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- PDB-5ggt: PD-L1 in complex with BMS-936559 Fab -

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Basic information

Entry
Database: PDB / ID: 5ggt
TitlePD-L1 in complex with BMS-936559 Fab
Components
  • IGK@ protein
  • IgG H chain
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / antibody
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHeo, Y.S.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of checkpoint blockade by monoclonal antibodies in cancer immunotherapy
Authors: Lee, J.Y. / Lee, H.T. / Shin, W. / Chae, J. / Choi, J. / Kim, S.H. / Lim, H. / Won Heo, T. / Park, K.Y. / Lee, Y.J. / Ryu, S.E. / Son, J.Y. / Lee, J.U. / Heo, Y.S.
History
DepositionJun 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
H: IgG H chain
L: IGK@ protein


Theoretical massNumber of molelcules
Total (without water)61,7283
Polymers61,7283
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-33 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.199, 91.555, 164.156
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: 13394.374 Da / Num. of mol.: 1 / Fragment: UNP residues 18-134 / Mutation: Q57E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9NZQ7
#2: Antibody IgG H chain


Mass: 25025.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Antibody IGK@ protein


Mass: 23308.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M imidazole, pH 9.0, 1.2M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14132 / % possible obs: 97.3 % / Redundancy: 5.9 % / Net I/σ(I): 26.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.161 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 712 5.04 %
Rwork0.2113 --
obs0.2141 14130 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→29.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4155 0 0 0 4155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054247
X-RAY DIFFRACTIONf_angle_d1.0585770
X-RAY DIFFRACTIONf_dihedral_angle_d15.9131531
X-RAY DIFFRACTIONf_chiral_restr0.04656
X-RAY DIFFRACTIONf_plane_restr0.006736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.0160.36571550.31512655X-RAY DIFFRACTION99
3.016-3.31910.32191380.27472665X-RAY DIFFRACTION98
3.3191-3.79850.30751530.23852633X-RAY DIFFRACTION97
3.7985-4.78230.23541310.17162670X-RAY DIFFRACTION96
4.7823-29.16280.21041350.17032795X-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)
12.46891.1907-0.37151.2910.35951.1594-0.3549-0.45680.50240.3026-0.0122-0.00920.352-0.05090.36610.45260.00580.05030.3608-0.06150.35638.083413.16783.0616
20.93020.63630.1552.94420.33252.39720.1892-0.7901-0.7964-0.0122-0.1240.07620.5585-0.289-0.1850.499-0.02640.03860.7259-0.03420.4915-5.15894.1323-4.7962
31.5544-0.75840.45910.0490.08121.69770.01370.62640.4671-0.31580.0309-0.1666-0.3810.1263-0.14450.2344-0.04580.03240.60510.05520.47887.047711.9131-11.7089
42.02123.00543.55330.73170.92821.08090.3969-0.1283-0.1899-0.83140.8072-1.09750.60971.0768-0.23840.5883-0.9148-0.4295-1.0167-0.33260.45487.02033.9687-17.4882
53.0188-0.6771-0.26011.39880.57042.6512-0.0555-0.1035-0.25670.09310.2796-0.53520.97260.3975-0.2240.36880.0271-0.05740.52460.01370.444912.87496.2796-8.5707
63.51251.73932.13453.24830.9031.94030.0081-0.2412-0.1672-0.11810.0206-0.19120.2944-0.0230.20640.37590.0229-0.01570.3398-0.02170.423215.421810.9268-1.0229
