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- PDB-3dd1: Crystal structure of glycogen phophorylase complexed with an anth... -

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Basic information

Entry
Database: PDB / ID: 3dd1
TitleCrystal structure of glycogen phophorylase complexed with an anthranilimide based inhibitor GSK254
ComponentsGlycogen phosphorylase, liver form
KeywordsTRANSFERASE / Glycogen Phosphorylase HLGP / Diabetes / Allosteric enzyme / Carbohydrate metabolism / Disease mutation / Glycogen metabolism / Glycogen storage disease / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate
Function / homology
Function and homology information


vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / AMP binding / necroptotic process / response to bacterium / pyridoxal phosphate binding / glucose homeostasis / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
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-25D / CAFFEINE / N-acetyl-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsNolte, R.T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy.
Authors: Thomson, S.A. / Banker, P. / Bickett, D.M. / Boucheron, J.A. / Carter, H.L. / Clancy, D.C. / Cooper, J.P. / Dickerson, S.H. / Garrido, D.M. / Nolte, R.T. / Peat, A.J. / Sheckler, L.R. / ...Authors: Thomson, S.A. / Banker, P. / Bickett, D.M. / Boucheron, J.A. / Carter, H.L. / Clancy, D.C. / Cooper, J.P. / Dickerson, S.H. / Garrido, D.M. / Nolte, R.T. / Peat, A.J. / Sheckler, L.R. / Sparks, S.M. / Tavares, F.X. / Wang, L. / Wang, T.Y. / Weiel, J.E.
History
DepositionJun 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen phosphorylase, liver form
B: Glycogen phosphorylase, liver form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,98817
Polymers194,6792
Non-polymers3,31015
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-27.5 kcal/mol
Surface area58070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.103, 124.103, 123.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLNGLNAA12 - 83014 - 832
2ASNASNBB23 - 83025 - 832
DetailsThe active form is a dimer, as seen in the asymmetric unit

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glycogen phosphorylase, liver form /


Mass: 97339.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Liver isoform / Gene: PYGL / Plasmid: T7 promoter / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P06737, 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
b-D-Glcp1NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 553 molecules

#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE / Caffeine (data page)


Mass: 194.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N4O2 / Comment: medication*YM
#5: Chemical ChemComp-25D / 2-cyclohexyl-N-[(3-{[(2,4,6-trimethylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]-D-alanine


Mass: 501.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H35N3O4
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Na MES pH 5.8-6.1, 12-25% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 25, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 83085 / Num. obs: 82440 / % possible obs: 99.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 14.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EM6

1em6


Resolution: 2.57→49.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.765 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.514 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20729 2049 3 %RANDOM
Rwork0.16744 ---
obs0.16865 65493 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.31 Å20 Å2
2---0.61 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.57→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13062 0 226 540 13828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02213650
X-RAY DIFFRACTIONr_bond_other_d0.0020.029286
X-RAY DIFFRACTIONr_angle_refined_deg1.0551.97518497
X-RAY DIFFRACTIONr_angle_other_deg0.81322613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54251626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77324.343654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0415.0062394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1571580
X-RAY DIFFRACTIONr_chiral_restr0.0540.22006
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022790
X-RAY DIFFRACTIONr_nbd_refined0.1940.22918
X-RAY DIFFRACTIONr_nbd_other0.1750.29585
X-RAY DIFFRACTIONr_nbtor_refined0.1790.26705
X-RAY DIFFRACTIONr_nbtor_other0.0810.26739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2666
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4371.58790
X-RAY DIFFRACTIONr_mcbond_other0.0621.53273
X-RAY DIFFRACTIONr_mcangle_it0.715213082
X-RAY DIFFRACTIONr_scbond_it0.74936254
X-RAY DIFFRACTIONr_scangle_it1.1454.55415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
4682medium positional0.280.5
6212loose positional0.485
4682medium thermal0.292
6212loose thermal0.5710
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 157 -
Rwork0.207 4853 -
obs--100 %

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