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- PDB-7nld: Structure of human Programmed cell death 1 ligand 1 (PD-L1) with ... -

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Basic information

Entry
Database: PDB / ID: 7nld
TitleStructure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / cancer / inhibitor
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 / transcription coactivator activity / adaptive immune response / 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-UGZ / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSala, D. / Magiera-Mularz, K. / Muszak, D. / Surmiak, E. / Grudnik, P. / Holak, T.A.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Terphenyl-Based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction.
Authors: Muszak, D. / Surmiak, E. / Plewka, J. / Magiera-Mularz, K. / Kocik-Krol, J. / Musielak, B. / Sala, D. / Kitel, R. / Stec, M. / Weglarczyk, K. / Siedlar, M. / Domling, A. / Skalniak, L. / Holak, T.A.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Programmed cell death 1 ligand 1
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
E: Programmed cell death 1 ligand 1
F: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5829
Polymers88,0736
Non-polymers1,5093
Water75742
1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8613
Polymers29,3582
Non-polymers5031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8613
Polymers29,3582
Non-polymers5031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Programmed cell death 1 ligand 1
hetero molecules

F: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)29,8613
Polymers29,3582
Non-polymers5031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Unit cell
Length a, b, c (Å)67.087, 75.255, 74.354
Angle α, β, γ (deg.)90.000, 96.290, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 6
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-UGZ / N-(2-((2'-chloro-3'-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-3-methoxy-[1,1'-biphenyl]-4-yl)(methyl)amino)ethyl)methanesulfonamide / ~{N}-[2-[[4-[2-chloranyl-3-(2,3-dihydro-1,4-benzodioxin-6-yl)phenyl]-2-methoxy-phenyl]methylamino]ethyl]methanesulfonamide


Mass: 503.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H27ClN2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M sodium cocdylate pH 6.5; 25% PEG4000

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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: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→47.01 Å / Num. obs: 32474 / % possible obs: 99 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.42 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1720 / CC1/2: 0.77 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O45

5o45


Resolution: 2.3→43.03 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2939 1606 4.99 %
Rwork0.2426 30584 -
obs0.2443 32190 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.6 Å2 / Biso mean: 56.2346 Å2 / Biso min: 28.02 Å2
Refinement stepCycle: final / Resolution: 2.3→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 102 42 5354
Biso mean--73.14 57.56 -
Num. residues----696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.37420.46531410.4129271697
2.3742-2.45910.44561380.3819263493
2.4591-2.55750.47261440.3579275298
2.5575-2.67390.41271460.3425277599
2.6739-2.81490.41361490.3069280799
2.8149-2.99120.34061480.3052280299
2.9912-3.22210.35251450.2832277598
3.2221-3.54620.34141490.2544281999
3.5462-4.0590.28011470.2232281699
4.059-5.11260.22071480.1824280999
5.1126-43.030.21361510.1968287999

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