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- PDB-5x8m: PD-L1 in complex with durvalumab -

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Basic information

Entry
Database: PDB / ID: 5x8m
TitlePD-L1 in complex with durvalumab
Components
  • Programmed cell death 1 ligand 1
  • durvalumab heavy chain
  • durvalumab light chain
KeywordsIMMUNE SYSTEM / complex / antibody
Function / homology
Function and homology information


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / negative regulation of T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / response to cytokine / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / receptor ligand activity / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.661 Å
AuthorsHeo, Y.S. / Lee, H.T.
CitationJournal: Sci Rep / Year: 2017
Title: Molecular mechanism of PD-1/PD-L1 blockade via anti-PD-L1 antibodies atezolizumab and durvalumab
Authors: Lee, H.T. / Lee, J.Y. / Lim, H. / Lee, S.H. / Moon, Y.J. / Pyo, H.J. / Ryu, S.E. / Shin, W. / Heo, Y.S.
History
DepositionMar 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
B: durvalumab heavy chain
C: durvalumab light chain


Theoretical massNumber of molelcules
Total (without water)63,2303
Polymers63,2303
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-28 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.950, 97.395, 153.564
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: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 14224.239 Da / Num. of mol.: 1 / Fragment: UNP residues 18-134 / Mutation: Q47E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9NZQ7
#2: Antibody durvalumab heavy chain


Mass: 25404.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#3: Antibody durvalumab light chain


Mass: 23601.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 17827 / % possible obs: 99.4 % / Redundancy: 3.2 % / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.661→46.419 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.43
RfactorNum. reflection% reflection
Rfree0.219 913 5.12 %
Rwork0.1809 --
obs0.1829 17827 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.661→46.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4201 0 0 73 4274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084300
X-RAY DIFFRACTIONf_angle_d1.1055831
X-RAY DIFFRACTIONf_dihedral_angle_d15.2381554
X-RAY DIFFRACTIONf_chiral_restr0.042649
X-RAY DIFFRACTIONf_plane_restr0.007746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6607-2.8010.30131540.22262253X-RAY DIFFRACTION97
2.801-2.97650.29341220.21952375X-RAY DIFFRACTION100
2.9765-3.20620.26361350.20592394X-RAY DIFFRACTION100
3.2062-3.52880.20861120.1822420X-RAY DIFFRACTION100
3.5288-4.03910.22331250.17022446X-RAY DIFFRACTION100
4.0391-5.08790.18321330.14532438X-RAY DIFFRACTION100
5.0879-46.42640.19271320.19132588X-RAY DIFFRACTION100

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