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- PDB-1r7y: Glycosyltransferase A in complex with 3-amino-acceptor analog inh... -

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Basic information

Entry
Database: PDB / ID: 1r7y
TitleGlycosyltransferase A in complex with 3-amino-acceptor analog inhibitor and uridine diphosphate
ComponentsGlycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
KeywordsTRANSFERASE / Glycoprotein / transmembrane / signal-anchor / blood group antigen
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 / : / Golgi cisterna membrane / : / 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 / : / Golgi cisterna membrane / : / 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
: / : / URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNguyen, H.P. / Seto, N.O.L. / Cai, Y. / Leinala, E.K. / Borisova, S.N. / Palcic, M.M. / Evans, S.V.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: The influence of an intramolecular hydrogen bond in differential recognition of inhibitory acceptor analogs by human ABO(H) blood group A and B glycosyltransferases
Authors: Nguyen, H.P. / Seto, N.O.L. / Cai, Y. / Leinala, E.K. / Borisova, S.N. / Palcic, M.M. / Evans, S.V.
History
DepositionOct 22, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8719
Polymers32,9991
Non-polymers1,8728
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
hetero molecules

A: Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,74118
Polymers65,9982
Non-polymers3,74316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9990 Å2
ΔGint-288 kcal/mol
Surface area21590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.500, 149.400, 79.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycosyltransferase A


Mass: 32999.148 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (Residues 63-345)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-hexyl 3-amino-3-deoxy-beta-D-galactopyranoside


Type: oligosaccharide / Mass: 409.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OCCCCCC_3*N][a1221m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][hexyl]{[(1+1)][b-D-Galp3N]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 146 molecules

#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.48 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Patenaude, S.I., (2002) Nat. Struct. Biol., 9, 685.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-8 mg/mlprotein1drop
270 mMADA1droppH7.5
350 mMsodium acetate1droppH4.6
440 mM1dropNaCl
55-8 mM1dropMnCl2
62.5 %(v/v)MPD1drop
75 %(v/v)glycerol1drop
82 %(w/v)PEG40001drop
90.3-0.5 mM3-chloro-Hg-2-methoxy-propylurea1drop
1050 mMADA1reservoirpH7.5
1110 mM1reservoirMnCl2
12100 mMammonium sulfate1reservoir
135 %(v/v)MPD1reservoir
1410 %(v/v)glycerol1reservoir
158-10 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.75→36.13 Å / Num. all: 31851 / Observed criterion σ(F): 0 / Biso Wilson estimate: 21.7 Å2 / Limit h max: 30 / Limit h min: 0 / Limit k max: 85 / Limit k min: 0 / Limit l max: 45 / Limit l min: 0 / Observed criterion F max: 577023.69 / Observed criterion F min: 0.71
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 32164 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.148

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→36.13 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3135 10 %random
Rwork0.208 ---
all-31951 --
obs-31389 98.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 58.1366 Å2 / ksol: 0.427441 e/Å3
Displacement parametersBiso max: 57.61 Å2 / Biso mean: 24.08 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2--1.01 Å20 Å2
3----0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å-0.02 Å
Luzzati d res high-1.75
Refinement stepCycle: LAST / Resolution: 1.75→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 59 139 2356
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_torsion_deg23.8
X-RAY DIFFRACTIONc_torsion_impr_deg0.8
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.75-1.810.24631010.20.21327310.0143165304196.1
1.81-1.890.22731610.30.19827590.0133149307597.7
1.89-1.970.21233110.60.19127770.0123159310898.4
1.97-2.070.24132310.30.19928140.0133173313798.9
2.07-2.20.2012989.50.19228500.0123179314899
2.2-2.370.2234210.90.19927980.0123165314099.2
2.37-2.610.213099.70.20228710.0123193318099.6
2.61-2.990.2183169.90.2128730.0123204318999.5
2.99-3.770.2042929.20.20228990.0123253319198.1
3.77-36.130.2182989.40.22828820.0133361318094.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate_AA.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5udp.paramudp.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.215 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.005
LS refinement shell
*PLUS
Rfactor Rfree: 0.224 / Rfactor Rwork: 0.194

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