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- PDB-2zb2: Human liver glycogen phosphorylase a complexed with glcose and 5-... -

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Basic information

Entry
Database: PDB / ID: 2zb2
TitleHuman liver glycogen phosphorylase a complexed with glcose and 5-chloro-N-[4-(1,2-dihydroxyethyl)phenyl]-1H-indole-2-carboxamide
ComponentsGlycogen phosphorylase, liver form
KeywordsTRANSFERASE / ALLOSTERIC SITE / ALLOSTERIC BINDING / Allosteric enzyme / Carbohydrate metabolism / Disease mutation / Glycogen metabolism / Glycogen storage disease / Glycosyltransferase / Nucleotide-binding / Phosphorylation / 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-A46 / alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKatayama, N. / Onda, K.
CitationJournal: Bioorg.Med.Chem. / Year: 2008
Title: Synthesis of 5-chloro-N-aryl-1H-indole-2-carboxamide derivatives as inhibitors of human liver glycogen phosphorylase a.
Authors: Onda, K. / Suzuki, T. / Shiraki, R. / Yonetoku, Y. / Negoro, K. / Momose, K. / Katayama, N. / Orita, M. / Yamaguchi, T. / Ohta, M. / Tsukamoto, S.
History
DepositionOct 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 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
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, liver form
B: Glycogen phosphorylase, liver form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,98412
Polymers194,8412
Non-polymers2,14310
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-42 kcal/mol
Surface area56020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.819, 123.819, 123.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glycogen phosphorylase, liver form /


Mass: 97420.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Liver / Gene: PYGL / Plasmid: pET42b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06737, glycogen phosphorylase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 405 molecules

#3: 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
#4: 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
#5: Chemical ChemComp-A46 / 5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide


Mass: 330.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15ClN2O3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 56.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM NaMES (pH6), 22.5 % MPD, 60mM D-glucose, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 18, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→49.4 Å / Num. obs: 79745 / % possible obs: 99.1 % / Rsym value: 0.374 / Net I/σ(I): 1.4
Reflection shellResolution: 2.42→2.49 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6036 / % possible all: 91.6

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Processing

Software
NameClassification
CrystalCleardata collection
CNXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EXV

1exv


Resolution: 2.45→49.18 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.307 7726 -RANDOM
Rwork0.261 ---
obs0.3 77428 99.4 %-
all-77428 --
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å22.29 Å20 Å2
2---1.4 Å20 Å2
3---2.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.45→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12876 0 140 397 13413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.339 1230 -
Rwork0.3 --
obs-11357 97.1 %

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