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- PDB-5ggs: PD-1 in complex with pembrolizumab Fab -

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Basic information

Entry
Database: PDB / ID: 5ggs
TitlePD-1 in complex with pembrolizumab Fab
Components
  • Programmed cell death protein 1
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of immune response / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of immune response / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response / PD-1 signaling / signaling receptor activity / adaptive immune response / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Programmed cell death protein 1 / Immunoglobulin V-Type / 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 protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.997 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heavy chain
B: light chain
C: heavy chain
D: light chain
Y: Programmed cell death protein 1
Z: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)125,7786
Polymers125,7786
Non-polymers00
Water14,340796
1
A: heavy chain
B: light chain
Z: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)62,8893
Polymers62,8893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-32 kcal/mol
Surface area23930 Å2
MethodPISA
2
C: heavy chain
D: light chain
Y: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)62,8893
Polymers62,8893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-32 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.170, 54.195, 104.039
Angle α, β, γ (deg.)105.69, 96.99, 96.06
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody heavy chain


Mass: 25237.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Antibody light chain


Mass: 23768.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Programmed cell death protein 1 / hPD-1


Mass: 13883.409 Da / Num. of mol.: 2 / Fragment: UNP residues 26-148 / Mutation: C93S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q15116
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, pH 6.5, 12% PEG500 MME, 6% PEG20,000, 50 mM ammonium acetate

