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- PDB-8p64: Co-crystal structure of PD-L1 with low molecular weight inhibitor -

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Basic information

Entry
Database: PDB / ID: 8p64
TitleCo-crystal structure of PD-L1 with low molecular weight inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsANTITUMOR PROTEIN / PD-L1 / inhibitor complex
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 / negative regulation of type II interferon 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 / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / positive regulation of T cell proliferation / negative regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / positive regulation of cell migration / receptor ligand activity / 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
: / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.312 Å
AuthorsPlewka, J. / Magiera-Mularz, K. / van der Straat, R. / Draijer, R. / Surmiak, E. / Butera, R. / Land, L. / Musielak, B. / Domling, A.
Funding support Poland, 1items
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-420F/17-00 Poland
CitationJournal: Rsc Med Chem / Year: 2024
Title: 1,5-Disubstituted tetrazoles as PD-1/PD-L1 antagonists.
Authors: van der Straat, R. / Draijer, R. / Surmiak, E. / Butera, R. / Land, L. / Magiera-Mularz, K. / Musielak, B. / Plewka, J. / Holak, T.A. / Domling, A.
History
DepositionMay 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 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: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2283
Polymers29,9082
Non-polymers3191
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-5 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.450, 73.450, 96.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 119 / Label seq-ID: 4 - 119

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14954.085 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 BL21(DE3) (bacteria) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-X1Q / ~{N}-[[1-[(~{E})-2-(2-methyl-3-phenyl-phenyl)ethenyl]-1,2,3,4-tetrazol-5-yl]methyl]ethanamine


Mass: 319.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.2 M S38 sodium citrate tribasic dihydrate 0.01 M sodium borate, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.31→48.04 Å / Num. obs: 4743 / % possible obs: 99.9 % / Redundancy: 10.55 % / CC1/2: 0.997 / Net I/σ(I): 9.39
Reflection shellResolution: 3.31→3.51 Å / Mean I/σ(I) obs: 0.96 / Num. unique obs: 743 / CC1/2: 0.423

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.312→38.336 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 39.532 / SU ML: 0.603 / Cross valid method: FREE R-VALUE / ESU R Free: 0.631
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2971 224 4.723 %
Rwork0.2343 4519 -
all0.237 --
obs-4743 99.853 %
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: 97.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.052 Å2-0.026 Å20 Å2
2---0.052 Å2-0 Å2
3---0.169 Å2
Refinement stepCycle: LAST / Resolution: 3.312→38.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 24 10 1799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121822
X-RAY DIFFRACTIONr_bond_other_d0.0040.0161684
X-RAY DIFFRACTIONr_ext_dist_refined_b00.017486
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.6452482
X-RAY DIFFRACTIONr_angle_other_deg0.8031.5643827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3345233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.0277.512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.78510273
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.6181076
X-RAY DIFFRACTIONr_chiral_restr0.1020.2288
X-RAY DIFFRACTIONr_chiral_restr_other0.2360.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02419
X-RAY DIFFRACTIONr_nbd_refined0.1980.2276
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21567
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2872
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3080.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3650.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2620.212
X-RAY DIFFRACTIONr_nbd_other0.3230.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3150.21
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_mcbond_it6.95110.71938
X-RAY DIFFRACTIONr_mcbond_other6.95110.71938
X-RAY DIFFRACTIONr_mcangle_it11.05319.2361169
X-RAY DIFFRACTIONr_mcangle_other11.04919.2421170
X-RAY DIFFRACTIONr_scbond_it6.74710.916884
X-RAY DIFFRACTIONr_scbond_other6.74510.916885
X-RAY DIFFRACTIONr_scangle_it10.81420.0021313
X-RAY DIFFRACTIONr_scangle_other10.8120.0011314
X-RAY DIFFRACTIONr_lrange_it17.117174.3647635
X-RAY DIFFRACTIONr_lrange_other17.116174.3527636
X-RAY DIFFRACTIONr_ncsr_local_group_10.1510.053254
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.150790.0501
12AX-RAY DIFFRACTIONLocal ncs0.150790.0501
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
3.312-3.3970.415130.3743290.3753420.7780.8711000.361
3.397-3.4890.423130.373210.3723350.8870.87999.70150.358
3.489-3.590.329140.3263030.3263170.9380.9071000.317
3.59-3.6990.464120.323000.3263120.9040.9191000.298
3.699-3.8190.325120.2732970.2763090.9190.9441000.233
3.819-3.9520.286220.2492710.2512930.9510.9511000.226
3.952-4.10.299110.2392800.2422910.9480.9581000.204
4.1-4.2650.303240.2032480.2112720.930.9721000.182
4.265-4.4520.196100.1992490.1992590.9540.9741000.167
4.452-4.6660.33180.1892540.1932620.9810.9751000.158
4.666-4.9150.22380.1692340.1712420.9660.9831000.145
4.915-5.2070.18890.1812160.1822250.9770.9741000.156
5.207-5.560.264230.1842050.1912290.9470.97899.56330.151
5.56-5.9950.3110.221900.2242010.9520.9641000.189
5.995-6.5510.37370.2371880.2421960.9690.9699.48980.192
6.551-7.2970.3880.2421700.2481780.9120.9561000.216
7.297-8.3760.325100.2031420.2111520.9470.9681000.18
8.376-10.1380.18840.1881360.1881400.9940.9761000.183
10.138-13.8610.43440.2211070.2261110.8060.9781000.211
13.861-38.3360.42610.463790.462810.8598.76540.433

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