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- PDB-13fl: Structure of FabS1CE2_P2a in complex with the N-terminal domain o... -

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Basic information

Entry
Database: PDB / ID: 13fl
TitleStructure of FabS1CE2_P2a in complex with the N-terminal domain of PD-L1
Components
  • (FabS1CE2_P2a ...) x 2
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / high-affinity binding / immune suppression / tumour growth suppressor / cell signalling / PD-L1
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 / TRIF-dependent toll-like receptor signaling pathway / negative regulation of T cell mediated immune response to tumor cell / 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 T cell activation / negative regulation of activated T cell proliferation ...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 / TRIF-dependent toll-like receptor signaling pathway / negative regulation of T cell mediated immune response to tumor cell / 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 T cell activation / 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 receptor signaling pathway / 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
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMallette, E. / Singer, A.U. / Blazer, L.L. / Adams, J.J. / Suits, M.D.L. / Sidhu, S.S.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-93725 Canada
Canadian Institutes of Health Research (CIHR)MOP-136944 Canada
CitationJournal: To Be Published
Title: A Strategy for Modular Assembly of Tetravalent Multispecific Antibodies
Authors: Mallette, E. / Blazer, L.L. / Hokanson, C.A. / Chen, C. / Perez, J.G. / Pavkenco, A. / Ploder, L. / Singer, A.U. / Suits, M.D.L. / Adams, J.J. / Sidhu, S.S.
History
DepositionMay 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FabS1CE2_P2a heavy chain
B: FabS1CE2_P2a light chain (Trastuzumab Fab Light Chain)
C: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5038
Polymers62,1143
Non-polymers3905
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.358, 239.679, 104.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-428-

HOH

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody FabS1CE2_P2a heavy chain


Mass: 24385.398 Da / Num. of mol.: 1 / Mutation: K123Q and E154G
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND SELECTED BY PHAGE DISPLAY.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSDCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody FabS1CE2_P2a light chain (Trastuzumab Fab Light Chain)


Mass: 23225.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND SELECTED BY PHAGE DISPLAY.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSDCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules C

