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- PDB-4y63: AAGlyB in complex with amino-acid analogues -

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Basic information

Entry
Database: PDB / ID: 4y63
TitleAAGlyB in complex with amino-acid analogues
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / AAGlyB / inhibitor
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-48O / Chem-BHE / : / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWang, S. / Cuesta-Seijo, J.A. / Striebeck, A. / Lafont, D. / Palcic, M.M. / Vidal, S.
CitationJournal: Chempluschem / Year: 2015
Title: Design of Glycosyltransferase Inhibitors: Serine Analogues as Pyrophosphate Surrogates?
Authors: Wang, S. / Cuesta-Seijo, J.A. / Striebeck, A. / Lafont, D. / Palcic, M.M. / Vidal, S.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7814
Polymers40,9471
Non-polymers8353
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-5 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.840, 149.150, 80.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

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Components

#1: Protein Histo-blood group ABO system transferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N- ...Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Histo-blood group A transferase / A transferase / Histo-blood group B transferase / B transferase / NAGAT


Mass: 40946.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli)
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-BHE / octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside / H-antigen acceptor / alpha-L-Fucp-(1,2)-Beta-D-Galp-O(CH2)7CH3


Mass: 438.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H38O10
#3: Chemical ChemComp-48O / 5'-deoxy-5'-{[(2S)-2-(triaza-1,2-dien-2-ium-1-yl)propanoyl]amino}uridine


Mass: 341.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N6O6
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350 ammonium sulfate MOPS MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.954 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.3→42.3 Å / Num. obs: 77776 / % possible obs: 99.6 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.69
Reflection shellResolution: 1.3→1.5 Å / Redundancy: 13 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.99 / Num. unique all: 26858 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KC1

4kc1


Resolution: 1.3→42.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.749 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18333 1556 2 %RANDOM
Rwork0.15937 ---
obs0.15984 76190 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å2-0 Å2
2--0.81 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.3→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 55 377 2747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022460
X-RAY DIFFRACTIONr_bond_other_d0.0030.022330
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.973351
X-RAY DIFFRACTIONr_angle_other_deg1.3223.015353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14822.564117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5815401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4931521
X-RAY DIFFRACTIONr_chiral_restr0.0780.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212720
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02607
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6251.1581137
X-RAY DIFFRACTIONr_mcbond_other0.621.1561136
X-RAY DIFFRACTIONr_mcangle_it0.8171.741422
X-RAY DIFFRACTIONr_mcangle_other0.8171.7411423
X-RAY DIFFRACTIONr_scbond_it1.0791.3391323
X-RAY DIFFRACTIONr_scbond_other1.0791.3381322
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1341.9441924
X-RAY DIFFRACTIONr_long_range_B_refined2.19211.4613084
X-RAY DIFFRACTIONr_long_range_B_other1.59610.2092842
X-RAY DIFFRACTIONr_rigid_bond_restr1.41234790
X-RAY DIFFRACTIONr_sphericity_free22.9265105
X-RAY DIFFRACTIONr_sphericity_bonded5.79354990
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 114 -
Rwork0.261 5590 -
obs--99.6 %

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