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- PDB-2y7j: Structure of human phosphorylase kinase, gamma 2 -

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Basic information

Entry
Database: PDB / ID: 2y7j
TitleStructure of human phosphorylase kinase, gamma 2
ComponentsPHOSPHORYLASE B KINASE GAMMA CATALYTIC CHAIN, TESTIS/LIVER ISOFORM
KeywordsTRANSFERASE
Function / homology
Function and homology information


phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / positive regulation of glycogen catabolic process / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / tau-protein kinase activity / glycogen metabolic process / generation of precursor metabolites and energy / calmodulin binding ...phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / positive regulation of glycogen catabolic process / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / tau-protein kinase activity / glycogen metabolic process / generation of precursor metabolites and energy / calmodulin binding / protein phosphorylation / protein serine/threonine kinase activity / enzyme binding / ATP binding / cytosol
Similarity search - Function
Phosphorylase kinase, gamma catalytic subunit / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Phosphorylase kinase, gamma catalytic subunit / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-B49 / Phosphorylase b kinase gamma catalytic chain, liver/testis isoform
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMuniz, J.R.C. / Shrestha, A. / Savitsky, P. / Wang, J. / Rellos, P. / Fedorov, O. / Burgess-Brown, N. / Brenner, B. / Berridge, G. / Elkins, J.M. ...Muniz, J.R.C. / Shrestha, A. / Savitsky, P. / Wang, J. / Rellos, P. / Fedorov, O. / Burgess-Brown, N. / Brenner, B. / Berridge, G. / Elkins, J.M. / Krojer, T. / Vollmar, M. / Che, K.H. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
CitationJournal: To be Published
Title: Structure of Human Phosphorylase Kinase, Gamma 2
Authors: Muniz, J.R.C. / Shrestha, A. / Savitsky, P. / Wang, J. / Rellos, P. / Fedorov, O. / Burgess-Brown, N. / Brenner, B. / Berridge, G. / Elkins, J.M. / Krojer, T. / Vollmar, M. / Che, K.H. / von ...Authors: Muniz, J.R.C. / Shrestha, A. / Savitsky, P. / Wang, J. / Rellos, P. / Fedorov, O. / Burgess-Brown, N. / Brenner, B. / Berridge, G. / Elkins, J.M. / Krojer, T. / Vollmar, M. / Che, K.H. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
History
DepositionJan 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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: PHOSPHORYLASE B KINASE GAMMA CATALYTIC CHAIN, TESTIS/LIVER ISOFORM
B: PHOSPHORYLASE B KINASE GAMMA CATALYTIC CHAIN, TESTIS/LIVER ISOFORM
C: PHOSPHORYLASE B KINASE GAMMA CATALYTIC CHAIN, TESTIS/LIVER ISOFORM
D: PHOSPHORYLASE B KINASE GAMMA CATALYTIC CHAIN, TESTIS/LIVER ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,2758
Polymers169,6814
Non-polymers1,5944
Water5,098283
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-33.1 kcal/mol
Surface area49220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.790, 91.420, 164.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3344, -0.8966, 0.2904), (-0.8178, 0.1229, -0.5622), (0.4684, -0.4255, -0.7743)
Vector: 9.4139, 5.1678, 12.3336)

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Components

#1: Protein
PHOSPHORYLASE B KINASE GAMMA CATALYTIC CHAIN, TESTIS/LIVER ISOFORM / PHOSPHORYLASE KINASE GAMMA 2 / PHK-GAMMA-T / PSK-C3 / PHOSPHORYLASE KINASE SUBUNIT GAMMA-2


Mass: 42420.254 Da / Num. of mol.: 4 / Fragment: RESIDUES 6-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R-LA / References: UniProt: P15735, phosphorylase kinase
#2: Chemical
ChemComp-B49 / N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide / SUNITINIB


