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- PDB-1z6q: Glycogen phosphorylase with inhibitor in the AMP site -

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Basic information

Entry
Database: PDB / ID: 1z6q
TitleGlycogen phosphorylase with inhibitor in the AMP site
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / GLYCOGEN METABOLISM / GLYCOGEN PHOSPHORYLASE B / INHIBITION / allosteric
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
Chem-195 / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKristiansen, M. / Andersen, B. / Iversen, L.F. / Westergaard, N.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Identification, synthesis and chracterization of new glycogen phosphorylase inhibitors binding to the allosteric AMP site
Authors: Kristiansen, M. / Andersen, B. / Iversen, L.F. / Westergaard, N.
History
DepositionMar 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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)98,1062
Polymers97,5191
Non-polymers5861
Water00
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,2124
Polymers195,0392
Non-polymers1,1732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6380 Å2
ΔGint-16 kcal/mol
Surface area55980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.5, 127.5, 115.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein Glycogen phosphorylase, muscle form / E.C.2.4.1.1 / Myophosphorylase


Mass: 97519.320 Da / Num. of mol.: 1 / Fragment: Glycogen Phosphorylase / Source method: isolated from a natural source / Details: gene PYGM / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-195 / 4-{2,4-BIS[(3-NITROBENZOYL)AMINO]PHENOXY}PHTHALIC ACID


Mass: 586.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H18N4O11

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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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: BES, EDTA, DTT, SPERMDINE, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 2, 1999
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→20 Å / Num. all: 60467 / Num. obs: 60467 / % possible obs: 99 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.03→2.06 Å / % possible all: 99

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3023 5 %RANDOM
Rwork0.21 ---
obs0.22 60467 --
all-60467 --
Refinement stepCycle: LAST / Resolution: 2.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 43 0 6685
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.029
X-RAY DIFFRACTIONx_angle_deg3.3

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