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- PDB-7wsl: PD-1 in complex with Dostarlimab -

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Basic information

Entry
Database: PDB / ID: 7wsl
TitlePD-1 in complex with Dostarlimab
Components
  • Programmed cell death protein 1
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / PD-1 / dostarlimab / antibody / cancer immunotherapy
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / adaptive immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / adaptive immune response / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.534 Å
AuthorsHeo, Y.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Molecular basis of PD-1 blockade by dostarlimab, the FDA-approved antibody for cancer immunotherapy.
Authors: Park, U.B. / Jeong, T.J. / Gu, N. / Lee, H.T. / Heo, Y.S.
History
DepositionJan 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: light chain
D: Programmed cell death protein 1
H: heavy chain


Theoretical massNumber of molelcules
Total (without water)62,8053
Polymers62,8053
Non-polymers00
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-30 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.600, 44.870, 76.960
Angle α, β, γ (deg.)93.800, 98.180, 97.950
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody light chain


Mass: 23565.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Programmed cell death protein 1 / hPD-1


Mass: 14855.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#3: Antibody heavy chain


Mass: 24384.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.53→28.543 Å / Num. obs: 73835 / % possible obs: 95.35 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.57 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.5
Reflection shellResolution: 1.53→1.59 Å / Num. unique obs: 7304 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ggs

