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- PDB-9mi7: Crystal Structure of ADI-64597 ((human Fab, with substituted IgG1... -

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Basic information

Entry
Database: PDB / ID: 9mi7
TitleCrystal Structure of ADI-64597 ((human Fab, with substituted IgG1-CH1 (HC-L128R and K147R) and substituted kappa constant domain (LC-Q124E, V133Q, and T178R))
Components
  • ADI-64597 Fab heavy chain
  • ADI-64597 Fab light chain
KeywordsIMMUNE SYSTEM / antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsBattles, M.B. / Welin, M. / Laursen, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Mabs / Year: 2025
Title: Design of orthogonal constant domain interfaces to aid proper heavy/light chain pairing of bispecific antibodies.
Authors: Barlow, K.A. / Battles, M.B. / Brown, M.E. / Canfield, K. / Lu, X. / Lynaugh, H. / Morrill, M. / Rappazzo, C.G. / Reyes, S.P. / Sandberg, C. / Sharkey, B. / Strong, C. / Zhao, J. / Sivasubramanian, A.
History
DepositionDec 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: ADI-64597 Fab heavy chain
L: ADI-64597 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3177
Polymers47,0262
Non-polymers2915
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-40 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.983, 65.983, 97.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody ADI-64597 Fab heavy chain


Mass: 23588.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: substituted IgG1-CH1 (HC-L128R and K147R) / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody ADI-64597 Fab light chain


Mass: 23437.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: kappa constant domain (LC-Q124E, V133Q, and T178R))
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ADI-64597 (human Fab) was received at concentration 16.5 mg/mL in a buffer containing 2 mM Tris-HCl pH 8.0 and 150 mM NaCl. PACT, BCS and JCSG+ screens (all from Molecular Dimensions Ltd.) ...Details: ADI-64597 (human Fab) was received at concentration 16.5 mg/mL in a buffer containing 2 mM Tris-HCl pH 8.0 and 150 mM NaCl. PACT, BCS and JCSG+ screens (all from Molecular Dimensions Ltd.) were set up using a mosquito crystallisation robot (STP Labtech). Sitting drops of 150 nL protein and 150 nL reservoir solution were left to equilibrate against a 40 uL reservoir at 20 C. After a few days, needle-like crystals were obtained in several conditions. The crystal used for data collection was obtained in the BCS screen, condition B10 (0.1 M HEPES pH 7.5, 22% w/v PEG Smear Broad)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.22→49.29 Å / Num. obs: 23297 / % possible obs: 99.7 % / Redundancy: 10.4 % / CC1/2: 0.998 / Net I/σ(I): 11.6
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2261 / CC1/2: 0.542 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→49.29 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2302 --
Rwork0.18 --
obs-23297 97.6 %
Refinement stepCycle: LAST / Resolution: 2.22→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 15 51 3306

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