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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: 1.99→50 Å / Num. obs: 71844 / % possible obs: 95.2 % / Redundancy: 1.9 % / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.997→30.038 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 3604 5.02 %
Rwork0.1795 --
obs0.1819 71844 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.997→30.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8443 0 0 796 9239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088653
X-RAY DIFFRACTIONf_angle_d1.16511752
X-RAY DIFFRACTIONf_dihedral_angle_d13.0463121
X-RAY DIFFRACTIONf_chiral_restr0.0491310
X-RAY DIFFRACTIONf_plane_restr0.0051517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9975-2.02370.26751140.21632341X-RAY DIFFRACTION84
2.0237-2.05150.26931540.22132595X-RAY DIFFRACTION95
2.0515-2.08080.28181250.22452604X-RAY DIFFRACTION91
2.0808-2.11180.30091420.22242594X-RAY DIFFRACTION96
2.1118-2.14480.26371610.20912642X-RAY DIFFRACTION96
2.1448-2.180.24661430.19942704X-RAY DIFFRACTION96
2.18-2.21750.25321250.19592612X-RAY DIFFRACTION96
2.2175-2.25780.2951330.21072587X-RAY DIFFRACTION91
2.2578-2.30130.28461160.20252609X-RAY DIFFRACTION95
2.3013-2.34820.26041430.18882691X-RAY DIFFRACTION96
2.3482-2.39920.26911260.19972655X-RAY DIFFRACTION97
2.3992-2.4550.25831400.20022697X-RAY DIFFRACTION96
2.455-2.51640.28051530.19652666X-RAY DIFFRACTION97
2.5164-2.58440.27211390.19512702X-RAY DIFFRACTION96
2.5844-2.66040.27011280.19432644X-RAY DIFFRACTION97
2.6604-2.74620.24781420.18892624X-RAY DIFFRACTION95
2.7462-2.84430.25291630.18342667X-RAY DIFFRACTION96
2.8443-2.95810.24181410.18312588X-RAY DIFFRACTION95
2.9581-3.09260.25331550.17842659X-RAY DIFFRACTION95
3.0926-3.25540.20721380.17262644X-RAY DIFFRACTION96
3.2554-3.45910.22191290.16712617X-RAY DIFFRACTION94
3.4591-3.72580.19411500.15472537X-RAY DIFFRACTION92
3.7258-4.09990.18061400.15122567X-RAY DIFFRACTION93
4.0999-4.69120.1661070.13812675X-RAY DIFFRACTION95
4.6912-5.9030.17871440.16372688X-RAY DIFFRACTION97
5.903-30.04150.21981530.20392631X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.265-1.42-0.35352.94360.77261.51320.06590.56740.1138-0.4511-0.07940.2048-0.0814-0.07190.0480.2366-0.03630.00290.2286-0.00110.17260.5312-11.8737-16.9038
23.38170.24140.36372.33770.0155-0.02960.0321-0.1204-0.16460.142-0.05580.12320.23520.0181-0.02450.2477-0.01460.00960.17820.00370.15880.0886-18.182-10.945
32.0844-1.8924-1.4831.77571.26521.839-0.0495-0.00990.0126-0.05560.0690.0154-0.03170.0554-0.00590.1531-0.0368-0.00150.11390.00070.1642-4.78421.0409-4.1245
42.39320.5091-0.49584.1911-0.30532.1770.01750.1938-0.09380.1829-0.0123-0.2831-0.19530.0406-0.01430.123-0.0084-0.01160.19110.00740.1436-12.269612.82120.862
52.60841.64231.57675.13495.89467.5398-0.19520.13910.3411-0.5942-0.15560.8386-0.4001-0.25030.30150.23430.0004-0.04440.29310.03490.2124-20.363916.0976-3.1867
62.3866-2.56880.3452.7458-0.36882.8256-0.1779-0.19410.15350.52710.30290.28540.01690.0329-0.06410.11510.0003-0.01440.1992-0.00180.103216.80720.63643.5696
73.0291-0.6672-0.73255.7959-1.14252.8834-0.06860.1668-0.38790.2132-0.0996-0.65260.51050.38630.11030.21660.06510.01220.21930.01780.283123.3255-12.0018-1.1864
83.29430.8063-0.53394.2740.23182.4475-0.04180.18160.0459-0.2476-0.0546-0.1278-0.05590.10950.0620.1344-0.0214-0.00150.1581-0.01330.127519.1246-2.2906-7.8564
92.60950.6686-0.69455.42511.0821.57560.03030.28240.2126-0.3315-0.04060.1687-0.13260.05990.00520.1638-0.002-0.01460.20460.03330.159515.35183.4527-4.4916
100.564-1.0968-1.07286.15463.13322.2756-0.0213-0.06930.02790.0160.1367-0.31260.0910.0784-0.14090.16660.0214-0.06020.1650.00450.208411.72530.03062.2443
117.81546.10242.17987.61261.58024.6891-0.1462-0.020.3814-0.22490.08490.57560.136-0.67680.09630.21570.01730.00950.26580.01610.2047-20.090313.415812.6346
