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- PDB-5o4y: Structure of human PD-L1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 5o4y
TitleStructure of human PD-L1 in complex with inhibitor
Components
  • PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2
  • Programmed cell death 1 ligand 1
KeywordsCELL CYCLE / PD-1 / Programmed Death 1 / PD-L1 / Programmed Death Ligand 1 / immune checkpoint / cancer
Function / homology
Function and homology information


positive regulation of tolerance induction to tumor cell / 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 / 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 ...positive regulation of tolerance induction to tumor cell / 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 / 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 / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMagiera, K. / Grudnik, P. / Dubin, G. / Holak, T.A.
Funding support Poland, 3items
OrganizationGrant numberCountry
National Science CenterUMO-2014/12/W/NZ1/00457 Poland
National Science CenterUMO-2012/07/E/NZ1/01907 Poland
European UnionMarie Curie FP7-Reintegration-Grant Poland
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Bioactive Macrocyclic Inhibitors of the PD-1/PD-L1 Immune Checkpoint.
Authors: Magiera-Mularz, K. / Skalniak, L. / Zak, K.M. / Musielak, B. / Rudzinska-Szostak, E. / Kocik, J. / Grudnik, P. / Sala, D. / Zarganes-Tzitzikas, T. / Shaabani, S. / Domling, A. / Dubin, G. / Holak, T.A.
History
DepositionMay 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: 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.name
Revision 1.2Dec 11, 2019Group: Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / refine_hist
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _refine_hist.d_res_high / _refine_hist.d_res_low
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Programmed cell death 1 ligand 1
C: Programmed cell death 1 ligand 1
E: Programmed cell death 1 ligand 1
A: PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2
D: PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2
F: PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2


Theoretical massNumber of molelcules
Total (without water)45,9806
Polymers45,9806
Non-polymers00
Water1,892105
1
B: Programmed cell death 1 ligand 1
D: PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2


Theoretical massNumber of molelcules
Total (without water)15,3272
Polymers15,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area6790 Å2
MethodPISA
2
C: Programmed cell death 1 ligand 1
F: PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2


Theoretical massNumber of molelcules
Total (without water)15,3272
Polymers15,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-9 kcal/mol
Surface area6760 Å2
MethodPISA
3
E: Programmed cell death 1 ligand 1
A: PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2


Theoretical massNumber of molelcules
Total (without water)15,3272
Polymers15,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area6900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.550, 80.950, 54.230
Angle α, β, γ (deg.)90.00, 104.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 13439.414 Da / Num. of mol.: 3
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: Protein/peptide PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS-GLY-NH2


Mass: 1887.191 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate (pH 5.5), 0.1 M Bis-Tris, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→29.78 Å / Num. obs: 18522 / % possible obs: 97.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.552

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 2.3→29.78 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 31.74
RfactorNum. reflection% reflection
Rfree0.262 935 5.06 %
Rwork0.198 --
obs0.201 18474 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 0 105 3210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.42120.40391320.30852498X-RAY DIFFRACTION99
2.4212-2.57280.30661610.27392493X-RAY DIFFRACTION99
2.5728-2.77140.35461260.26342472X-RAY DIFFRACTION97
2.7714-3.050.29341200.23082496X-RAY DIFFRACTION97
3.05-3.49080.27751470.22523X-RAY DIFFRACTION99
3.4908-4.39570.22961220.16172508X-RAY DIFFRACTION98
4.3957-29.78280.19861270.15462549X-RAY DIFFRACTION97

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