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- PDB-5dk3: Crystal Structure of Pembrolizumab, a full length IgG4 antibody -

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Basic information

Entry
Database: PDB / ID: 5dk3
TitleCrystal Structure of Pembrolizumab, a full length IgG4 antibody
Components
  • Heavy Chain
  • Light Chain
KeywordsIMMUNE SYSTEM / Cancer / Antibody / subclasses / IgG4 / melanoma
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / sucrose
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsScapin, G. / Prosise, W. / Reichert, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of full-length human anti-PD1 therapeutic IgG4 antibody pembrolizumab.
Authors: Scapin, G. / Yang, X. / Prosise, W.W. / McCoy, M. / Reichert, P. / Johnston, J.M. / Kashi, R.S. / Strickland, C.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_radiation_wavelength / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light Chain
B: Heavy Chain
F: Light Chain
G: Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,95414
Polymers145,8694
Non-polymers4,08510
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19280 Å2
ΔGint-102 kcal/mol
Surface area59230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.830, 110.830, 264.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules AFBG

#1: Antibody Light Chain


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


Mass: 49166.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)

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Sugars , 3 types, 5 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
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, 486 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 3.22 Å3/Da / Density % sol: 61.75 % / Description: Rods
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.8-2.2 M NH4H2PO4, 100 mM TRIS / PH range: 8.0 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→110.83 Å / Num. obs: 654220 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 53.08 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.5
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
2.28-2.557.50.7233184254244670.8570.282
5.09-110.836.80.03246.75629882760.9990.013

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→33.38 Å / Cor.coef. Fo:Fc: 0.9421 / Cor.coef. Fo:Fc free: 0.9225 / SU R Cruickshank DPI: 0.627 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.207 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 4386 5.06 %RANDOM
Rwork0.1843 ---
obs0.1863 86694 99.99 %-
Displacement parametersBiso mean: 64.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.259 Å20 Å20 Å2
2--6.9585 Å20 Å2
3----7.2175 Å2
Refine analyzeLuzzati coordinate error obs: 0.308 Å
Refinement stepCycle: LAST / Resolution: 2.28→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19507 0 268 481 20256
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0120259HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1836518HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4320SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes221HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2940HARMONIC5
X-RAY DIFFRACTIONt_it20259HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion15.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1455SEMIHARMONIC5
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_contact21020SEMIHARMONIC4
LS refinement shellResolution: 2.28→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2375 300 4.8 %
Rwork0.2055 5945 -
all0.2071 6245 -
obs--99.99 %
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)
10.93920.3592-0.24951.2899-0.62650.78650.0189-0.0025-0.07450.1406-0.0772-0.04-0.0440.10070.0583-0.07950.01330.0682-0.1176-0.0563-0.038910.9073-19.7359-68.1115
20.2033-0.01330.04561.062-0.53120.2826-0.0173-0.0802-0.00180.2327-0.0236-0.1109-0.120.03540.0409-0.05-0.00760.0715-0.0913-0.0395-0.048711.8349-28.8997-54.1121
30.31931.1402-1.89650.37111.3190.19790.01370.00460.0085-0.07110.01580.014-0.0146-0.0453-0.0294-0.0633-0.00060.30220.03230.0591-0.02014.501-48.5158-28.3024
42.8746-2.2086-0.12733.34841.1434.6285-0.3306-0.7365-0.22510.46490.6004-0.14860.85380.2923-0.2698-0.19250.1108-0.084-0.07180.0896-0.38327.2615-2.39145.9137
50.32440.3638-1.06681.1945-0.45280.3098-0.00320.0258-0.0012-0.023-0.00640.01680.0315-0.02460.00960.0389-0.14150.1461-0.17890.04730.097227.4109-30.0513-38.4026
60.0950.01820.10792.36991.2830.594-0.0113-0.1770.0450.12560.0091-0.0590.0123-0.00680.0022-0.0723-0.01450.03670.02150.0249-0.14292.7046-26.5963-16.4152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|218 }A1 - 218
2X-RAY DIFFRACTION2{ B|1 - B|444 }B1 - 444
3X-RAY DIFFRACTION3{ G|501 - G|507 }G501 - 507
4X-RAY DIFFRACTION4{ F|1 - F|218 }F1 - 218
5X-RAY DIFFRACTION5{ B|505 - B|511 }B505 - 511
6X-RAY DIFFRACTION6{ G|1 - G|444 }G1 - 444

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