123.95212.3975-3.79811.8715-2.05913.5679-0.0863-0.2535-0.0815-0.0302-0.0154-0.02070.08940.14620.07050.18910.0048-0.01630.1795-0.0320.1548-5.095611.005814.6951
135.00391.1306-2.81391.4660.43253.1901-0.29020.3064-0.2425-0.16680.2057-0.07390.4009-0.12380.1150.1540.0592-0.06350.1470.0040.1517-3.64279.57310.9511
147.64381.6734-1.50673.38930.24133.7494-0.0765-0.3052-0.19610.1362-0.14550.21470.1756-0.31520.26560.21540.001-0.00550.19030.05110.1397-16.45548.36720.1315
153.83242.3232-3.72162.3033-1.41994.20980.1238-0.06150.7168-0.09-0.05110.1669-0.18020.0094-0.10960.2037-0.0066-0.03540.1171-0.01970.1452-7.755916.96321.8145
162.571-2.5345-2.21294.8412.0364.1999-0.0765-0.3007-0.3930.18440.0833-0.23530.20640.0207-0.09550.18250.0277-0.01380.15080.05060.1921-9.6914-5.730851.6006
173.3807-0.5238-0.90852.87660.61721.4439-0.0278-0.25210.02070.18390.0682-0.09140.09210.0112-0.09570.1602-0.0165-0.00180.1714-0.00560.1424-14.88894.454151.7844
186.2264-0.4063-1.42274.95430.81716.2561-0.090.1755-0.2201-0.1299-0.29720.56190.0058-0.50440.13310.1638-0.0211-0.01670.22880.03110.2331-24.80594.082848.7416
195.45682.21054.18724.36323.05533.78990.0357-0.3293-0.3180.2381-0.10450.17940.0808-0.32790.03920.180.00430.01550.20850.04850.1972-20.4618-2.490554.3943
202.0195-1.6505-1.09761.85181.13861.67210.0260.0455-0.03730.0524-0.0657-0.04380.0036-0.10570.0550.1664-0.05460.00240.13580.01740.1468-4.679-2.379242.6261
215.00141.0462-1.10031.95751.13581.08160.1776-0.0239-0.24070.2706-0.1103-0.0416-0.04610.0065-0.06990.24250.0325-0.00850.15080.04760.239811.3075-12.361137.539
223.03841.0586-0.01813.18520.58072.7009-0.14820.52120.53460.00880.1617-0.1125-0.00970.38280.01510.18650.0031-0.01140.15790.02850.192913.9751-8.690433.8683
237.59772.6139-4.38344.5804-1.16276.18120.0095-0.5234-0.66380.4019-0.2409-0.42490.26760.26080.24670.25780.0115-0.07580.20910.02140.211415.8578-17.342940.5923
245.91-2.33451.15551.14030.10241.7920.04440.3345-0.1678-0.1137-0.0171-0.14010.02720.0429-0.02950.21160.03230.01490.13320.0370.1181-2.664418.209333.5915
258.37880.82822.62193.80571.14953.3781-0.07040.1319-0.05520.0764-0.04980.3872-0.1123-0.48160.14520.16790.0204-0.0040.09010.05730.1714-15.804523.113838.4068
260.8796-0.5673-0.5780.99130.47530.70950.04210.01440.03960.0408-0.00390.00830.0152-0.0496-0.04240.1744-0.0013-0.02750.17380.01650.1699-0.998112.159938.9462
271.12651.1551.19423.38353.37143.4450.011-0.02870.0708-0.0666-0.17470.261-0.0256-0.0990.14060.1413-0.03040.03590.17250.00590.1589.935-2.488722.4063
281.09390.7118-0.54086.05013.84154.5410.1603-0.1102-0.04720.3654-0.21910.10630.2003-0.27040.0610.13720.0361-0.01510.15360.03980.178.3829-1.192226.0221
292.44120.1011-1.12547.56692.41313.7828-0.05580.1737-0.1215-0.0908-0.29590.31140.355-0.17740.30970.2142-0.0079-0.06230.21620.00470.15368.5043-14.027816.9459
301.41171.65890.52772.90372.29342.5090.1108-0.0026-0.1013-0.0308-0.0927-0.8089-0.08370.1125-0.00020.14120.0050.00950.24130.00990.168116.1324-4.553415.2365
316.21690.27840.82255.86160.27338.19950.0470.44120.42520.7598-0.0261-0.1925-0.8660.2577-0.06960.51770.02120.02220.21380.07310.4577-28.677732.205664.8318
324.207-0.4072-0.53343.65390.875.66430.12510.4526-0.19720.2229-0.01460.7738-0.7168-0.7401-0.21380.35930.13650.10550.36010.01210.5661-39.327926.298361.8588
335.22950.4294-1.22526.6879-0.55675.15770.2934-0.1330.4746-0.1185-0.06590.0849-0.90210.1245-0.25790.30570.06540.04020.286-0.0590.3087-24.959426.102358.8393
345.10274.8665-2.42585.9787-4.75935.61840.1455-1.3432-0.52491.3949-0.3126-0.62850.21570.60880.16680.88410.210.01990.56030.24720.7332-27.13913.051571.3459
353.49641.2683-1.49945.7930.5431.49930.21820.1715-0.0085-0.5399-0.02240.71270.0217-0.4906-0.08190.33370.0449-0.01730.33060.01630.3006-30.290218.519853.6005
