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- PDB-6nnv: PD-L1 IgV domain complex with macro-cyclic peptide -

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Basic information

Entry
Database: PDB / ID: 6nnv
TitlePD-L1 IgV domain complex with macro-cyclic peptide
Components
  • Programmed cell death 1 ligand 1
  • macrocyclic peptide
KeywordsIMMUNE SYSTEM / Fragment-based screening / Structure-based design / PD-L1 inhibitor / Cancer drug discovery / Immunotherapy
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: 1.92 Å
AuthorsZhao, B. / Perry, E.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)5T32GM065086 United States
National Science Foundation (NSF, United States)0922862 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR025677 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR026915 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2019
Title: Fragment-based screening of programmed death ligand 1 (PD-L1).
Authors: Perry, E. / Mills, J.J. / Zhao, B. / Wang, F. / Sun, Q. / Christov, P.P. / Tarr, J.C. / Rietz, T.A. / Olejniczak, E.T. / Lee, T. / Fesik, S.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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

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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
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
I: macrocyclic peptide
J: macrocyclic peptide
K: macrocyclic peptide
L: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)65,5838
Polymers65,5838
Non-polymers00
Water5,008278
1
A: Programmed cell death 1 ligand 1
J: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,3962
Polymers16,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area7020 Å2
MethodPISA
2
B: Programmed cell death 1 ligand 1
I: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,3962
Polymers16,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area7340 Å2
MethodPISA
3
C: Programmed cell death 1 ligand 1
K: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,3962
Polymers16,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-10 kcal/mol
Surface area7480 Å2
MethodPISA
4
D: Programmed cell death 1 ligand 1
L: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,3962
Polymers16,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area7160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.840, 61.683, 80.895
Angle α, β, γ (deg.)90.00, 90.17, 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: 14542.585 Da / Num. of mol.: 4 / Fragment: UNP residues 18-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9NZQ7
#2: Protein/peptide
macrocyclic peptide


Mass: 1853.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 41912 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.055 / Rrim(I) all: 0.105 / Rsym value: 0.061 / Χ2: 1.149 / Net I/σ(I): 10.1
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.338 / Num. unique obs: 2469 / Rpim(I) all: 0.237 / Rrim(I) all: 0.415 / Rsym value: 0.367 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BIK

