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- PDB-5j89: Structure of human Programmed cell death 1 ligand 1 (PD-L1) with ... -

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Basic information

Entry
Database: PDB / ID: 5j89
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 / Programmed cell death 1 ligand 1 / cell cycle
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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6GX / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZak, K.M. / Grudnik, P. / Guzik, K. / Zieba, B.J. / Musielak, B. / Doemling, P. / Dubin, G. / Holak, T.A.
Funding support Poland, 5items
OrganizationGrant numberCountry
European CommissionaMarie Curie FP7-Reintegration-Grant Poland
National Science CentreUMO-2012/06/A/ST5/00224 Poland
National Science CentreUMO-2011/01/D/NZ1/01169 Poland
European UnionPOIG.02.01.00-12-064/08 Poland
European UnionPOIG.02.01.00-12-167/08 Poland
CitationJournal: Oncotarget / Year: 2016
Title: Structural basis for small molecule targeting of the programmed death ligand 1 (PD-L1).
Authors: Zak, K.M. / Grudnik, P. / Guzik, K. / Zieba, B.J. / Musielak, B. / Domling, A. / Dubin, G. / Holak, T.A.
History
DepositionApr 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8387
Polymers66,9374
Non-polymers9013
Water3,747208
1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8883
Polymers33,4692
Non-polymers4201
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)33,9504
Polymers33,4692
Non-polymers4822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.834, 85.093, 161.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 16734.254 Da / Num. of mol.: 4
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-6GX / N-{2-[({2-methoxy-6-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]pyridin-3-yl}methyl)amino]ethyl}acetamide


Mass: 419.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29N3O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.01M Tris pH=8.5, 0.3M sodium chloride, 27% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.2→42.55 Å / Num. obs: 29405 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 6.3 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 2.2→42.547 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.256 1490 5.07 %
Rwork0.2023 --
obs0.2051 29405 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 66 208 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084004
X-RAY DIFFRACTIONf_angle_d1.0055450
X-RAY DIFFRACTIONf_dihedral_angle_d18.612357
X-RAY DIFFRACTIONf_chiral_restr0.06613
X-RAY DIFFRACTIONf_plane_restr0.006694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27110.32581160.26232500X-RAY DIFFRACTION99
2.2711-2.35220.30891320.24562481X-RAY DIFFRACTION100
2.3522-2.44640.35071210.23682499X-RAY DIFFRACTION99
2.4464-2.55770.30681390.24312511X-RAY DIFFRACTION99
2.5577-2.69260.30871360.24132481X-RAY DIFFRACTION100
2.6926-2.86120.29031320.23142522X-RAY DIFFRACTION100
2.8612-3.08210.26551370.23772510X-RAY DIFFRACTION100
3.0821-3.39210.271470.22222560X-RAY DIFFRACTION100
3.3921-3.88270.28231350.19652535X-RAY DIFFRACTION100
3.8827-4.89070.20431420.15182601X-RAY DIFFRACTION100
4.8907-42.55440.19441530.17222715X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7069-1.46560.64164.9322-2.93156.0591-0.2148-0.54020.34510.0861-0.1071-0.7068-0.3030.07920.22790.1558-0.0196-0.07280.3528-0.08480.365415.700529.0107196.4752
21.0846-0.3756-0.0275.4175-0.51941.5779-0.075-0.0354-0.2185-0.05150.18641.00750.0889-0.0447-0.08890.13940.0478-0.01990.25630.03610.38195.698725.6882195.475
