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- PDB-7vux: Complex structure of PD1 and 609A-Fab -

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Basic information

Entry
Database: PDB / ID: 7vux
TitleComplex structure of PD1 and 609A-Fab
Components
  • Heavy chain of Fab fragment
  • Light chain of Fab fragment
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / PD1 Fab complex
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / adaptive immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / THREONINE / Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsHuang, H. / Zhu, Z. / Zhao, J. / Jiang, L. / Yang, H. / Deng, L. / Meng, X. / Ding, J. / Yang, S. / Zhao, L. ...Huang, H. / Zhu, Z. / Zhao, J. / Jiang, L. / Yang, H. / Deng, L. / Meng, X. / Ding, J. / Yang, S. / Zhao, L. / Xu, W. / Wang, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2022
Title: A strategy for the efficient construction of anti-PD1-based bispecific antibodies with desired IgG-like properties.
Authors: Zhao, J. / Jiang, L. / Yang, H. / Deng, L. / Meng, X. / Ding, J. / Yang, S. / Zhao, L. / Xu, W. / Wang, X. / Zhu, Z. / Huang, H.
History
DepositionNov 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death protein 1
H: Heavy chain of Fab fragment
L: Light chain of Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,17822
Polymers61,7903
Non-polymers1,38819
Water14,214789
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-45 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.290, 68.410, 77.310
Angle α, β, γ (deg.)90.000, 99.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Programmed cell death protein 1 / Protein PD-1 / hPD-1


Mass: 15313.052 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain of Fab fragment


Mass: 23037.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: mammal environmental sample (environmental samples)
#3: Antibody Light chain of Fab fragment


Mass: 23439.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: mammal environmental sample (environmental samples)

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Non-polymers , 7 types, 808 molecules

#4: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium formate, pH 6.6, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.64→48.91 Å / Num. obs: 70749 / % possible obs: 99.7 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.045 / Rrim(I) all: 0.067 / Net I/σ(I): 12.5
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3505 / CC1/2: 0.842 / Rpim(I) all: 0.413 / Rrim(I) all: 0.618 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WT9

5wt9


Resolution: 1.64→48.91 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.959 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 3529 5 %RANDOM
Rwork0.1596 ---
obs0.1617 67222 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.66 Å2 / Biso mean: 20.227 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0.43 Å2
2---0.07 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.64→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 94 789 5110
Biso mean--36.44 34.03 -
Num. residues----551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134751
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174238
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.6476492
X-RAY DIFFRACTIONr_angle_other_deg1.4721.5729907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.7135.402647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29221.435216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23515735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8311531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026281
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021028
LS refinement shellResolution: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 263 -
Rwork0.407 4947 -
all-5210 -
obs--99.87 %

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