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- PDB-1noi: COMPLEX OF GLYCOGEN PHOSPHORYLASE WITH A TRANSITION STATE ANALOGU... -

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Basic information

Entry
Database: PDB / ID: 1noi
TitleCOMPLEX OF GLYCOGEN PHOSPHORYLASE WITH A TRANSITION STATE ANALOGUE NOJIRIMYCIN TETRAZOLE AND PHOSPHATE IN THE T AND R STATES
ComponentsGLYCOGEN PHOSPHORYLASE
KeywordsGLYCOGEN PHOSPHORYLASE / TRANSFERASE / 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
NOJIRIMYCINE TETRAZOLE / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsJohnson, L.N. / Mitchell, E.P.
Citation
Journal: Biochemistry / Year: 1996
Title: Ternary complex crystal structures of glycogen phosphorylase with the transition state analogue nojirimycin tetrazole and phosphate in the T and R states.
Authors: Mitchell, E.P. / Withers, S.G. / Ermert, P. / Vasella, A.T. / Garman, E.F. / Oikonomakos, N.G. / Johnson, L.N.
#1: Journal: Helv.Chim.Acta / Year: 1991
Title: Synthesis of a Glucose Derived Tetrazole as a New Beta-Glucosidase Inhibitor
Authors: Ermert, P. / Vasella, A.T.
#2: Journal: Nature / Year: 1989
Title: The Allosteric Transition of Glycogen Phosphorylase
Authors: Barford, D. / Johnson, L.N.
History
DepositionMar 12, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE
B: GLYCOGEN PHOSPHORYLASE
C: GLYCOGEN PHOSPHORYLASE
D: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,44616
Polymers389,2694
Non-polymers2,17712
Water15,925884
1
A: GLYCOGEN PHOSPHORYLASE
B: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7238
Polymers194,6342
Non-polymers1,0896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-20 kcal/mol
Surface area59260 Å2
MethodPISA
2
C: GLYCOGEN PHOSPHORYLASE
D: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7238
Polymers194,6342
Non-polymers1,0896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-21 kcal/mol
Surface area59000 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19060 Å2
ΔGint-60 kcal/mol
Surface area113870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.000, 190.000, 88.200
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GLYCOGEN PHOSPHORYLASE


Mass: 97317.242 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-NTZ / NOJIRIMYCINE TETRAZOLE


Mass: 202.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10N4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-40 mg/mlGPb11
21 mMIMP11
31 mMspermine11
410 mMBES11
50.1 mMEDTA11
60.02 %sodium azide11

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionNum. obs: 107826 / % possible obs: 88 % / Observed criterion σ(I): 3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 9999 Å / Num. measured all: 263189
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.56 Å / % possible obs: 74 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.273 -
Rwork0.171 -
obs0.171 104617
Displacement parametersBiso mean: 34.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26768 0 136 884 27788
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOP19X.TOP ?
X-RAY DIFFRACTION2PARMA.NJT (NORJIRIMYCIN TTOP.NJT (NORJIRIMYCIN TETRAZOLE)
X-RAY DIFFRACTION3PARAM.PLP (PYRIDOXAL PHOS
X-RAY DIFFRACTION4PARAM.PO4 (PHOSPHATE)

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