362.5817-1.3520.13171.3364-0.10313.47760.29860.26460.17590.20470.01670.4075-0.2562-0.5091-0.29430.27370.05980.08460.3095-0.01270.4474-35.444323.887159.5767
373.51850.34260.58453.72121.60015.13030.3212-1.1555-0.40250.7483-0.4305-0.19930.06640.2555-0.07120.55420.09620.02040.24390.0740.3653-28.916223.912565.6943
383.9992-0.3891-0.87576.13241.49735.89420.2846-0.1664-0.67010.0238-0.3272-0.87370.40510.76590.01570.3650.14640.0470.44990.02470.403831.2376-28.3662-24.4845
395.0951-0.8235-3.41119.0471-0.97417.90260.08090.7443-0.8591-0.5930.44990.12870.044-0.1974-0.49040.19730.02720.01950.2408-0.02550.287623.9095-23.565-23.7774
404.9128-0.81853.97765.3865-1.37988.3510.3230.4436-0.2107-0.6536-0.30740.21450.3966-0.55710.10950.25810.06950.02930.4363-0.0530.21218.0965-24.2332-26.3691
416.69481.1710.53892.29360.66160.64080.1339-0.7744-1.21180.5286-0.0561-0.39330.2751-0.1581-0.05820.41250.0167-0.0240.41820.09290.420720.0115-27.9135-14.7603
424.15390.32980.91186.81380.82446.3014-0.13810.4946-1.00190.16880.15730.17950.91460.12130.1930.4840.120.03460.3282-0.02130.445126.4498-33.9775-21.1393
432.0512-2.4871-1.70925.28791.96573.4550.37260.17750.6628-0.4768-0.3859-0.0493-0.3497-0.0867-0.13190.44560.13580.04820.4812-0.02560.340525.6606-17.7367-24.384
445.03030.7106-0.50827.4252-1.074.93960.10351.1319-0.2814-1.1753-0.070.30360.5028-0.3660.05050.37330.03310.01620.5133-0.05960.235526.5176-26.8574-31.7602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 197 )
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 220 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 18 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 36 )
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 79 )
9X-RAY DIFFRACTION9chain 'B' and (resid 80 through 94 )
10X-RAY DIFFRACTION10chain 'B' and (resid 95 through 117 )
11X-RAY DIFFRACTION11chain 'B' and (resid 118 through 132 )
12X-RAY DIFFRACTION12chain 'B' and (resid 133 through 154 )
13X-RAY DIFFRACTION13chain 'B' and (resid 155 through 178 )
14X-RAY DIFFRACTION14chain 'B' and (resid 179 through 201 )
15X-RAY DIFFRACTION15chain 'B' and (resid 202 through 217 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 17 )
17X-RAY DIFFRACTION17chain 'C' and (resid 18 through 52 )
18X-RAY DIFFRACTION18chain 'C' and (resid 53 through 64 )
19X-RAY DIFFRACTION19chain 'C' and (resid 65 through 83 )
20X-RAY DIFFRACTION20chain 'C' and (resid 84 through 141 )
21X-RAY DIFFRACTION21chain 'C' and (resid 142 through 164 )
22X-RAY DIFFRACTION22chain 'C' and (resid 165 through 198 )
23X-RAY DIFFRACTION23chain 'C' and (resid 199 through 220 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 18 )
25X-RAY DIFFRACTION25chain 'D' and (resid 19 through 36 )
26X-RAY DIFFRACTION26chain 'D' and (resid 37 through 132 )
27X-RAY DIFFRACTION27chain 'D' and (resid 133 through 154 )
28X-RAY DIFFRACTION28chain 'D' and (resid 155 through 178 )
29X-RAY DIFFRACTION29chain 'D' and (resid 179 through 201 )
30X-RAY DIFFRACTION30chain 'D' and (resid 202 through 217 )
31X-RAY DIFFRACTION31chain 'Y' and (resid 33 through 38 )
32X-RAY DIFFRACTION32chain 'Y' and (resid 39 through 58 )
33X-RAY DIFFRACTION33chain 'Y' and (resid 59 through 70 )
34X-RAY DIFFRACTION34chain 'Y' and (resid 71 through 75 )
35X-RAY DIFFRACTION35chain 'Y' and (resid 76 through 99 )
36X-RAY DIFFRACTION36chain 'Y' and (resid 100 through 127 )
37X-RAY DIFFRACTION37chain 'Y' and (resid 128 through 146 )
38X-RAY DIFFRACTION38chain 'Z' and (resid 31 through 62 )
39X-RAY DIFFRACTION39chain 'Z' and (resid 63 through 70 )
40X-RAY DIFFRACTION40chain 'Z' and (resid 71 through 82 )
41X-RAY DIFFRACTION41chain 'Z' and (resid 83 through 99 )
42X-RAY DIFFRACTION42chain 'Z' and (resid 100 through 118 )
43X-RAY DIFFRACTION43chain 'Z' and (resid 119 through 133 )
44X-RAY DIFFRACTION44chain 'Z' and (resid 134 through 143 )

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