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- PDB-5o45: Structure of human PD-L1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 5o45
TitleStructure of human PD-L1 in complex with inhibitor
Components
  • PHE-MEA-9KK-SAR-ASP-VAL-MEA-TYR-SAR-TRP-TYR-LEU-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: 0.99 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
European CommissionMarie Curie FP7-Reintegration-Grant Poland
National Science CenterUMO-2012/07/E/NZ1/01907 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 26, 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 1.2Jan 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
A: Programmed cell death 1 ligand 1
B: PHE-MEA-9KK-SAR-ASP-VAL-MEA-TYR-SAR-TRP-TYR-LEU-CCS-GLY-NH2


Theoretical massNumber of molelcules
Total (without water)16,6062
Polymers16,6062
Non-polymers00
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.814, 53.682, 80.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14792.861 Da / Num. of mol.: 1
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-MEA-9KK-SAR-ASP-VAL-MEA-TYR-SAR-TRP-TYR-LEU-CCS-GLY-NH2


Mass: 1813.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M imidazole malate (pH 8.5) 27% PEG 10000

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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: 0.99→44.735 Å / Num. obs: 73554 / % possible obs: 94.29 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19.7
Reflection shellResolution: 0.99→1.025 Å / Rmerge(I) obs: 0.887 / CC1/2: 0.723

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c3t
Resolution: 0.99→44.735 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1367 3738 5.08 %
Rwork0.1123 69796 -
obs0.1136 73534 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.11 Å2 / Biso mean: 16.6353 Å2 / Biso min: 5.49 Å2
Refinement stepCycle: final / Resolution: 0.99→44.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 244 378 1648
Biso mean--13.12 35.47 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021336
X-RAY DIFFRACTIONf_angle_d1.761833
X-RAY DIFFRACTIONf_chiral_restr0.134193
X-RAY DIFFRACTIONf_plane_restr0.011244
X-RAY DIFFRACTIONf_dihedral_angle_d23.71522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.99-1.00250.21751410.21772394253590
1.0025-1.01570.1991280.20762457258591
1.0157-1.02960.24331200.18252483260391
1.0296-1.04440.19081420.17352452259491
1.0444-1.05990.17641460.16022467261391
1.0599-1.07650.16071370.15752501263892
1.0765-1.09420.14831360.13872489262592
1.0942-1.1130.14011340.12652474260892
1.113-1.13330.12711410.11042519266093
1.1333-1.15510.1171360.10332508264493
1.1551-1.17860.10781200.10182586270693
1.1786-1.20430.1191490.10622499264893
1.2043-1.23230.12741370.10592555269294
1.2323-1.26310.14221250.10242567269294
1.2631-1.29730.13361420.10132577271995
1.2973-1.33540.12461370.10322597273495
1.3354-1.37850.14421220.10282615273795
1.3785-1.42780.12231610.09862589275096
1.4278-1.4850.12541560.09792609276596
1.485-1.55260.11011410.09492632277396
1.5526-1.63440.10861270.09432683281097
1.6344-1.73680.11491420.10152665280797
1.7368-1.87090.12541390.10112710284997
1.8709-2.05920.10931230.10662710283397
2.0592-2.35720.14771430.10732754289798
2.3572-2.96970.13961480.11832804295299
2.9697-44.78030.15271650.11632900306598

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