5ggs


Resolution: 1.534→28.543 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1783 3690 5 %
Rwork0.1606 70133 -
obs0.1615 73823 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.54 Å2 / Biso mean: 26.0142 Å2 / Biso min: 8.87 Å2
Refinement stepCycle: final / Resolution: 1.534→28.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 0 740 4846
Biso mean---37.06 -
Num. residues----534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5344-1.55460.27181300.2385247687
1.5546-1.57580.25531360.206257591
1.5758-1.59840.20171400.1958268894
1.5984-1.62220.1921390.1834262695
1.6222-1.64760.2511410.1825268193
1.6476-1.67460.20291400.1872268695
1.6746-1.70340.25231400.1787266495
1.7034-1.73440.22021430.1781271495
1.7344-1.76780.19771400.1743265996
1.7678-1.80380.19241430.1722270694
1.8038-1.84310.21641410.1766269396
1.8431-1.88590.20631430.1757270994
1.8859-1.93310.17181420.1701269796
1.9331-1.98530.21331430.167270995
1.9853-2.04370.17941400.165267496
2.0437-2.10970.19371420.1648270296
2.1097-2.18510.18421450.1666273596
2.1851-2.27250.20961430.1695273297
2.2725-2.37590.18851450.1686275197
2.3759-2.50110.17081440.1674274197
2.5011-2.65770.17041460.1688276797
2.6577-2.86270.21421430.1703272597
2.8627-3.15050.15961440.1626272897
3.1505-3.60560.17691450.1449274797
3.6056-4.53970.14191440.1321275097
4.5397-28.5430.1421480.1472279899
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)
14.3137-1.88252.65333.6826-0.57763.59110.0818-0.34080.04040.48860.07980.01870.3561-0.2739-0.0450.28410.00440.0350.16190.01410.1269.588614.040135.8363
21.4845-0.11760.25882.72660.23662.2602-0.01370.0489-0.01340.20610.02520.11790.1325-0.0265-0.00220.0773-0.00730.01650.08510.01550.09759.502311.345624.4454
34.5316-4.57452.04955.0677-1.31692.2444-0.0206-0.4065-0.26360.39770.25520.57330.0469-0.2948-0.05110.1419-0.00790.07470.15130.03770.18783.99598.181129.1475
41.47670.32240.51521.50190.4992.32240.0222-0.0708-0.10240.25430.10550.08950.2417-0.0616-0.12120.11610.00120.01440.10480.00560.123110.6515.176826.5726
52.89390.52764.47560.09040.79117.08110.3853-0.0905-0.10050.2587-0.144-0.04280.56220.1129-0.18820.3102-0.0069-0.0590.18170.00510.138620.56114.280145.0218
64.38482.9693-0.98669.4801-1.66864.84250.1911-0.17620.2753-0.2795-0.3161-0.1665-0.44510.55540.08250.269-0.0145-0.00420.2097-0.01370.117534.659640.894250.186
70.49620.29280.20739.58061.97611.84020.0211-0.01410.0211-0.3131-0.15030.35990.0675-0.15650.13980.25490.0183-0.06410.20250.0110.147523.450730.224450.2704
80.7835-0.6075-0.45665.6132.2522.72750.1106-0.0045-0.0312-0.4461-0.0409-0.0307-0.0428-0.0597-0.05390.24790.0132-0.06860.20350.00610.148423.627328.549846.5339
92.03090.72560.70322.18281.11683.1667-0.0558-0.09350.3133-0.6147-0.11640.2911-0.8092-0.03710.19070.38310.0343-0.02240.1528-0.03030.163327.000245.070150.1098
102.3752.3903-0.16768.8815-0.41232.10130.206-0.03210.05680.3422-0.17810.2820.0613-0.2013-0.01320.23560.01060.00890.2169-0.02150.126124.258533.946758.7157
110.30180.69140.3821.62730.76352.65420.02860.0032-0.0706-0.2071-0.22320.3010.0369-0.24870.19270.1451-0.02440.01990.201-0.02810.2223-4.1392-0.6929-3.8072
127.46417.20587.23176.95386.94317.7716-0.01130.11721.2095-0.2651-0.4250.74080.0463-0.59780.53120.46020.00290.01540.36420.0450.5179-2.171717.65832.4402
136.7334-0.7275-0.21962.15151.31272.7109-0.0142-0.5358-0.39770.6627-0.22670.09410.5441-0.35980.16470.2369-0.08390.03290.22680.00310.14711.2437-0.23977.3052
142.38973.7553.71075.94485.86945.85180.0368-0.0246-0.40820.36170.2387-0.43880.56340.4015-0.33350.18040.00880.04150.20990.01380.281412.32074.31254.6844
151.09610.7309-0.08766.8325-4.35753.0012-0.01850.01190.1025-0.2838-0.057-0.3142-0.1499-0.06630.15580.24850.00170.01050.1962-0.00970.19382.30975.7332-5.6772
166.0735-1.7159-0.88086.8115-0.38617.84260.1813-0.3626-0.86410.3104-0.4605-0.93450.66220.36990.32050.2407-0.0050.00510.15780.02920.32875.2932-12.6873-2.5443
170.9456-1.0679-0.34474.90283.25463.3014-0.0160.037-0.16580.0978-0.34660.30910.2034-0.33730.4110.1246-0.03610.03910.1949-0.0060.2344-3.93680.45813.6164
180.17590.14780.18163.42711.78351.8438-0.04730.0295-0.0297-0.25130.1374-0.3961-0.13260.1567-0.12220.0751-0.02560.03210.150.00910.162119.701426.18439.7001
192.12320.51151.75092.42830.05914.7907-0.0101-0.03710.1020.05130.03210.1339-0.1085-0.21660.00560.0504-0.01440.0130.09930.01340.13889.490427.609615.4925
201.01470.37851.03196.4713.48745.1411-0.08480.19580.1217-0.53070.1019-0.1496-0.3510.1374-0.03420.0953-0.03110.02180.11880.03770.130414.283530.77686.6676
210.80410.4440.63830.41680.42621.0174-0.0522-0.0068-0.0170.14460.04930.0113-0.02530.0008-0.02360.1480.0016-0.0060.12520.01120.147421.560430.782723.4548
221.7344-0.27210.32163.0043-0.6621.5551-0.016-0.0653-0.0457-0.07240.0235-0.0624-0.01740.0828-0.00270.25360.0456-0.01320.1582-0.00290.10835.475331.706540.7175
236.4008-1.08733.3894.9406-2.7652.93820.01050.2186-0.0231-0.216-0.1679-0.6328-0.06240.5680.11580.30360.02310.05250.2241-0.00730.22244.348134.807539.0383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 18 )L1 - 18
2X-RAY DIFFRACTION2chain 'L' and (resid 19 through 61 )L19 - 61
3X-RAY DIFFRACTION3chain 'L' and (resid 62 through 75 )L62 - 75
4X-RAY DIFFRACTION4chain 'L' and (resid 76 through 101 )L76 - 101
5X-RAY DIFFRACTION5chain 'L' and (resid 102 through 113 )L102 - 113
6X-RAY DIFFRACTION6chain 'L' and (resid 114 through 128 )L114 - 128
7X-RAY DIFFRACTION7chain 'L' and (resid 129 through 150 )L129 - 150
8X-RAY DIFFRACTION8chain 'L' and (resid 151 through 174 )L151 - 174
9X-RAY DIFFRACTION9chain 'L' and (resid 175 through 188 )L175 - 188
10X-RAY DIFFRACTION10chain 'L' and (resid 189 through 212 )L189 - 212
11X-RAY DIFFRACTION11chain 'D' and (resid 31 through 55 )D31 - 55
12X-RAY DIFFRACTION12chain 'D' and (resid 56 through 62 )D56 - 62
13X-RAY DIFFRACTION13chain 'D' and (resid 63 through 82 )D63 - 82
14X-RAY DIFFRACTION14chain 'D' and (resid 83 through 94 )D83 - 94
15X-RAY DIFFRACTION15chain 'D' and (resid 95 through 110 )D95 - 110
16X-RAY DIFFRACTION16chain 'D' and (resid 111 through 118 )D111 - 118
17X-RAY DIFFRACTION17chain 'D' and (resid 119 through 147 )D119 - 147
18X-RAY DIFFRACTION18chain 'H' and (resid 1 through 33 )H1 - 33
19X-RAY DIFFRACTION19chain 'H' and (resid 34 through 64 )H34 - 64
20X-RAY DIFFRACTION20chain 'H' and (resid 65 through 83 )H65 - 83
21X-RAY DIFFRACTION21chain 'H' and (resid 84 through 137 )H84 - 137
22X-RAY DIFFRACTION22chain 'H' and (resid 138 through 193 )H138 - 193
23X-RAY DIFFRACTION23chain 'H' and (resid 194 through 216 )H194 - 216

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