31.42810.04790.50640.0598-0.22691.2240.309-0.0596-0.6703-0.2383-0.01370.34840.429-0.3604-0.10430.3668-0.0294-0.34790.61220.12970.61020.4826.6543186.8634
40.82360.7574-0.14415.36371.67063.8090.4828-0.2601-0.0042-1.09070.4453-0.6486-0.3723-0.9873-0.65380.54360.0082-0.11110.6378-0.00310.9616-3.666428.4794185.5154
52.5631.4287-0.85640.892-0.54990.3395-0.61470.8070.0012-0.60440.59030.5080.0912-0.29350.73650.5432-0.255-0.18490.5787-0.12381.5631-4.744617.1002190.3477
62.53271.28860.7741.95050.4630.9172-0.10020.1889-0.32870.5429-0.26231.11620.1535-0.28450.26740.23140.0350.10760.2853-0.04670.6221.289529.7218198.7586
71.32131.02620.6644.61781.04830.39990.0144-0.013-0.0245-0.70990.16321.21930.0422-0.1946-0.15270.1223-0.0745-0.07980.3210.00780.42915.796721.754191.9601
82.27543.0829-2.05625.8778-4.64784.5448-0.18210.3327-0.235-0.37060.35150.23630.17990.1781-0.10330.13050.0104-0.03190.2243-0.05480.26911.956218.8612193.9116
96.7533-0.93690.44115.7261-2.49036.88330.34760.65620.3531-0.6359-0.09451.77420.1582-0.3472-0.32280.2272-0.0105-0.0960.34020.09460.6514-0.4528-0.772195.173
101.3648-0.4125-0.51945.85931.20612.6636-0.010.0834-0.09990.61340.09870.69840.8182-0.2192-0.15280.2441-0.0036-0.04570.19050.06870.31348.5561-10.5499196.1034
112.63760.15981.23143.13561.01113.0616-0.086-0.0875-0.35030.242-0.03890.56510.5159-0.25330.0970.4305-0.0375-0.03070.20060.03710.332611.9771-22.5162194.2805
123.8304-2.4703-0.37136.21111.52512.54810.74710.47310.3417-1.2804-0.5887-0.2618-0.54270.5364-0.29880.435-0.01550.07510.3521-0.06610.187519.5833-15.9985188.5409
134.5429-3.1028-1.32384.69841.20591.80610.3453-0.3390.6072-0.7593-0.4197-1.0668-0.20130.7026-0.65120.13240.04270.45190.5335-0.11290.636223.6317-14.4459190.5728
141.5053-0.5482-0.51272.1395-0.7850.86710.1998-0.348-0.1096-1.3407-0.0486-1.22540.0340.522-0.27120.6916-0.0396-0.13220.4624-0.04341.017126.7304-12.3613194.025
151.2604-0.3094-1.04592.5665-2.57924.096-0.4019-0.419-0.20710.81240.371-0.87790.41260.3858-0.2040.33920.0851-0.09170.2933-0.07740.360818.6114-19.527200.624
161.481-1.10840.26827.5876-0.06581.6347-0.07120.05310.0713-0.34630.3212-0.35260.27430.1212-0.24130.263-0.0393-0.01730.2431-0.02350.182715.6539-13.1124194.3648
171.72030.0274-0.25046.70537.04358.4714-0.11270.2778-0.0745-0.48480.20880.46490.4888-0.0627-0.09130.3731-0.0281-0.07650.20040.02130.25429.8708-8.5822190.0209
184.50421.68660.5574.9116-0.20043.3837-0.01820.0411-0.24870.21420.2329-0.60980.13480.3777-0.22930.19140.0275-0.06790.2366-0.04750.280718.996910.7024201.439
191.2524-0.7570.24594.84852.053.5559-0.12470.10160.1336-0.5057-0.25020.3988-0.7799-0.6660.23280.30810.1593-0.16880.68910.03920.16186.650728.8745170.7233
202.5679-1.765-1.173.9791.16662.8997-0.1512-0.41450.2322-0.58840.2539-0.1832-0.3984-0.0063-0.02040.2616-0.0467-0.04580.3731-0.00010.207916.714727.8031167.3275
214.21340.3076-0.69816.00371.462.4109-0.592-0.77660.47970.7867-0.0059-0.00670.36510.76610.4660.46420.2085-0.08420.5198-0.10450.283817.201932.4538178.5944
221.4102-0.5744-0.09162.1882.83113.9864-0.3454-0.7898-0.08180.85040.8182-0.10851.08250.7444-0.14670.44850.2423-0.12740.8376-0.06810.241721.107227.8136180.6224
233.5463-1.6097-0.81122.0027-0.60120.8911-0.5891-0.6621.27821.00651.4044-0.88440.19931.17640.31370.45360.3819-0.23950.9374-0.34250.801727.372228.5626178.8141
245.022-2.33050.57866.4082-0.33924.5922-0.3699-0.27151.0162-0.46330.3867-1.0894-0.44150.32720.06110.3348-0.0579-0.04190.4004-0.07670.45820.683636.0874168.3842
252.4499-0.9441-0.61254.06660.45513.0535-0.3988-0.43850.1528-0.12480.3509-0.22040.03060.32990.06550.22110.0965-0.03690.4188-0.00630.179918.813925.2044173.0851