74.87485.25952.21225.33292.3831.76190.2940.169-0.4529-0.1952-0.1351-0.52840.0954-0.1171-0.02410.3932-0.03070.01630.3753-0.01950.34932.826414.4739-7.5719
80.31250.2323-0.55012.74670.39011.29740.0542-0.95640.6010.2512-0.3166-0.0565-0.85320.44060.08780.2839-0.12850.06060.40340.05790.37038.300918.44560.2609
92.4519-0.3208-0.40771.55910.00153.3328-0.05860.10290.23440.302-0.17020.0567-0.26830.22190.07490.30640.0497-0.03380.3951-0.02720.4687-7.208223.6527-35.4929
102.24170.64250.51762.6886-0.75594.2233-0.31860.27130.18340.041-0.42780.17220.2647-1.53130.7040.3155-0.0475-0.10610.3322-0.01020.335-8.103614.619-28.2337
111.5670.9230.26172.8226-0.95713.658-0.0440.33870.32450.3608-0.2351-0.14570.13510.4580.11560.2648-0.0219-0.03210.46640.02960.40820.102217.9246-27.1726
120.3817-0.4686-0.42060.2753-0.58531.5896-0.0184-0.14550.0857-0.0707-0.0332-0.1155-0.00340.10080.15240.2665-0.0730.00040.31910.01260.3856-10.245915.4608-42.0079
134.10090.27711.50732.5151.20023.3688-0.01310.50590.16150.0236-0.46730.3650.0986-0.98850.66090.3897-0.0063-0.05820.6195-0.08930.4001-21.740219.1082-58.7578
141.49372.11940.09362.83140.2034-0.01480.26940.53-1.021-0.3717-0.6328-0.5922-0.1483-0.0520.07410.2925-0.0057-0.09430.4344-0.11350.4565-8.911216.1132-58.6276
150.8182-0.18890.63530.760.23170.9041-0.1259-0.38680.1795-0.4001-0.22450.5272-0.5099-1.09770.24970.48260.0696-0.13490.7202-0.13880.4446-26.455721.5669-63.7452
163.0011-1.15141.31010.3709-0.35442.9624-0.42560.359-1.0432-0.16550.5260.60480.89760.42210.1250.67240.01490.02770.41970.04940.4331-14.4529-6.7878-39.5816
171.57710.87710.21381.41760.35691.80640.09050.1256-0.167-0.10690.02890.05250.3866-0.0825-0.12780.3563-0.0165-0.00580.2547-0.00730.2475-15.7203-2.7878-29.5639
180.97730.1388-0.06250.0567-0.72142.721-0.1250.2119-0.0324-0.02910.1456-0.08850.3195-0.25950.00370.3922-0.06390.00120.2582-0.08880.324-16.91213.5593-54.2281
19-0.0067-0.2061-0.35150.05780.67591.1535-0.0545-0.2784-0.7105-0.22961.0373-1.70920.04230.2225-0.44610.4671-0.1741-0.19960.55960.03840.7756-8.3814.8091-70.5314
202.2254-0.9889-2.77333.7478-0.24534.070.1309-0.67510.12350.2224-0.55570.7182-0.3436-0.28020.21170.5101-0.0756-0.0690.6611-0.19730.6007-25.183.4437-53.3754
211.3614-0.1410.09121.50550.30461.8808-0.05430.3080.0103-0.23320.0043-0.32380.3063-0.1934-0.01620.43610.01040.04920.515-0.17050.4031-14.48045.7933-74.9861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 73 )
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 94 )
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 109 )
7X-RAY DIFFRACTION7chain 'A' and (resid 110 through 119 )
8X-RAY DIFFRACTION8chain 'A' and (resid 120 through 133 )
9X-RAY DIFFRACTION9chain 'H' and (resid 2 through 24 )
10X-RAY DIFFRACTION10chain 'H' and (resid 25 through 44 )
11X-RAY DIFFRACTION11chain 'H' and (resid 45 through 83 )
12X-RAY DIFFRACTION12chain 'H' and (resid 84 through 147 )
13X-RAY DIFFRACTION13chain 'H' and (resid 148 through 175 )
14X-RAY DIFFRACTION14chain 'H' and (resid 176 through 187 )
15X-RAY DIFFRACTION15chain 'H' and (resid 188 through 223 )
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 18 )
17X-RAY DIFFRACTION17chain 'L' and (resid 19 through 75 )
18X-RAY DIFFRACTION18chain 'L' and (resid 76 through 149 )
19X-RAY DIFFRACTION19chain 'L' and (resid 150 through 162 )
20X-RAY DIFFRACTION20chain 'L' and (resid 163 through 173 )
21X-RAY DIFFRACTION21chain 'L' and (resid 174 through 210 )

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