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- PDB-8znl: PD-L1 de novo designed binder with picomolar binding affinity -

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Basic information

Entry
Database: PDB / ID: 8znl
TitlePD-L1 de novo designed binder with picomolar binding affinity
Components
  • PD-L1 de novo binder
  • Programmed cell death 1 ligand 1
KeywordsDE NOVO PROTEIN / PD-L1 / picomolar binding affinity
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 / response to cytokine / positive regulation of T cell proliferation / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
BROMIDE ION / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsZhao, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)8227130865 China
CitationJournal: To Be Published
Title: PD-L1 de novo binder
Authors: Zhao, L.
History
DepositionMay 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PD-L1 de novo binder
B: Programmed cell death 1 ligand 1
C: PD-L1 de novo binder
D: Programmed cell death 1 ligand 1
E: PD-L1 de novo binder
F: Programmed cell death 1 ligand 1
G: PD-L1 de novo binder
H: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,75612
Polymers80,4378
Non-polymers3204
Water7,116395
1
A: PD-L1 de novo binder
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1893
Polymers20,1092
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-6 kcal/mol
Surface area9000 Å2
MethodPISA
2
C: PD-L1 de novo binder
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1893
Polymers20,1092
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-5 kcal/mol
Surface area9030 Å2
MethodPISA
3
E: PD-L1 de novo binder
F: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1893
Polymers20,1092
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-4 kcal/mol
Surface area9030 Å2
MethodPISA
4
G: PD-L1 de novo binder
H: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1893
Polymers20,1092
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-6 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.872, 58.956, 63.299
Angle α, β, γ (deg.)92.520, 90.020, 94.800
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
PD-L1 de novo binder


Mass: 6988.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein
Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 13121.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: buffer containing 0.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide; 0.1 M (Imidazole/MES) pH6.5, 12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.77→30.46 Å / Num. obs: 60509 / % possible obs: 96.04 % / Redundancy: 2.7 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.97 / CC star: 0.992 / Rmerge(I) obs: 0.1528 / Rpim(I) all: 0.1096 / Rrim(I) all: 0.1891 / Net I/σ(I): 4.26
Reflection shellResolution: 1.77→1.833 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 6050 / CC1/2: 0.673 / CC star: 0.897 / Rpim(I) all: 0.3927 / Rrim(I) all: 0.6735 / % possible all: 95.56

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→30.46 Å / SU ML: 0.2822 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.6008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 2960 4.89 %
Rwork0.2009 57544 -
obs0.2045 60504 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.57 Å2
Refinement stepCycle: LAST / Resolution: 1.77→30.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5648 0 4 395 6047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00635738
X-RAY DIFFRACTIONf_angle_d0.83177717
X-RAY DIFFRACTIONf_chiral_restr0.0529861
X-RAY DIFFRACTIONf_plane_restr0.0065995
X-RAY DIFFRACTIONf_dihedral_angle_d16.05232273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.38171320.2782805X-RAY DIFFRACTION95.45
1.8-1.830.35581390.25342682X-RAY DIFFRACTION95.59
1.83-1.860.3541390.23392747X-RAY DIFFRACTION95.5
1.86-1.90.34771530.22182698X-RAY DIFFRACTION95.9
1.9-1.940.27461440.20312718X-RAY DIFFRACTION95.3
1.94-1.980.28011410.19972727X-RAY DIFFRACTION95.82
1.98-2.030.30971350.19942770X-RAY DIFFRACTION95.65
2.03-2.080.28171430.19452681X-RAY DIFFRACTION96.28
2.08-2.130.27821260.19242763X-RAY DIFFRACTION95.95
2.13-2.20.27131420.19562743X-RAY DIFFRACTION96.13
2.2-2.270.3121220.20262778X-RAY DIFFRACTION95.93
2.27-2.350.26431340.1942754X-RAY DIFFRACTION95.85
2.35-2.440.28121250.19792747X-RAY DIFFRACTION96.21
2.44-2.550.25661370.19622730X-RAY DIFFRACTION96.37
2.55-2.690.28941330.20182765X-RAY DIFFRACTION96.5
2.69-2.860.27921640.20582725X-RAY DIFFRACTION96.33
2.86-3.080.26061840.20512696X-RAY DIFFRACTION96.13
3.08-3.380.25741480.20162734X-RAY DIFFRACTION96.13
3.38-3.870.27071270.18952757X-RAY DIFFRACTION96.36
3.87-4.880.25121340.18042773X-RAY DIFFRACTION96.51
4.88-30.460.24181580.2082751X-RAY DIFFRACTION97.42

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