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- PDB-1b4d: AMIDOCARBAMATE INHIBITOR OF GLYCOGEN PHOSPHORYLASE -

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Basic information

Entry
Database: PDB / ID: 1b4d
TitleAMIDOCARBAMATE INHIBITOR OF GLYCOGEN PHOSPHORYLASE
ComponentsPROTEIN (GLYCOGEN PHOSPHORYLASE B)
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE / INHIBITOR BINDING / AMIDOCARBAMATE
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-CRA / INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsTsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W.J.
Citation
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.
#1: Journal: Synlett / Year: 1997
Title: Stereospecific Synthesis of Spirohydantoins of Beta-Glucopyranose:Inhibitors of Glycogen Phosphorylase
Authors: Krulle, T.M. / De La Fuente, C. / Watson, K.A. / Gregoriou, M. / Johnson, L.N. / Tsitsanou, K.E. / Zographos, S.E. / Oikonomakos, N.G. / Fleet, G.W.J.
#2: Journal: Protein Sci. / Year: 1995
Title: N-Acetyl-Beta-D-Glucopyranosylamine:A Potent T-State Inhibitor of Glycogen Phosphorylase. A Comparison with Alpha-D-Glucose
Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J.F. / Fleet, G.W.J. / Acharya, K.R.
#3: Journal: Biochemistry / Year: 1991
Title: Glucose Analogue Inhibitors of Glycogen Phosphorylase: The Design of Potential Drugs for Diabetes
Authors: Martin, J.L. / Veluraja, K. / Ross, K. / Johnson, L.N. / Fleet, G.W. / Ramsden, N.G. / Bruce, I. / Orchard, M.G. / Oikonomakos, N.G. / Papageorgiou, A.C. / Leonidas, D.D. / Tsitoura, H.S.
History
DepositionDec 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: 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: Data collection / Derived calculations
Category: diffrn_source / struct_conn ...diffrn_source / struct_conn / struct_site / struct_site_gen
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag ..._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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: PROTEIN (GLYCOGEN PHOSPHORYLASE B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1674
Polymers97,2911
Non-polymers8763
Water14,772820
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.680, 126.680, 115.350
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 B)


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: Sugar ChemComp-CRA / 1-DEOXY-1-METHOXYCARBAMIDO-BETA-D-GLUCO-2-HEPTULOPYRANOSONAMIDE


Type: D-saccharide / Mass: 280.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H16N2O8
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 289 K / pH: 6.7
Details: CO-CRYSTALLIZED COMPLEX WAS OBTAINED FROM 0.01 M BES, PH 6.7, 0.003 M DTT, 0.001 M SPERMINE, 0.0001 M SODIUM EDTA, 0.02 % SODIUM AZIDE AND 0.01 M AMIDOCARBAMATE AT 16 DEGREES C. JUST BEFORE ...Details: CO-CRYSTALLIZED COMPLEX WAS OBTAINED FROM 0.01 M BES, PH 6.7, 0.003 M DTT, 0.001 M SPERMINE, 0.0001 M SODIUM EDTA, 0.02 % SODIUM AZIDE AND 0.01 M AMIDOCARBAMATE AT 16 DEGREES C. JUST BEFORE DATA COLLECTION, THE CRYSTALS WERE TRANSFERRED TO A FRESH SOLUTION OF THE ABOVE BUFFER CONTAINING 30% GLYCEROL FOR 30-60 SEC., temperature 289K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Oct 18, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 62995 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.67
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 6.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1A8I

1a8i


Resolution: 2→20 Å / Cross valid method: FREE R-FACTOR / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3967 5 %RANDOM
Rwork0.182 ---
obs0.182 62895 99.4 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6542 0 57 820 7419
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.182 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

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