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- PDB-6xkr: Structure of Sasanlimab Fab in complex with PD-1 -

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Basic information

Entry
Database: PDB / ID: 6xkr
TitleStructure of Sasanlimab Fab in complex with PD-1
Components
  • Programmed cell death protein 1
  • Sasanlimab Fab Heavy chain
  • Sasanlimab Fab Light chain
KeywordsANTITUMOR PROTEIN/IMMUNE SYSTEM / anti-PD-1 / Fab / Complex / Immuno-Oncology / ANTITUMOR PROTEIN / ANTITUMOR PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS / adaptive immune response / 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: 2.59 Å
AuthorsKimberlin, C.R. / Chin, S.M.
CitationJournal: Mol.Cancer Ther. / Year: 2020
Title: Pharmacologic Properties and Preclinical Activity of Sasanlimab, A High-affinity Engineered Anti-Human PD-1 Antibody.
Authors: Al-Khami, A.A. / Youssef, S. / Abdiche, Y. / Nguyen, H. / Chou, J. / Kimberlin, C.R. / Chin, S.M. / Kamperschroer, C. / Jessen, B. / Kern, B. / Budimir, N. / Dillon, C.P. / Xu, A. / Clark, J. ...Authors: Al-Khami, A.A. / Youssef, S. / Abdiche, Y. / Nguyen, H. / Chou, J. / Kimberlin, C.R. / Chin, S.M. / Kamperschroer, C. / Jessen, B. / Kern, B. / Budimir, N. / Dillon, C.P. / Xu, A. / Clark, J.D. / Chou, J. / Kraynov, E. / Rajpal, A. / Lin, J.C. / Salek-Ardakani, S.
History
DepositionJun 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
H: Sasanlimab Fab Heavy chain
L: Sasanlimab Fab Light chain
P: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4918
Polymers65,0303
Non-polymers4605
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-34 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.453, 90.622, 176.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody Sasanlimab Fab Heavy chain


Mass: 24860.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Sasanlimab Fab Light chain


Mass: 24372.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Programmed cell death protein 1 / / hPD-1


Mass: 15796.501 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15116
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.5M LiCl, 0.1M Citric Acid, pH 4, 22% w/v PEG 6000, 0.5% w/v ODG
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→49.32 Å / Num. obs: 21538 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 47.89 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.423 / Rpim(I) all: 0.121 / Rrim(I) all: 0.44 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.59-2.7112.93.4623263225340.4130.9963.6040.8100
8.97-49.3110.80.05866476150.9990.0180.06131.799.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B8C

