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- PDB-6umv: Human apo PD-1 double mutant -

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Basic information

Entry
Database: PDB / ID: 6umv
TitleHuman apo PD-1 double mutant
ComponentsProgrammed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 / immune checkpoint
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 / MOLECULAR REPLACEMENT / Resolution: 1.424 Å
AuthorsTang, S. / Kim, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.
Authors: Tang, S. / Kim, P.S.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6413
Polymers14,5701
Non-polymers712
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area6840 Å2
Unit cell
Length a, b, c (Å)46.199, 46.199, 89.407
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 14570.252 Da / Num. of mol.: 1 / Fragment: UNP residues 33-150 / Mutation: T76P, A132V
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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.89 Å3/Da / Density % sol: 34.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium chloride, 100 mM Tris-HCl, pH 8.0, 36% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 21337 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 21.92 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.034 / Rrim(I) all: 0.1 / Χ2: 3.27 / Net I/σ(I): 11.2 / Num. measured all: 162777
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.42-1.443.60.78310340.7790.3820.8730.98597.5
1.44-1.4740.52310240.8110.2810.5970.59398.7
1.47-1.54.20.45610440.8630.2410.5190.64599
1.5-1.535.20.44610400.9120.2080.4940.77899.7
1.53-1.5660.41710630.9080.1780.4540.81699.9
1.56-1.66.50.43810440.9280.1750.4730.86799.9
1.6-1.647.20.51110560.9310.1950.5480.895100
1.64-1.687.80.43210370.9550.160.4611.10699.8
1.68-1.738.30.39910560.970.1450.4251.19699.9
1.73-1.797.80.31210510.9650.1180.3351.62199.9
1.79-1.859.30.25810740.9820.0880.2732.007100
1.85-1.939.40.22110590.9810.0750.2342.75699.9
1.93-2.019.40.17210650.9880.0580.1823.183100
2.01-2.129.30.17610510.990.060.1873.721100
2.12-2.258.50.12710760.9890.0460.1364.12899.9
2.25-2.439.70.10810840.9940.0370.1153.705100
2.43-2.679.60.09810850.9950.0330.1044.117100
2.67-3.069.30.08810950.9960.0310.0945.359100
3.06-3.858.90.07911120.9960.0280.0847.84699.8
3.85-508.10.06911870.9950.0270.0749.66899.7

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RRQ

3rrq


Resolution: 1.424→36.52 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.78
RfactorNum. reflection% reflection
Rfree0.1894 2007 9.42 %
Rwork0.1605 --
obs0.1633 21296 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.36 Å2 / Biso mean: 30.5379 Å2 / Biso min: 15.05 Å2
Refinement stepCycle: final / Resolution: 1.424→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 2 84 961
Biso mean--39.16 39.43 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161104
X-RAY DIFFRACTIONf_angle_d1.6361543
X-RAY DIFFRACTIONf_chiral_restr0.111173
X-RAY DIFFRACTIONf_plane_restr0.019214
X-RAY DIFFRACTIONf_dihedral_angle_d10.556444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.424-1.45960.26281410.1991133598
1.4596-1.49910.23351370.1727135599
1.4991-1.54320.21651410.14851348100
1.5432-1.5930.18911410.12361367100
1.593-1.64990.19191410.14351358100
1.6499-1.7160.21931430.13581350100
1.716-1.79410.21671390.1431342100
1.7941-1.88860.18021370.14271376100
1.8886-2.0070.18831480.13551393100
2.007-2.16190.19161390.14331366100
2.1619-2.37940.20221490.15251383100
2.3794-2.72360.21681480.17481413100
2.7236-3.43110.17371440.16931412100
3.4311-36.520.17531590.16971491100

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