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- PDB-9fxt: L2A5 Fab in complex with STn-Ser -

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Basic information

Entry
Database: PDB / ID: 9fxt
TitleL2A5 Fab in complex with STn-Ser
Components
  • Anti kappa Variable Heavy Chain
  • L2A5 Fab Heavy Chain
  • L2A5 Fab Light Chain
KeywordsSUGAR BINDING PROTEIN / Antibody / Fab
Function / homology: / DI(HYDROXYETHYL)ETHER / SERINE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLaugieri, M.E. / Ereno Orbea, J. / Jimenez Barbero, J. / Oyenarte, I.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI) Spain
European Commission101079417European Union
CitationJournal: Jacs Au / Year: 2025
Title: Decoding the Molecular Basis of the Specificity of an Anti-sTn Antibody.
Authors: Soares, C.O. / Laugieri, M.E. / Grosso, A.S. / Natale, M. / Coelho, H. / Behren, S. / Yu, J. / Cai, H. / Franconetti, A. / Oyenarte, I. / Magnasco, M. / Gimeno, A. / Ramos, N. / Chai, W. / ...Authors: Soares, C.O. / Laugieri, M.E. / Grosso, A.S. / Natale, M. / Coelho, H. / Behren, S. / Yu, J. / Cai, H. / Franconetti, A. / Oyenarte, I. / Magnasco, M. / Gimeno, A. / Ramos, N. / Chai, W. / Corzana, F. / Westerlind, U. / Jimenez-Barbero, J. / Palma, A.S. / Videira, P.A. / Ereno-Orbea, J. / Marcelo, F.
History
DepositionJul 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: L2A5 Fab Heavy Chain
I: L2A5 Fab Heavy Chain
K: Anti kappa Variable Heavy Chain
L: L2A5 Fab Light Chain
M: L2A5 Fab Light Chain
V: Anti kappa Variable Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,58620
Polymers117,4026
Non-polymers2,18414
Water3,909217
1
H: L2A5 Fab Heavy Chain
K: Anti kappa Variable Heavy Chain
M: L2A5 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6098
Polymers58,7013
Non-polymers9085
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: L2A5 Fab Heavy Chain
L: L2A5 Fab Light Chain
V: Anti kappa Variable Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,97712
Polymers58,7013
Non-polymers1,2769
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.355, 125.277, 190.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 3 types, 6 molecules HIKVLM

#1: Antibody L2A5 Fab Heavy Chain


Mass: 23231.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Anti kappa Variable Heavy Chain


Mass: 12155.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody L2A5 Fab Light Chain


Mass: 23313.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 1 types, 2 molecules

#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 512.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sialyl-Tn (sTn) antigen is a truncated O-glycan containing a sialic acid alpha-2,6 linked to N-acetylgalactosamine (GalNAc) alpha-O-serine or to N-acetylgalactosamine (GalNAc) alpha-O-threonine.
References: BIRD: PRD_002573
DescriptorTypeProgram
DNeup5Aca2-6DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 229 molecules

#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking, Oligosaccharide / Class: Antigen / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
Details: Sialyl-Tn (sTn) antigen is a truncated O-glycan containing a sialic acid alpha-2,6 linked to N-acetylgalactosamine (GalNAc) alpha-O-serine or to N-acetylgalactosamine (GalNAc) alpha-O-threonine.
References: BIRD: PRD_002573
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsActivation of an aberrant glycosylation pathway in cancer cells can lead to expression of the onco- ...Activation of an aberrant glycosylation pathway in cancer cells can lead to expression of the onco-foetal sialyl-Tn (sTn) antigen.
Has ligand of interestY
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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 22% PEG 3350, 0.1M NH4Cl pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.67019 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.67019 Å / Relative weight: 1
ReflectionResolution: 2.3→47.69 Å / Num. obs: 52514 / % possible obs: 99.9 % / Redundancy: 23.27 % / CC1/2: 0.998 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.17 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Num. unique obsCC1/2Rrim(I) allDiffraction-IDRmerge(I) obs
2.3-2.4459420.31.31
2.44-2.6169830.470.961
2.61-2.8167230.730.571
2.81-3.0861900.90.31
3.08-3.4455430.970.161
3.44-3.9748310.980.0910.08
3.97-4.8641080.9940.061
4.86-6.8331370.9930.0621

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5109: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.69 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3121 2636 5.03 %
Rwork0.261 --
obs0.2635 52436 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7749 0 144 217 8110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.652
X-RAY DIFFRACTIONf_dihedral_angle_d13.6622773
X-RAY DIFFRACTIONf_chiral_restr0.0431267
X-RAY DIFFRACTIONf_plane_restr0.0041393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.38381350.32942447X-RAY DIFFRACTION96
2.34-2.390.35821270.31052543X-RAY DIFFRACTION98
2.39-2.440.37051270.3092640X-RAY DIFFRACTION100
2.44-2.490.36981400.31182553X-RAY DIFFRACTION100
2.49-2.550.38171310.32032652X-RAY DIFFRACTION100
2.55-2.610.39341360.32892549X-RAY DIFFRACTION100
2.61-2.680.47581480.31732633X-RAY DIFFRACTION100
2.68-2.760.35841410.3062537X-RAY DIFFRACTION100
2.76-2.850.36441680.29182639X-RAY DIFFRACTION100
2.85-2.950.3321340.27482552X-RAY DIFFRACTION100
2.95-3.070.31131310.27092638X-RAY DIFFRACTION100
3.07-3.210.28261370.26962633X-RAY DIFFRACTION100
3.21-3.380.35071500.28422587X-RAY DIFFRACTION100
3.38-3.590.30071310.26432650X-RAY DIFFRACTION100
3.59-3.870.30231340.25012643X-RAY DIFFRACTION100
3.87-4.250.27161460.23622648X-RAY DIFFRACTION100
4.25-4.870.2531430.22032692X-RAY DIFFRACTION100
4.87-6.130.29451390.23982710X-RAY DIFFRACTION100
6.13-47.690.29441380.23632854X-RAY DIFFRACTION100

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