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- PDB-2amv: THE STRUCTURE OF GLYCOGEN PHOSPHORYLASE B WITH AN ALKYL-DIHYDROPY... -

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Basic information

Entry
Database: PDB / ID: 2amv
TitleTHE STRUCTURE OF GLYCOGEN PHOSPHORYLASE B WITH AN ALKYL-DIHYDROPYRIDINE-DICARBOXYLIC ACID
ComponentsPROTEIN (GLYCOGEN PHOSPHORYLASE)
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE / GLYCOGEN METABOLISM / DIABETES / INHIBITORS / GLYCOSYLTRANSFERASE
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-BIN / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsZographos, S.E. / Oikonomakos, N.G. / Johnson, L.N.
Citation
Journal: Structure / Year: 1997
Title: The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor.
Authors: Zographos, S.E. / Oikonomakos, N.G. / Tsitsanou, K.E. / Leonidas, D.D. / Chrysina, E.D. / Skamnaki, V.T. / Bischoff, H. / Goldmann, S. / Watson, K.A. / Johnson, L.N.
#1: Journal: Protein Sci. / Year: 1999
Title: Effects of Commonly Used Cryoprotectants on Glycogen Phosphorylase Activity and Structure
Authors: Tsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W.
#2: Journal: Glycogen Phosphorylase B: Description of the Protein Structure
Year: 1991
Title: Glycogen Phosphorylase B: Description of the Protein Structure
Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallographic Binding Studies on the Allosteric Inhibitor Glucose-6- Phosphate to T State Glycogen Phosphorylase b
Authors: Johnson, L.N. / Snape, P. / Martin, J.L. / Acharya, K.R. / Barford, D. / Oikonomakos, N.G.
History
DepositionOct 13, 1998Deposition site: BNL / Processing site: RCSB
SupersessionOct 21, 1998ID: 1amv
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0374
Polymers97,2911
Non-polymers7463
Water10,070559
1
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules

A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,0758
Polymers194,5822
Non-polymers1,4926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules

A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,0758
Polymers194,5822
Non-polymers1,4926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)127.110, 127.110, 115.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (GLYCOGEN PHOSPHORYLASE)


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-BIN / 2,3-DICARBOXY-4-(2-CHLORO-PHENYL)-1-ETHYL-5-ISOPROPOXYCARBONYL-6-METHYL-PYRIDINIUM


Mass: 406.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21ClNO6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 289 K / pH: 6.7
Details: PHOSPHORYLASE B WAS COCRYSTALLISED WITH 1 MM W1807 IN A MEDIUM CONSISTING OF 27-28 MG/ML ENZYME, 1 MM SPERMINE, 3 MM DTT, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (16 DEG C)., temperature 289K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMW180711
227-28 mg/mlenzyme11
31 mMspermine11
43 mMdithiothreitol11
510 mMBES11
60.1 mMEDTA11
70.02 %sodium azide11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 39549 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.6 / % possible all: 95.9
Reflection
*PLUS
Num. measured all: 242759
Reflection shell
*PLUS
% possible obs: 95.9 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→30 Å / Cross valid method: R FREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 -5 %RANDOM
Rwork0.201 ---
obs0.201 39513 94 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 49 559 7350
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.8
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2

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