5b8c


Resolution: 2.59→49.311 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 1075 5.01 %
Rwork0.2185 20397 -
obs0.221 21472 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.71 Å2 / Biso mean: 56.6599 Å2 / Biso min: 18.64 Å2
Refinement stepCycle: final / Resolution: 2.59→49.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 30 107 4257
Biso mean--75.8 45.48 -
Num. residues----548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024250
X-RAY DIFFRACTIONf_angle_d0.4785798
X-RAY DIFFRACTIONf_chiral_restr0.041654
X-RAY DIFFRACTIONf_plane_restr0.004743
X-RAY DIFFRACTIONf_dihedral_angle_d2.1972500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.59-2.70790.37171300.36782453
2.7079-2.85070.38661320.3282518
2.8507-3.02920.35741320.29942507
3.0292-3.26310.31711330.2532516
3.2631-3.59140.30181320.22682531
3.5914-4.11080.28051360.20042566
4.1108-5.17830.1921360.15472581
5.1783-49.3110.22321440.18912725
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)
10.77240.29720.02792.87440.37991.53740.0412-0.2020.0444-0.1107-0.078-0.0776-0.17250.04030.05340.3161-0.00110.03980.41020.07910.4159.145971.184343.5779
20.07510.64010.09311.68080.1212-0.05410.014-0.0184-0.05160.16270.0398-0.17410.1074-0.0507-0.00010.42860.01440.04760.3982-00.41827.057784.343334.303
31.1111-0.8105-0.47012.47851.4333.5428-0.1690.1593-0.05650.0365-0.05980.1608-0.3079-0.34680.18780.27520.017-0.01030.3394-0.01480.3357-1.683498.697424.3979
43.49160.9307-0.85152.7101-1.19593.58230.12910.1081-0.1058-0.4687-0.1122-0.16010.59650.06340.02020.45840.07260.09070.32360.0230.40615.517464.229321.2933
50.6837-0.3853-0.65961.4178-0.32351.3567-0.165-0.14350.0807-0.10.1216-0.2994-0.0897-0.00110.00940.42320.0255-0.01430.38930.0250.393210.821386.215919.8524
61.79720.2484-0.34943.42361.04343.0847-0.1793-0.04510.2129-0.4110.3174-0.0731-0.51960.3465-0.11910.5377-0.00020.03610.43550.02860.386613.727102.860814.9624
75.938-0.681-0.08754.9067-1.04523.6471-0.72660.2962-0.9042-0.76390.71230.77360.0599-0.58430.07290.8206-0.06190.04040.49670.03390.60170.936938.375221.6303
81.74510.67170.64332.8239-1.00771.38590.261-0.3112-1.03852.234-0.6735-1.2699-0.6318-0.59050.35571.13140.10750.06790.74390.1130.91094.903741.394339.4092
92.75550.4893-1.4112.63310.68972.8174-0.11550.4518-0.0889-0.98750.0983-1.0256-0.48220.64210.25360.96970.01190.13250.5524-0.00950.68943.66248.515825.6009
105.06481.53061.28175.5134-2.29132.2155-0.56991.34280.743-0.38230.88250.41-0.8387-0.7182-0.2661.0136-0.0872-0.07660.56920.03970.66685.270452.314620.2263
110.5455-0.14271.08590.11120.01933.1675-0.11260.5446-0.2114-0.5141-0.32251.11850.62160.67360.14830.85640.0414-0.00210.77960.1150.8445-5.836355.673326.1694
121.93812.0926-0.55232.4347-1.94828.9807-0.43870.06750.1234-0.18790.1264-0.43940.452-1.63420.34040.43680.0953-0.04470.59240.04080.5571-4.907841.491728.3838
134.0859-0.21331.09833.1982-0.59144.1967-0.2383-0.40060.2757-0.0423-0.5143-0.38040.3478-0.28980.84050.9599-0.2133-0.17771.26430.22950.6925-4.140247.410.1258
142.36280.143-0.42371.18820.7295.43730.1195-0.20280.1984-0.92610.306-0.48070.0689-0.1357-0.52230.73620.03180.15190.18650.04310.51548.329448.34530.8442
153.561.05380.71273.84831.34524.3228-0.69631.0940.0993-0.96330.3684-0.006-0.4161.6230.1911.05480.03090.24350.53560.06870.65757.367542.313420.3269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 83 )H1 - 83
2X-RAY DIFFRACTION2chain 'H' and (resid 84 through 138 )H84 - 138
3X-RAY DIFFRACTION3chain 'H' and (resid 139 through 218 )H139 - 218
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 81 )L1 - 81
5X-RAY DIFFRACTION5chain 'L' and (resid 82 through 143 )L82 - 143
6X-RAY DIFFRACTION6chain 'L' and (resid 144 through 220 )L144 - 220
7X-RAY DIFFRACTION7chain 'P' and (resid 32 through 55 )P32 - 55
8X-RAY DIFFRACTION8chain 'P' and (resid 56 through 62 )P56 - 62
9X-RAY DIFFRACTION9chain 'P' and (resid 63 through 70 )P63 - 70
10X-RAY DIFFRACTION10chain 'P' and (resid 71 through 82 )P71 - 82
11X-RAY DIFFRACTION11chain 'P' and (resid 83 through 94 )P83 - 94
12X-RAY DIFFRACTION12chain 'P' and (resid 95 through 111 )P95 - 111
13X-RAY DIFFRACTION13chain 'P' and (resid 112 through 118 )P112 - 118
14X-RAY DIFFRACTION14chain 'P' and (resid 119 through 133 )P119 - 133
15X-RAY DIFFRACTION15chain 'P' and (resid 134 through 144 )P134 - 144

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