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- PDB-6k0y: Study of the interactions of a novel monoclonal antibody, mAb059c... -

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Basic information

Entry
Database: PDB / ID: 6k0y
TitleStudy of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor
Components
  • Antibody Heavy ChainImmunoglobulin heavy chain
  • Antibody Light ChainImmunoglobulin light chain
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 Complex / Immune Checkpoint / Inhibitor
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS / adaptive immune response / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, J.X. / Wang, G.Q.
CitationJournal: Sci Rep / Year: 2019
Title: Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor.
Authors: Liu, J. / Wang, G. / Liu, L. / Wu, R. / Wu, Y. / Fang, C. / Zhou, X. / Jiao, J. / Gu, Y. / Zhou, H. / Xie, Z. / Sun, Z. / Chen, D. / Dai, K. / Wang, D. / Tang, W. / Yang, T.T.C.
History
DepositionMay 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Antibody Heavy Chain
B: Antibody Light Chain
C: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9267
Polymers62,6783
Non-polymers2484
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Crystals are washed two times and then dissolved in well solution; running SDS-PAGE indicates two components (PD-1 and Fab).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-31 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.952, 102.590, 137.723
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: Antibody Antibody Heavy Chain / Immunoglobulin heavy chain


Mass: 23275.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Antibody Light Chain / Immunoglobulin light chain


Mass: 23447.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Programmed cell death protein 1 / / hPD-1


Mass: 15954.713 Da / Num. of mol.: 1 / 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)
Variant (production host): BL21 / References: UniProt: Q15116
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.35 Å3/Da / Density % sol: 47.78 % / Description: single long shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2M NaCl , 0.1M Tris pH 8, 14% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 6, 2019 / Details: Q315r
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→41.9 Å / Num. obs: 62244 / % possible obs: 98.2 % / Redundancy: 10 % / CC1/2: 0.994 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.053 / Net I/σ(I): 30.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2532 / CC1/2: 0.796 / Rrim(I) all: 0.421 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGS

5ggs


Resolution: 1.7→41.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.339 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21447 3095 5 %RANDOM
Rwork0.17106 ---
obs0.17317 59148 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.745 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0 Å2
2--1.14 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.7→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 16 492 4684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134287
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173846
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.655830
X-RAY DIFFRACTIONr_angle_other_deg1.1941.578964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3795544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13722.111199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04115681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4941525
X-RAY DIFFRACTIONr_chiral_restr0.0460.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0461.6542185
X-RAY DIFFRACTIONr_mcbond_other1.0451.6532184
X-RAY DIFFRACTIONr_mcangle_it1.5362.4792726
X-RAY DIFFRACTIONr_mcangle_other1.5362.482727
X-RAY DIFFRACTIONr_scbond_it1.0981.8052102
X-RAY DIFFRACTIONr_scbond_other1.0971.8062103
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4552.6163105
X-RAY DIFFRACTIONr_long_range_B_refined2.79620.0144585
X-RAY DIFFRACTIONr_long_range_B_other2.56819.6054485
X-RAY DIFFRACTIONr_rigid_bond_restr0.86938133
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 199 -
Rwork0.191 3633 -
obs--82.27 %

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