3bik


Resolution: 1.92→29.099 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 31.55
RfactorNum. reflection% reflection
Rfree0.2531 1677 4.02 %
Rwork0.2147 --
obs0.2176 41672 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→29.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 536 278 4561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044465
X-RAY DIFFRACTIONf_angle_d1.0466060
X-RAY DIFFRACTIONf_dihedral_angle_d9.4142410
X-RAY DIFFRACTIONf_chiral_restr0.154654
X-RAY DIFFRACTIONf_plane_restr0.006761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9203-1.97670.31961270.27973206X-RAY DIFFRACTION89
1.9767-2.04050.29871350.25263226X-RAY DIFFRACTION91
2.0405-2.11340.26411200.25193270X-RAY DIFFRACTION91
2.1134-2.19790.24891520.23483278X-RAY DIFFRACTION92
2.1979-2.29790.28511300.24683186X-RAY DIFFRACTION90
2.2979-2.41890.24921330.23593344X-RAY DIFFRACTION94
2.4189-2.57020.28681400.24763331X-RAY DIFFRACTION94
2.5702-2.76840.26591400.23583383X-RAY DIFFRACTION94
2.7684-3.04630.25821320.2273386X-RAY DIFFRACTION95
3.0463-3.48580.25371470.20563420X-RAY DIFFRACTION95
3.4858-4.38640.23961360.18253461X-RAY DIFFRACTION96
4.3864-22.5350.20581370.17263515X-RAY DIFFRACTION96
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)
10.05170.0404-0.04320.0981-0.15170.37840.0022-0.0323-0.00920.0138-0.0176-0.01070.04020.1030.01220.18990.01-0.03180.4143-0.04320.023649.125826.271433.0999
20.04130.03280.27380.5332-0.42622.6148-0.01160.0601-0.0312-0.0806-0.0754-0.0470.23510.19780.05060.18520.0148-0.00620.4460.01050.081740.973-7.149914.7078
31.1815-0.43730.67681.03660.9492.2914-0.12250.08780.1657-0.1204-0.0354-0.1016-0.61140.36740.14050.2783-0.0535-0.02530.38730.02270.071639.06146.348718.8617
40.0131-0.0690.05290.4735-0.42950.54920.00630.0630.01170.1059-0.0239-0.0365-0.04830.11520.00810.1339-0.01180.00280.4322-0.02450.028440.8184-4.981222.0634
50.5527-0.2696-0.02051.8932-0.35341.5858-0.0353-0.04190.09090.1034-0.084-0.0247-0.29490.05470.13420.1482-0.0054-0.04340.442-0.03280.095369.39423.077916.0089
61.36650.5485-0.06171.45750.26650.7556-0.09060.0383-0.165-0.15720.0075-0.10350.22470.26870.08420.21330.0060.03810.4116-0.02670.066169.5233-8.523813.532
70.24270.257-0.49720.4004-0.85961.8866-0.0456-0.05030.0127-0.0728-0.00890.0128-0.0788-0.15130.00230.17250.01360.00520.3047-0.01350.036966.96250.85958.0293
81.54452.0427-2.15092.9603-3.0153.11330.1994-0.02520.146-0.0131-0.04810.0171-0.50150.1062-0.16270.33030.05940.07780.39710.00270.144771.917937.838928.6116
90.7893-0.2517-0.6950.95110.58053.412-0.01660.05690.0174-0.0374-0.0065-0.0935-0.00530.30330.04060.2447-0.0127-0.01340.35060.03840.074780.321534.308315.7382
100.0274-0.03240.00170.07830.00310.0006-0.07490.22440.03030.01270.0181-0.0498-0.06730.11320.04620.3424-0.0563-0.03510.3889-0.00070.104178.581128.545239.5101
110.64610.0989-0.54331.5640.52762.3647-0.01250.0264-0.0071-0.022-0.01130.02670.1095-0.04250.00210.1178-0.02010.00350.25110.00050.041672.387322.470222.3408
120.60340.50350.76230.99990.23131.24610.04110.0797-0.0820.06630.0712-0.11910.19740.2162-0.19690.14520.014-0.02810.4404-0.0270.075280.614822.440523.6114
130.79110.05571.40120.6234-0.92644.17860.18270.2409-0.0889-0.1841-0.1018-0.06270.23590.4934-0.08340.2561-0.0126-0.03240.3859-0.02660.095479.112127.29978.5254
140.8395-0.1340.49172.264-2.31075.88120.0018-0.00890.03210.06560.0237-0.016-0.00310.0030.020.1531-0.0037-0.00250.05010.03840.070970.715128.698226.077
150.03820.0768-0.08450.5136-0.91261.7206-0.0729-0.04330.0082-0.03350.08860.0280.1846-0.08770.00130.19190.0056-0.0010.2689-0.00290.037874.860636.390411.4607
160.14380.0978-0.12460.74030.15341.21570.00150.039-0.0421-0.1297-0.0095-0.0180.25150.06650.0050.24360.0096-0.01180.3762-0.0240.040647.663725.632625.324
170.1737-0.2479-0.71132.09421.74633.21830.05710.18020.1249-0.3796-0.0374-0.2984-0.48720.9111-0.02890.2115-0.0455-0.00560.42580.04540.111447.369939.356125.7454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 79 through 142 )
2X-RAY DIFFRACTION2chain 'D' and (resid 18 through 53 )
3X-RAY DIFFRACTION3chain 'D' and (resid 54 through 84 )
4X-RAY DIFFRACTION4chain 'D' and (resid 85 through 140 )
5X-RAY DIFFRACTION5chain 'A' and (resid 18 through 53 )
6X-RAY DIFFRACTION6chain 'A' and (resid 54 through 94 )
7X-RAY DIFFRACTION7chain 'A' and (resid 95 through 136 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 53 )
11X-RAY DIFFRACTION11chain 'B' and (resid 54 through 68 )
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 101 )
13X-RAY DIFFRACTION13chain 'B' and (resid 102 through 109 )
14X-RAY DIFFRACTION14chain 'B' and (resid 110 through 119 )
15X-RAY DIFFRACTION15chain 'B' and (resid 120 through 140 )
16X-RAY DIFFRACTION16chain 'C' and (resid 18 through 61 )
17X-RAY DIFFRACTION17chain 'C' and (resid 62 through 78 )

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