Mass: 398.474 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H27FN4O2 / Comment: medication, anticancer, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 1.95 Å3/Da / Density % sol: 36.99 % / Description: NONE
Crystal growDetails: 25% PEG 3350; 0.1 M BIS-TRIS 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→63.32 Å / Num. obs: 46408 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 56.58 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→61.14 Å / Cor.coef. Fo:Fc: 0.9393 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 2343 5.05 %RANDOM
Rwork0.1819 ---
obs0.1836 46353 --
Displacement parametersBiso mean: 51.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.3782 Å20 Å20 Å2
2---2.9162 Å20 Å2
3---3.2943 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 2.5→61.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8940 0 116 283 9339
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019318HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0812635HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4273SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes248HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1386HARMONIC5
X-RAY DIFFRACTIONt_it9318HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion2.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1188SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10788SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2722 183 5.57 %
Rwork0.2133 3100 -
all0.2166 3283 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5490.13330.15512.30570.84952.4548-0.10630.0740.05320.07450.01610.265-0.2144-0.03730.0902-0.0810.01780.0010.0140.0348-0.0961-24.5224-3.117447.2739
22.0918-2.90022.07090.68751.179400.0137-0.0505-0.1750.0190.103-0.1399-0.02450.2315-0.1167-0.03030.1520.02580.1951-0.0389-0.0943-10.0438-24.727833.1752
30.6004-0.67370.35882.27510.19942.99940.0502-0.0220.17980.221-0.0470.18680.40790.1184-0.0033-0.04380.0116-0.0414-0.0669-0.0248-0.1138-25.2961-19.931441.7306
43.08570.61140.30250.8666-0.180900.01680.03820.02880.1774-0.10720.04010.0701-0.12870.0904-0.1272-0.1009-0.1152-0.01120.0070.2985-43.4873-20.728136.8591
50-1.33020.02514.34931.11353.50090.06560.1161-0.0252-0.4808-0.09070.54420.4256-0.05880.0250.0219-0.0146-0.0812-0.0282-0.0092-0.0983-31.2986-22.408628.2363
63.3249-1.21411.0542.9897-0.91416.4938-0.02270.4148-0.3923-0.084-0.03770.03550.54420.50830.06040.05850.0456-0.0655-0.138-0.1211-0.2295-24.6404-29.940126.2073
72.3497-0.45321.57481.1648-0.51832.57470.1458-0.01840.03570.0796-0.0549-0.3538-0.10840.1848-0.0909-0.0599-0.00980.0108-0.1043-0.044-0.0695-2.036-3.2267-6.7566
81.206-2.91042.7321.9945-2.91040.9978-0.02480.01610.1956-0.2038-0.08510.2739-0.23930.1440.10990.1789-0.1520.00490.0391-0.1414-0.00883.115914.1691-3.9376
92.2242.91042.167602.84782.857-0.0128-0.1330.1808-0.21340.1116-0.0957-0.06280.2266-0.09880.0032-0.03370.0051-0.023-0.0576-0.02457.22510.9966-2.8629
100.90180.36791.13814.31221.77242.2577-0.00640.2091-0.3028-0.42530.4113-0.3430.43880.1757-0.405-0.0736-0.0425-0.0281-0.0344-0.0037-0.041311.78131.124312.7587
110.12861.4167-0.19777.06372.271500.09430.07560.05450.36610.1660.0143-0.16480.0612-0.2603-0.0447-0.0662-0.02140.01630.0291-0.113511.641315.374518.5428
123.25381.8735-0.37437.2407-0.44798.21350.0112-0.5065-0.47140.54420.0935-0.3617-0.15970.3735-0.1047-0.0285-0.1084-0.152-0.1337-0.0155-0.213114.59386.403727.6853
131.92220.0511-0.30020.5961-0.34242.32470.05920.0601-0.03530.0666-0.0516-0.06890.0735-0.0664-0.00760.00690.0144-0.0745-0.0608-0.0351-0.0833-20.2557-1.0067-10.6763
142.35680.69950.04283.3277-0.0243.07680.11510.10160.29230.21870.02520.18-0.2195-0.4897-0.1402-0.05070.0782-0.0347-0.00430.0273-0.1076-38.23963.1254-1.4931
151.11181.8381-2.13762.7507-0.98910.8239-0.0230.06190.04220.01340.080.03010.0436-0.0678-0.0570.1574-0.152-0.1511-0.10850.0010.0981-39.4227-20.0129-1.7411
160.53060.11080.06221.1984-2.62651.18880.01210.01890.01790.49650.26880.4756-0.2185-0.5442-0.28080.0360.0459-0.0097-0.05310.0235-0.0723-39.5436-8.276911.4855
172.8807-1.1365-0.49170-1.00622.2666-0.0225-0.03830.11460.0429-0.0598-0.0124-0.06440.00560.08220.05380.10240.1520.04330.152-0.0449-48.33821.812918.098
183.2495-2.9104-1.28291.51650.99072.75220.00540.13230.05520.17750.09740.4286-0.1689-0.5423-0.1028-0.22120.07080.04960.16270.1059-0.006-52.8069-0.72294.6583
190.26690.9278-0.08754.8411-0.36213.72810.03660.3491-0.05940.06980.1661-0.0949-0.16860.3721-0.2027-0.15780.0380.0180.0195-0.0098-0.1145-26.693215.923345.2118
201.7555-1.9173-0.19092.43020.37481.45430.0050.0469-0.02670.0255-0.00180.0493-0.0255-0.0133-0.0032-0.040.0302-0.04330.13120.07550.2247-4.856715.347445.9389
211.37290.5868-2.91040.9147-1.17453.24830.1081-0.24610.21010.00820.16260.1006-0.39010.421-0.2707-0.1273-0.0701-0.00250.05-0.0322-0.1236-19.835625.78542.6683
228.31550.3133-0.98662.1522-0.20994.14450.24660.47580.5442-0.1090.05110.37-0.2527-0.5442-0.2977-0.1851-0.02290.0249-0.01310.0708-0.1184-19.454830.928827.3812
238.31552.6403-2.30550.52540.11590.02610.12260.52990.1525-0.11270.0960.036-0.1449-0.1316-0.2186-0.0828-0.0142-0.03880.14030.0096-0.1128-5.245630.555723.1368
247.8335-0.4026-2.91044.3395-1.16658.31550.12220.54420.5217-0.2560.02270.2824-0.224-0.0795-0.1448-0.3040.0095-0.00830.15260.152-0.2687-11.928733.541813.559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 10 - 118)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 119 - 131)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 132 - 178)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 179 - 186)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 187 - 232)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 233 - 292)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 11 - 55)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 56 - 82)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 83 - 110)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 111 - 183)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 184 - 229)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 230 - 293)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 10 - 111)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 112 - 178)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 179 - 186)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 187 - 246)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 247 - 257)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 258 - 292)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 11 - 55)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 56 - 72)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 73 - 111)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 112 - 183)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 184 - 231)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 232 - 293)

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