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- PDB-1z6p: Glycogen phosphorylase AMP site inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 1z6p
TitleGlycogen phosphorylase AMP site inhibitor complex
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / GLYCOGEN METABOLISM / GLYCOGEN PHOSPHORYLASE B / INHIBITION / allosteric
Function / homology
Function and homology information


SHG alpha-glucan phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / glycogen phosphorylase activity / glycogen phosphorylase / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Phosphorylase pyridoxal-phosphate attachment site / Glycogen/starch/alpha-glucan phosphorylase / Glycosyl transferase, family 35 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-{2-[(3-NITROBENZOYL)AMINO]PHENOXY}PHTHALIC ACID / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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)97,9422
Polymers97,5191
Non-polymers4221
Water2,180121
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,8834
Polymers195,0392
Non-polymers8452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6080 Å2
ΔGint-31 kcal/mol
Surface area56240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.470, 127.470, 115.800
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: muscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-194 / 4-{2-[(3-NITROBENZOYL)AMINO]PHENOXY}PHTHALIC ACID


Mass: 422.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14N2O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: BES, EDTA. DTT, SPERMINE, 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: 2.4→20 Å / Num. all: 36575 / Num. obs: 36575 / % possible obs: 97 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.44 Å / % possible all: 48

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1828 5 %random
Rwork0.2 ---
all-36572 --
obs-36572 97 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 31 121 6794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.031
X-RAY DIFFRACTIONx_angle_deg3.6

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