#3: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14502.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 19-132 / Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Plasmid: PSDCSTA
Details (production host): C-terminal 6-His tag with thrombin cleavage site N-terminal to 6His
Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q9NZQ7
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 98 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 5.5M Sodium Formate, 0.1M Sodium Acetate trihydrate pH4.6, final pH 5.8, cryoprotected in paratone oil
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2026 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.97→40.412 Å / Num. obs: 27786 / % possible obs: 90.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.122 / Rrim(I) all: 0.266 / Net I/σ(I): 8.3
Reflection shellResolution: 1.97→2.282 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.879 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1389 / CC1/2: 0.213 / Rpim(I) all: 0.922 / Rrim(I) all: 2.095 / % possible all: 74.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→40.41 Å / SU ML: 0.2372 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2386 1324 4.94 %
Rwork0.1987 25503 -
obs0.2007 26827 64.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.32 Å2
Refinement stepCycle: LAST / Resolution: 2.22→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 21 94 4297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934316
X-RAY DIFFRACTIONf_angle_d1.06435872
X-RAY DIFFRACTIONf_chiral_restr0.0589666
X-RAY DIFFRACTIONf_plane_restr0.0102750
X-RAY DIFFRACTIONf_dihedral_angle_d17.20021545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.310.341210.3627X-RAY DIFFRACTION14.31
2.31-2.410.4137430.3296845X-RAY DIFFRACTION19.49
2.41-2.540.3706620.31491286X-RAY DIFFRACTION29.47
2.54-2.70.3263990.30631906X-RAY DIFFRACTION44.02
2.7-2.910.35621680.28983175X-RAY DIFFRACTION72.77
2.91-3.20.28952100.23954237X-RAY DIFFRACTION96.8
3.2-3.660.23522360.18984400X-RAY DIFFRACTION99.98
3.66-4.620.18282120.14444447X-RAY DIFFRACTION100
4.62-40.410.19652730.16484580X-RAY DIFFRACTION99.96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29847405715-1.15962420815-0.4872895358434.74292936216-0.4348292308570.5323272925290.3618684067650.481366520336-0.187320864369-0.333098197054-0.118480165204-0.5413711731740.06509054051420.117134705247-0.2081824894970.2772149839990.02015672026220.1267397352170.321402041125-0.1658206471450.433719621479-6.22867734143-28.86427972220.533334618557
20.6338935658920.0509221534069-0.093737154980.2823389633040.1059953942531.59686744917-0.1844974335540.183902364635-0.080095387884-0.343705586630.116631111815-0.364568789667-0.09643049661730.07463743849830.02493828643240.250906001535-0.01491686909470.07116883908570.189887524997-0.04879885331390.195796202613-8.77220061408-18.7359334341.74679042378
32.2777717967-0.2526833378570.4084216584463.034040245090.9744304339342.32802094523-0.05408826353120.106247736982-0.201633385237-0.01720986161610.0462642503571-0.538539278999-0.04954743832180.349942587411-0.006170280870170.168281442807-0.0101033270533-0.003245775797260.156001425079-0.06144447279840.232810835939-6.71066317082-22.03549171838.70834325483
42.49642282283-0.892117463874-1.19120274556.136600818932.691299166053.743301429890.2322944187630.402476830491-0.011560232728-0.514306823814-0.2793193802440.00482520853883-0.307156043821-0.3585931608440.04896918866320.1531854469530.008045404223780.1662662581620.23844370584-0.1333444207370.0082084308154-19.566253363-15.69158595393.73526535437
51.171946085360.3552746827360.01668505472922.95038201691-0.3496271220620.2689481232380.0868663951294-0.0509216837526-0.1923384394150.3757734755070.00384281612685-0.09132588335090.0903985207095-0.0855990266616-0.1050172110960.2297225946190.0255521761147-0.05268339053450.27998660142-0.1082838251640.390130306681-14.5621539226-54.12867794911.79031654803
63.110244958510.20190425086-0.670733083572.11720826295-0.4325346767341.13084186262-0.279615822107-0.07337591315790.470513019765-0.3495573686080.1412780831690.08273519459950.0877465305616-0.04032409073410.1147188241910.3390094713250.0363812166947-0.1377702816930.229912363127-0.07928583649310.480721127966-17.3746761494-54.6446292271-3.84023741862
70.9891902684640.298837407586-0.04083438263622.432935443530.3036350521120.3693265102030.07138666071530.0320032396521-0.3941483933220.041229243655-0.1719373140980.4796661817980.161047479322-0.2940517068220.1234290635930.210170889785-0.05540305773730.08110933548990.268749108856-0.1133764304520.333745740895-31.2356625353-24.62428668029.67682364884
83.064854695011.12946152413-0.5425319042642.498188541960.1257996057452.695340907780.120474174621-0.238487323533-0.3499712181950.1572980488140.01372205944150.2779061937640.420804473620.264011985859-0.1193180425010.3608017601660.0539974412474-0.1005133318220.266587893795-0.09030800977560.451323653748-26.6794397852-60.41509337288.72317682205
93.849220055190.5464731083171.612053214961.807779306010.6498986681892.8589111673-0.139652918159-0.02479951316650.3603410279310.1761990303290.01168746236360.392515237376-0.275296005196-0.155836108480.1606570078590.185507442865-0.01331128452280.02024934326810.195981342644-0.07062709089870.183436096551-17.0200269223-2.7053812865219.2461232436
102.879623170940.1493815767271.890355150174.095183772346.764893279382.00130723729-0.090148568624-0.912131655706-0.1921028049341.1833819799-0.0352279694461-0.04851494438140.575847787569-0.3803829460340.1291855900080.489842103991-0.05844744143510.03770050576640.42338852296-0.08763972307180.173519275027-9.37112414603-0.39017039037837.5526794683
111.484643555210.6102570508660.4233180377361.06818530118-0.01932033014572.59734728754-0.168033015598-0.01622116377320.227271927738-0.00880961782537-0.09016550942940.200578701678-0.416991412102-0.2860907506250.1787760234810.2949380906930.0340580730985-0.1527008537330.219260775898-0.09585346277060.170268474095-9.510483088088.0381936173521.8809510144
122.142707700660.2746072102840.4662071881082.206585901070.7784285827213.13859478786-0.01293005849410.3553674609140.197642737643-0.345275445635-0.122622696480.208914717053-0.2827762741330.1431496785670.140265324520.187256452863-0.015491271136-0.01984553891840.168546506816-0.02372514600250.153925936326-11.7019502124-0.66099111933615.8634911546
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 17 )AA1 - 171 - 17
22chain 'A' and (resid 18 through 39 )AA18 - 3918 - 39
33chain 'A' and (resid 40 through 98 )AA40 - 9840 - 98
44chain 'A' and (resid 99 through 113 )AA99 - 11399 - 113
55chain 'A' and (resid 114 through 140 )AA114 - 140114 - 140
66chain 'A' and (resid 141 through 220 )AA141 - 220141 - 220
77chain 'B' and (resid 1 through 113 )BC1 - 1131 - 113
88chain 'B' and (resid 114 through 210 )BC114 - 210114 - 210
99chain 'C' and (resid 19 through 41 )C000D19 - 411 - 23
1010chain 'C' and (resid 42 through 49 )C000D42 - 4924 - 31
1111chain 'C' and (resid 50 through 101 )C000D50 - 10132 - 83
1212chain 'C' and (resid 102 through 133 )C000D102 - 13384 - 115

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