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- PDB-8sjk: Pembrolizumab Caffeine crystal -

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Basic information

Entry
Database: PDB / ID: 8sjk
TitlePembrolizumab Caffeine crystal
Components
  • ANTIBODY HEAVY CHAIN
  • ANTIBODY LIGHT CHAIN
KeywordsIMMUNE SYSTEM / CANCER / ANTIBODY / SUBCLASSES / IGG4 / MELANOMA / NSCLC
Function / homologysucrose / CAFFEINE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLarpent, P. / Codan, L. / Bothe, J.R. / Stueber, D. / Reichert, P. / Fischmann, T. / Su, Y. / Pabit, S. / Gupta, S. / Iuzzolino, L. / Cote, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Mol Pharm. / Year: 2024
Title: Small-Angle X-ray Scattering as a Powerful Tool for Phase and Crystallinity Assessment of Monoclonal Antibody Crystallites in Support of Batch Crystallization.
Authors: Larpent, P. / Codan, L. / Bothe, J.R. / Iuzzolino, L. / Pabit, S. / Gupta, S. / Fischmann, T. / Su, Y. / Reichert, P. / Stueber, D. / Cote, A.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 21, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIBODY LIGHT CHAIN
B: ANTIBODY HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1306
Polymers72,9342
Non-polymers2,1964
Water5,405300
1
A: ANTIBODY LIGHT CHAIN
B: ANTIBODY HEAVY CHAIN
hetero molecules

hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1306
Polymers72,9342
Non-polymers2,1964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6890 Å2
ΔGint4 kcal/mol
Surface area32320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.800, 113.900, 175.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody ANTIBODY LIGHT CHAIN


Mass: 23768.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)
#2: Antibody ANTIBODY HEAVY CHAIN


Mass: 49166.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)

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Sugars , 2 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1317.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-1/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 301 molecules

#5: Chemical ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 6.8
Details: 0.1M Na HEPES pH 6.8 0.2%W/V Caffeine, 12% PEG3350, 3% DEXTRAN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→40.81 Å / Num. obs: 33863 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.147 / Net I/σ(I): 14.1
Reflection shellResolution: 2.22→2.453 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2412 / CC1/2: 0.542 / Rpim(I) all: 0.048 / Rrim(I) all: 0.147 / % possible all: 15.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
MOLREP11.4.06phasing
Aimless8.5.28data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→40.81 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.323 / SU Rfree Blow DPI: 0.234
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1635 4.83 %RANDOM
Rwork0.186 ---
obs0.189 33850 76.3 %-
Displacement parametersBiso mean: 37.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.0323 Å20 Å20 Å2
2--1.6237 Å20 Å2
3----1.6561 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.22→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 0 149 300 5415
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110067HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1318117HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2178SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1446HARMONIC5
X-RAY DIFFRACTIONt_it10067HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion15.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion715SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10192SEMIHARMONIC4
LS refinement shellResolution: 2.22→2.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.251 -4.82 %
Rwork0.225 --
all0.226 83 -
obs--2.2 %
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)
10.7126-0.00090.1490.71410.35012.67890.0393-0.07230.10250.01920.0360.04510.0165-0.0453-0.0753-0.12350.0078-0.0199-0.0897-0.0024-0.0764-19.0468-20.059910.202
20.16870.0392-0.22760.7975-0.07920.4877-0.0340.00310.01030.0487-0.03510.03960.11320.00020.0691-0.07910.0052-0.0205-0.041-0.0188-0.1426-13.9824-41.363616.5759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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