266.0795-4.5411-5.36863.87255.03617.4368-0.4278-0.433-0.2311-0.23920.28310.25290.1215-0.22290.35450.22620.0463-0.00160.4053-0.00290.239312.35620.6839173.0672
270.92862.30510.72527.03561.99460.59550.3249-0.5024-1.2547-0.19930.1239-1.87740.57350.2744-0.01590.32990.16440.06910.64740.18690.660729.21574.3307169.78
280.40460.76180.00214.8215-1.23150.6196-0.34150.1461-0.2683-1.38110.1778-0.89020.81980.36060.05630.80480.22090.20730.43650.02660.460423.1977-7.4957167.1996
291.88871.0127-1.01012.650.85731.8879-0.3214-0.13930.0751-0.48870.0178-0.19941.10090.16870.13541.23440.360.34920.40980.04210.614925.4186-24.6228170.4229
303.2757-1.43810.11946.73730.77032.3091-0.4507-0.1933-0.6288-0.49340.60120.69371.0605-0.32370.05541.11310.0870.09320.54620.06950.402713.0158-16.2048173.4267
312.4766-1.7327-0.41544.95180.54561.0136-0.2740.1215-0.7815-1.3712-0.03350.79750.57620.09780.08751.15230.0449-0.08040.4820.0040.476411.1679-16.3994166.4146
320.40820.8428-0.38621.8627-0.4081.5779-0.27120.5555-0.1999-1.0585-0.1454-0.02041.14090.2564-1.52521.43310.12610.20440.5080.09710.212216.6613-10.2669163.056
332.0569-1.1545-0.36426.3936-1.85781.1127-0.3346-0.26860.014-0.55120.421-0.15910.8949-0.3168-0.24380.85480.12410.14330.4337-0.01070.235317.4759-10.9228173.6626
340.7171-1.22240.40075.1812-4.1514.0598-0.0695-0.10290.1599-0.39370.0343-0.65260.38090.51820.15920.56920.13840.12290.424-0.04590.377621.9439-6.2742173.8299
352.0623-0.64192.44456.29270.26263.08020.1322-1.2465-0.05550.8651-0.62672.12530.4875-0.60360.38980.4455-0.08970.22170.4686-0.14930.47599.103411.2742163.0771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 18 through 26 )
2X-RAY DIFFRACTION2chain 'C' and (resid 27 through 61 )
3X-RAY DIFFRACTION3chain 'C' and (resid 62 through 68 )
4X-RAY DIFFRACTION4chain 'C' and (resid 69 through 78 )
5X-RAY DIFFRACTION5chain 'C' and (resid 79 through 84 )
6X-RAY DIFFRACTION6chain 'C' and (resid 85 through 101 )
7X-RAY DIFFRACTION7chain 'C' and (resid 102 through 120 )
8X-RAY DIFFRACTION8chain 'C' and (resid 121 through 131 )
9X-RAY DIFFRACTION9chain 'C' and (resid 132 through 142 )
10X-RAY DIFFRACTION10chain 'A' and (resid 18 through 35 )
11X-RAY DIFFRACTION11chain 'A' and (resid 36 through 49 )
12X-RAY DIFFRACTION12chain 'A' and (resid 50 through 61 )
13X-RAY DIFFRACTION13chain 'A' and (resid 62 through 68 )
14X-RAY DIFFRACTION14chain 'A' and (resid 69 through 84 )
15X-RAY DIFFRACTION15chain 'A' and (resid 85 through 91 )
16X-RAY DIFFRACTION16chain 'A' and (resid 92 through 120 )
17X-RAY DIFFRACTION17chain 'A' and (resid 121 through 131 )
18X-RAY DIFFRACTION18chain 'A' and (resid 132 through 144 )
19X-RAY DIFFRACTION19chain 'D' and (resid 18 through 26 )
20X-RAY DIFFRACTION20chain 'D' and (resid 27 through 49 )
21X-RAY DIFFRACTION21chain 'D' and (resid 50 through 59 )
22X-RAY DIFFRACTION22chain 'D' and (resid 60 through 68 )
23X-RAY DIFFRACTION23chain 'D' and (resid 69 through 84 )
24X-RAY DIFFRACTION24chain 'D' and (resid 85 through 94 )
25X-RAY DIFFRACTION25chain 'D' and (resid 95 through 120 )
26X-RAY DIFFRACTION26chain 'D' and (resid 121 through 131 )
27X-RAY DIFFRACTION27chain 'D' and (resid 132 through 141 )
28X-RAY DIFFRACTION28chain 'B' and (resid 18 through 38 )
29X-RAY DIFFRACTION29chain 'B' and (resid 39 through 49 )
30X-RAY DIFFRACTION30chain 'B' and (resid 50 through 68 )
31X-RAY DIFFRACTION31chain 'B' and (resid 69 through 94 )
32X-RAY DIFFRACTION32chain 'B' and (resid 95 through 105 )
33X-RAY DIFFRACTION33chain 'B' and (resid 106 through 120 )
34X-RAY DIFFRACTION34chain 'B' and (resid 121 through 131 )
35X-RAY DIFFRACTION35chain 'B' and (resid 132 through 142 )

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