.07710.0028-0.07610.18188.51233.03366.596
391.90262.3401-2.26144.9178-3.27059.2524-0.54240.2122-0.6074-0.75720.2546-0.42960.6965-0.28230.28780.0983-0.06330.13380.0148-0.13960.094415.58138.4656.068
408.77755.5017-7.106318.1457-5.340613.1753-0.2533-0.5552-1.17030.1015-0.4034-1.376-0.00290.61190.6567-0.0820.02170.00140.02160.07130.311711.57829.25474.083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 8
2X-RAY DIFFRACTION2H9 - 15
3X-RAY DIFFRACTION3H16 - 29
4X-RAY DIFFRACTION4H30 - 39
5X-RAY DIFFRACTION5H40 - 46
6X-RAY DIFFRACTION6H47 - 60
7X-RAY DIFFRACTION7H61 - 67
8X-RAY DIFFRACTION8H68 - 75
9X-RAY DIFFRACTION9H76 - 82
10X-RAY DIFFRACTION10H83 - 95
11X-RAY DIFFRACTION11H96 - 102
12X-RAY DIFFRACTION12H103 - 115
13X-RAY DIFFRACTION13H116 - 134
14X-RAY DIFFRACTION14H135 - 141
15X-RAY DIFFRACTION15H142 - 149
16X-RAY DIFFRACTION16H150 - 165
17X-RAY DIFFRACTION17H166 - 181
18X-RAY DIFFRACTION18H182 - 193
19X-RAY DIFFRACTION19H194 - 206
20X-RAY DIFFRACTION20H207 - 213
21X-RAY DIFFRACTION21L1 - 22
22X-RAY DIFFRACTION22L23 - 29
23X-RAY DIFFRACTION23L30 - 43
24X-RAY DIFFRACTION24L44 - 57
25X-RAY DIFFRACTION25L58 - 76
26X-RAY DIFFRACTION26L77 - 81
27X-RAY DIFFRACTION27L82 - 93
28X-RAY DIFFRACTION28L94 - 105
29X-RAY DIFFRACTION29L106 - 123
30X-RAY DIFFRACTION30L124 - 133
31X-RAY DIFFRACTION31L134 - 142
32X-RAY DIFFRACTION32L143 - 154
33X-RAY DIFFRACTION33L155 - 162
34X-RAY DIFFRACTION34L163 - 168
35X-RAY DIFFRACTION35L169 - 175
36X-RAY DIFFRACTION36L176 - 183
37X-RAY DIFFRACTION37L184 - 189
38X-RAY DIFFRACTION38L190 - 195
39X-RAY DIFFRACTION39L196 - 208
40X-RAY DIFFRACTION40L209 - 213

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