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- PDB-3np7: Glycogen phosphorylase complexed with 2,5-dihydroxy-3-(beta-D-glu... -

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Basic information

Entry
Database: PDB / ID: 3np7
TitleGlycogen phosphorylase complexed with 2,5-dihydroxy-3-(beta-D-glucopyranosyl)-chlorobenzene and 2,5-dihydroxy-4-(beta-D-glucopyranosyl)-chlorobenzene
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Glycogenolysis / type 2 diabetes / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan 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
Chem-Z15 / Chem-Z16 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsAlexacou, K.-M.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Halogen-substituted (C-beta-D-glucopyranosyl)-hydroquinone regioisomers: synthesis, enzymatic evaluation and their binding to glycogen phosphorylase.
Authors: Alexacou, K.M. / Zhang, Y.Z. / Praly, J.P. / Zographos, S.E. / Chrysina, E.D. / Oikonomakos, N.G. / Leonidas, D.D.
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Jun 19, 2013Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: 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
Revision 2.2Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4394
Polymers97,5191
Non-polymers9203
Water4,504250
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,8798
Polymers195,0392
Non-polymers1,8406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4940 Å2
ΔGint-25 kcal/mol
Surface area56420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.728, 128.728, 116.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glycogen phosphorylase, muscle form / / Myophosphorylase


Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-Z15 / (1S)-1,5-anhydro-1-(4-chloro-2,5-dihydroxyphenyl)-D-glucitol


Type: D-saccharide / Mass: 306.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15ClO7
#3: Sugar ChemComp-Z16 / (1S)-1,5-anhydro-1-(3-chloro-2,5-dihydroxyphenyl)-D-glucitol


Type: D-saccharide / Mass: 306.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15ClO7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 50.16 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA and 3 mM DTT. Crystals soaked with 100 mM inhibitor in BES for 21 hours, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2004
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 60600 / Num. obs: 60600 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.8
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2641 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2PRJ

2prj


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.023 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22013 3070 5.1 %RANDOM
Rwork0.19559 ---
obs0.19683 57482 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.411 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--1.1 Å20 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6623 0 60 250 6933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.9659276
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1215810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65323.571350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.276151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1781559
X-RAY DIFFRACTIONr_chiral_restr0.0720.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025237
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.22862
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24648
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2348
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5471.54189
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93826540
X-RAY DIFFRACTIONr_scbond_it1.20433069
X-RAY DIFFRACTIONr_scangle_it1.9734.52736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 177 -
Rwork0.247 3711 -
obs-3070 87.04 %

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