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- PDB-2prj: Binding of N-acetyl-beta-D-glucopyranosylamine to Glycogen Phosph... -

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Basic information

Entry
Database: PDB / ID: 2prj
TitleBinding of N-acetyl-beta-D-glucopyranosylamine to Glycogen Phosphorylase B
ComponentsGLYCOGEN PHOSPHORYLASE
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / N-acetyl-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsOikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J.F. / Fleet, G.W.J. / Acharya, K.R.
Citation
Journal: Protein Sci. / Year: 1995
Title: N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose.
Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J. / Fleet, G.W. / Acharya, K.R.
#1: Journal: Biochemistry / Year: 1994
Title: The Design of Inhibitors of Glycogen Phosphorylase: A Study of Alpha and Beta Glucoheptonamides and 1-Thio-Beta-D-Glucose Compounds
Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Son, J.C. / Bichard, C.J.F. / Orchard, M.G. / Fleet, G.W.J. / Oikonomakos, N.G. / Leonidas, D.D. / Kontou, M. / Papageorgiou, A.C.
History
DepositionDec 11, 1998Deposition site: PDBE / Processing site: RCSB
SupersessionDec 16, 1998ID: 1PRJ
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1084
Polymers97,2911
Non-polymers8173
Water4,666259
1
A: GLYCOGEN PHOSPHORYLASE
hetero molecules

A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,2168
Polymers194,5822
Non-polymers1,6336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8520 Å2
ΔGint-27 kcal/mol
Surface area58610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.500, 128.500, 116.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein GLYCOGEN PHOSPHORYLASE / E.C.2.4.1.1


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-NBG / N-acetyl-beta-D-glucopyranosylamine / 1-N-ACETYL-BETA-D-GLUCOSAMINE / N-acetyl-beta-D-glucosylamine / N-acetyl-D-glucosylamine / N-acetyl-glucosylamine


Type: D-saccharide / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
b-D-Glcp1NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.47 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: GLYCOGEN PHOSPHORYLASE WAS CO-CRYSTALLISED WITH 20 MM N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE IN A MEDIUM CONSISTING OF 20-30 MG/ML ENZYME, 1 MM IMP, 1 MM SPERMINE, 10 MM BES, 3 MM ...Details: GLYCOGEN PHOSPHORYLASE WAS CO-CRYSTALLISED WITH 20 MM N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE IN A MEDIUM CONSISTING OF 20-30 MG/ML ENZYME, 1 MM IMP, 1 MM SPERMINE, 10 MM BES, 3 MM DITHIOTHREITOL, 0.1 MM EDTA, 0.02% (W/V) SODIUM AZIDE, PH 6.7 AT 16 C, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE11
2BES11
3DITHIOTHREITOL11
4NAN311
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetailsSol-ID
120 mM1-GlcNAc1in a medium consisting
220-30 mg/mlenzyme1
31 mMIMP1
41 mMspermine1
510 mMBES11
63 mMdithiothreitol11
70.1 mMEDTA11
80.02 %(w/v)sodium azide11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Date: Aug 9, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.17 Å / Num. obs: 35730 / % possible obs: 81.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.4 Å / % possible all: 46.5
Reflection
*PLUS
% possible obs: 84 % / Num. measured all: 62732

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 2.3→18.17 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 --RANDOM
Rwork0.181 ---
obs0.181 35730 81.6 %-
all-35730 --
Refinement stepCycle: LAST / Resolution: 2.3→18.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 53 259 7061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 34607 / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.7

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