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- PDB-8r6q: Co-crystal structure of PD-L1 with low molecular weight inhibitor -

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Basic information

Entry
Database: PDB / ID: 8r6q
TitleCo-crystal structure of PD-L1 with low molecular weight inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / immunotherapy / SMIs
Function / homology
Function and homology information


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / receptor ligand activity / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / 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
Chem-WEW / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsPlewka, J. / Surmiak, E. / Magiera-Mularz, K. / Kalinowska-Tluscik, J.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2020/39/D/ST4/01344 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Solubilizer Tag Effect on PD-L1/Inhibitor Binding Properties for m -Terphenyl Derivatives.
Authors: Surmiak, E. / Zaber, J. / Plewka, J. / Wojtanowicz, G. / Kocik-Krol, J. / Kruc, O. / Muszak, D. / Rodriguez, I. / Musielak, B. / Viviano, M. / Castellano, S. / Skalniak, L. / Magiera-Mularz, ...Authors: Surmiak, E. / Zaber, J. / Plewka, J. / Wojtanowicz, G. / Kocik-Krol, J. / Kruc, O. / Muszak, D. / Rodriguez, I. / Musielak, B. / Viviano, M. / Castellano, S. / Skalniak, L. / Magiera-Mularz, K. / Holak, T.A. / Kalinowska-Tluscik, J.
History
DepositionNov 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1447
Polymers29,3582
Non-polymers7865
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-32 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.088, 109.991, 51.823
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: Protein Programmed cell death 1 ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14678.759 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-WEW / (3~{R})-1-[[4-[2-chloranyl-3-(2,3-dihydro-1,4-benzodioxin-6-yl)phenyl]-2-methoxy-phenyl]methyl]-~{N}-(2-hydroxyethyl)pyrrolidine-3-carboxamide


Mass: 523.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31ClN2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 27 % w/v PEG 3350, 0.1 M Bis-Tris propane, pH 7.0 and 0.2 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.17→46.88 Å / Num. obs: 16333 / % possible obs: 99.7 % / Redundancy: 6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.094 / Rrim(I) all: 0.173 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.95-46.885.30.0552800.9990.0350.065
2.17-2.246.30.76213760.7340.4840.905

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→46.88 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: FREE R-VALUE / ESU R: 0.331 / ESU R Free: 0.237
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2894 865 5.308 %
Rwork0.2708 15432 -
all0.272 --
obs-16297 99.597 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.169 Å2-0 Å20 Å2
2---0.013 Å2-0 Å2
3----0.156 Å2
Refinement stepCycle: LAST / Resolution: 2.17→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 49 46 2119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122117
X-RAY DIFFRACTIONr_angle_refined_deg0.9831.6572869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.859514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30810364
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.46410100
X-RAY DIFFRACTIONr_chiral_restr0.050.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021573
X-RAY DIFFRACTIONr_nbd_refined0.210.2895
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2106
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.25
X-RAY DIFFRACTIONr_mcbond_it3.8373.131006
X-RAY DIFFRACTIONr_mcangle_it5.5085.6171254
X-RAY DIFFRACTIONr_scbond_it5.2993.8291111
X-RAY DIFFRACTIONr_scangle_it7.6226.7791615
X-RAY DIFFRACTIONr_lrange_it11.57436.0023144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.17-2.2260.383680.37411050.37411730.8420.881000.363
2.226-2.2870.369660.36110960.36211620.8590.8961000.344
2.287-2.3530.368620.34910560.3511180.8770.8991000.328
2.353-2.4260.354570.36210080.36110680.870.89599.71910.342
2.426-2.5050.427710.3499990.35510710.8250.90499.90660.33
2.505-2.5930.283640.3329840.32910500.9460.92199.80950.312
2.593-2.690.361560.3179130.329700.9180.92999.89690.292
2.69-2.80.299450.3059110.3059590.9230.93499.68720.285
2.8-2.9240.377360.3028880.3049270.9060.93899.67640.286
2.924-3.0660.312460.2988610.2999110.9390.93799.56090.285
3.066-3.2310.298480.2777740.2788330.9280.94798.67950.272
3.231-3.4260.338530.2727260.2767840.920.9599.36220.271
3.426-3.6610.362300.2747340.2787680.9230.95199.47920.279
3.661-3.9520.255280.2676660.2676970.9410.94999.56960.276
3.952-4.3260.287300.2296380.2316770.9450.96498.67060.245
4.326-4.8320.179250.215580.2085860.9860.96999.48810.237
4.832-5.5690.228350.2294940.2295330.9670.96599.24950.255
5.569-6.7970.26150.2384460.2384630.950.96799.5680.263
6.797-9.5130.181260.2123450.213740.980.97399.19790.253
9.513-46.880.24340.232300.232360.9810.96399.15250.293

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