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- PDB-9v11: The Fab fragment of Osemitamab (TST001), a therapeutic antibody t... -

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Basic information

Entry
Database: PDB / ID: 9v11
TitleThe Fab fragment of Osemitamab (TST001), a therapeutic antibody targeting claudin 18.2
Components
  • Fab of Osemitamab (TST001), Heavy chain
  • Fab of Osemitamab (TST001), Light chain
KeywordsANTITUMOR PROTEIN / CLDN18.2 / gastric cancer / antibody / crystal
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.728 Å
AuthorsWang, X. / Sun, Z. / Zhou, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Recognition of human claudin 18.2 by therapeutic antibodies
Authors: Wang, X. / Sun, Z. / Zhou, X.
History
DepositionMay 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab of Osemitamab (TST001), Heavy chain
L: Fab of Osemitamab (TST001), Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,37214
Polymers51,2192
Non-polymers1,15312
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-179 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.512, 106.144, 112.148
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: Antibody Fab of Osemitamab (TST001), Heavy chain


Mass: 27096.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab of Osemitamab (TST001), Light chain


Mass: 24122.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.5 M ammonium sulfate, 0.1 M HEPES pH 7.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98655 Å / Relative weight: 1
ReflectionResolution: 1.728→47.972 Å / Num. obs: 46681 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Rrim(I) all: 0.12 / Net I/σ(I): 12.1
Reflection shellResolution: 1.728→1.758 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.423 / Num. unique obs: 2286 / Rpim(I) all: 0.402 / Rrim(I) all: 1.48

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimless0.7.4data scaling
XDSBUILT 20230630data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.728→47.972 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 2254 4.84 %
Rwork0.1995 --
obs0.2008 46594 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.728→47.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 60 261 3609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063445
X-RAY DIFFRACTIONf_angle_d0.8514696
X-RAY DIFFRACTIONf_dihedral_angle_d14.4342035
X-RAY DIFFRACTIONf_chiral_restr0.057517
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.728-1.76540.44671490.36022678X-RAY DIFFRACTION100
1.7654-1.80640.46171440.34542727X-RAY DIFFRACTION100
1.8064-1.85160.33461490.30032684X-RAY DIFFRACTION100
1.8516-1.90170.36061370.27672764X-RAY DIFFRACTION100
1.9017-1.95760.28221180.2532746X-RAY DIFFRACTION100
1.9576-2.02080.26741310.23762742X-RAY DIFFRACTION100
2.0208-2.09310.28161320.20952741X-RAY DIFFRACTION100
2.0931-2.17690.23721270.20182778X-RAY DIFFRACTION100
2.1769-2.27590.23671430.20352751X-RAY DIFFRACTION100
2.2759-2.39590.241540.19772729X-RAY DIFFRACTION100
2.3959-2.5460.27831520.20482742X-RAY DIFFRACTION100
2.546-2.74260.24151640.19922778X-RAY DIFFRACTION100
2.7426-3.01850.22621230.19832815X-RAY DIFFRACTION100
3.0185-3.45520.17941150.17952820X-RAY DIFFRACTION100
3.4552-4.35280.17671560.15882843X-RAY DIFFRACTION100
4.3528-47.9720.1861600.17813002X-RAY DIFFRACTION100
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)
11.15441.09480.38235.6735-0.13814.16150.0418-0.023-0.0299-0.15570.0408-0.01760.2960.1651-0.04060.1222-0.0013-0.03290.25530.01460.2279-8.2962-14.95332.6898
20.0697-0.87490.16913.4738-0.53063.92220.0384-0.08630.02060.0445-0.06320.02510.14720.14780.00070.0881-0.0012-0.01920.27240.00110.2545-9.764-11.431830.9326
34.80310.85782.07662.99750.91752.6473-0.1905-0.0475-0.05490.0780.10230.1988-0.072-0.29890.08340.16990.0030.04430.23770.01290.1564-25.07093.059612.3473
43.73450.33855.79073.46980.80769.709-0.7605-0.71540.52350.49620.50480.1865-0.9376-0.86610.10170.3940.16520.07070.5274-0.00920.3272-30.77248.814215.9882
53.2543-0.44450.57131.3978-0.10232.38720.37560.3174-0.3684-1.0595-0.0331-0.08650.7820.4148-0.3580.91830.08190.04820.3007-0.02160.3661-5.1904-25.20717.8616
64.75631.6402-0.23174.1781-1.04861.92240.0448-0.5568-0.98140.2788-0.0703-0.42010.84210.39860.021.22150.32840.14880.45350.15690.5359-1.0545-36.400822.978
74.9417-2.0405-1.6522.02860.29147.8208-0.03350.0728-0.084-0.45180.09190.00510.7435-0.3294-0.09050.4535-0.0491-0.05920.2370.00720.2427-13.7697-22.08517.5647
81.527-0.6631.10242.5823-0.04542.69670.3281-0.332-0.3733-1.28330.06520.09561.0457-0.2117-0.24431.2561-0.0207-0.09380.2508-0.0370.3338-12.5789-32.744414.4414
94.44390.57061.05573.31662.72062.8745-0.0083-0.015-0.4634-0.78260.25930.30540.7758-0.1622-0.19730.6917-0.0669-0.05660.2160.03180.3059-13.77-23.173510.7477
100.7376-0.59830.41780.8491-0.78522.74790.0989-0.00960.0243-0.264-0.0474-0.08560.36780.0205-0.03690.1467-0.04890.03910.2424-0.00660.2719-15.4093-5.768.6698
110.76191.25530.89523.73543.53223.78660.0413-0.02680.02930.2125-0.0685-0.1044-0.036-0.0219-0.00230.2197-0.0015-0.00620.23920.01050.2572-16.46712.9518-1.5319
120.60511.16420.44675.6394-2.81146.62860.2464-0.0419-0.07450.5863-0.224-0.2383-0.01330.1503-0.01250.13930.05370.06350.239-0.02150.2423-15.5533-0.40930.9205
132.1704-0.3575-0.62497.28131.74087.92040.0636-0.0890.2631-0.01210.0691-0.4396-0.77290.0374-0.11780.2123-0.02890.04890.2421-0.01310.2757-16.4114-1.0589
143.3175-1.4999-1.539.62476.80725.03520.05490.09780.1566-0.876-0.05850.2826-0.6059-0.37140.15880.3120.03550.02590.2930.03260.2551-21.47138.2814-9
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 67 )
2X-RAY DIFFRACTION2chain 'H' and (resid 68 through 124 )
3X-RAY DIFFRACTION3chain 'H' and (resid 125 through 208 )
4X-RAY DIFFRACTION4chain 'H' and (resid 209 through 219 )
5X-RAY DIFFRACTION5chain 'L' and (resid 1 through 25 )
6X-RAY DIFFRACTION6chain 'L' and (resid 26 through 38 )
7X-RAY DIFFRACTION7chain 'L' and (resid 39 through 54 )
8X-RAY DIFFRACTION8chain 'L' and (resid 55 through 81 )
9X-RAY DIFFRACTION9chain 'L' and (resid 82 through 96 )
10X-RAY DIFFRACTION10chain 'L' and (resid 97 through 134 )
11X-RAY DIFFRACTION11chain 'L' and (resid 135 through 156 )
12X-RAY DIFFRACTION12chain 'L' and (resid 157 through 180 )
13X-RAY DIFFRACTION13chain 'L' and (resid 181 through 204 )
14X-RAY DIFFRACTION14chain 'L' and (resid 205 through 219 )

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