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- PDB-1em6: HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP... -

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Basic information

Entry
Database: PDB / ID: 1em6
TitleHUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP-526,423
ComponentsLIVER GLYCOGEN PHOSPHORYLASE
KeywordsTRANSFERASE / allosteric site / allosteric binding
Function / homology
Function and homology information


purine nucleobase binding / vitamin binding / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / bile acid binding / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / AMP binding ...purine nucleobase binding / vitamin binding / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / bile acid binding / glycogen catabolic process / 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 / cytoplasm / cytosol
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-CP4 / N-acetyl-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsRath, V.L. / Ammirati, M. / Danley, D.E. / Ekstrom, J.L. / Hynes, T.R. / Olson, T.V. / Hoover, D.J.
CitationJournal: Chem.Biol. / Year: 2000
Title: Human liver glycogen phosphorylase inhibitors bind at a new allosteric site.
Authors: Rath, V.L. / Ammirati, M. / Danley, D.E. / Ekstrom, J.L. / Gibbs, E.M. / Hynes, T.R. / Mathiowetz, A.M. / McPherson, R.K. / Olson, T.V. / Treadway, J.L. / Hoover, D.J.
History
DepositionMar 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / 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_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 1.4Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIVER GLYCOGEN PHOSPHORYLASE
B: LIVER GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1118
Polymers194,5532
Non-polymers1,5586
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-41 kcal/mol
Surface area54020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.314, 123.314, 122.319
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 LIVER GLYCOGEN PHOSPHORYLASE


Mass: 97276.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PBLUEBACII / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / 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 , 4 types, 741 molecules

#3: Chemical ChemComp-CP4 / BIS[5-CHLORO-1H-INDOL-2-YL-CARBONYL-AMINOETHYL]-ETHYLENE GLYCOL / CP-526423 / 1,2-BIS(2-(5-CHLOROINDOLE-2-CARBONYLAMINO)ETHOXY)ETHANE


Mass: 503.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24Cl2N4O4
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 105649 / Num. obs: 103325 / % possible obs: 97.8 % / Observed criterion σ(F): -2 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.359 / Num. unique all: 9224 / % possible all: 87.1
Reflection
*PLUS
Lowest resolution: 99 Å
Reflection shell
*PLUS
% possible obs: 87.1 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.2→99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 194745.34 / Data cutoff high rms absF: 194745.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS default
RfactorNum. reflection% reflectionSelection details
Rfree0.264 9800 10 %RANDOM
Rwork0.233 ---
all0.237 105689 --
obs0.234 97974 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.103 Å2 / ksol: 0.349441 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å21.65 Å20 Å2
2---1.48 Å20 Å2
3---2.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12760 0 102 737 13599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it0.491.5
X-RAY DIFFRACTIONc_mcangle_it0.892
X-RAY DIFFRACTIONc_scbond_it0.82
X-RAY DIFFRACTIONc_scangle_it1.122.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 1392 9.9 %
Rwork0.307 12669 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARWATER.TOP
X-RAY DIFFRACTION3ALL.PARALL.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.34 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.307 / Rfactor obs: 0.307

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