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- PDB-6u77: yGsy2p in complex with small molecule -

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Basic information

Entry
Database: PDB / ID: 6u77
TitleyGsy2p in complex with small molecule
ComponentsGlycogen [starch] synthase isoform 2
KeywordsTRANSFERASE/INHIBITOR / Inhibitor / Glycogen Synthase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


Glycogen synthesis / glycogen(starch) synthase / glycogen (starch) synthase activity / glycogen biosynthetic process / molecular function inhibitor activity / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Glycogen synthase / Glycogen synthase
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Chem-VMC / Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsTang, B. / Hurley, T.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-DK079887 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery and Development of Small-Molecule Inhibitors of Glycogen Synthase.
Authors: Tang, B. / Frasinyuk, M.S. / Chikwana, V.M. / Mahalingan, K.K. / Morgan, C.A. / Segvich, D.M. / Bondarenko, S.P. / Mrug, G.P. / Wyrebek, P. / Watt, D.S. / DePaoli-Roach, A.A. / Roach, P.J. / Hurley, T.D.
History
DepositionAug 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen [starch] synthase isoform 2
B: Glycogen [starch] synthase isoform 2
C: Glycogen [starch] synthase isoform 2
D: Glycogen [starch] synthase isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,23212
Polymers320,7994
Non-polymers2,4338
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)192.257, 206.557, 205.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLUGLU5AA2 - 162 - 16
211SERSERGLUGLU5BB2 - 162 - 16
311SERSERGLUGLU5CC2 - 162 - 16
411SERSERGLUGLU5DD2 - 162 - 16
121ARGARGASNASN4AA20 - 5020 - 50
221ARGARGASNASN4BB20 - 5020 - 50
321ARGARGASNASN4CC20 - 5020 - 50
421ARGARGASNASN4DD20 - 5020 - 50
131METMETLEULEU4AA73 - 12573 - 125
231METMETLEULEU4BB73 - 12573 - 125
331METMETLEULEU4CC73 - 12573 - 125
431METMETLEULEU4DD73 - 12573 - 125
141ASPASPLEULEU4AA134 - 201134 - 201
241ASPASPLEULEU4BB134 - 201134 - 201
341ASPASPLEULEU4CC134 - 201134 - 201
441ASPASPLEULEU4DD134 - 201134 - 201
151TYRTYRPHEPHE4AA228 - 276228 - 276
251TYRTYRPHEPHE4BB228 - 276228 - 276
351TYRTYRPHEPHE4CC228 - 276228 - 276
451TYRTYRPHEPHE4DD228 - 276228 - 276
161LYSLYSASPASP4AA600 - 620600 - 620
261LYSLYSASPASP4BB600 - 620600 - 620
361LYSLYSASPASP4CC600 - 620600 - 620
461LYSLYSASPASP4DD600 - 620600 - 620
112GLYGLYASPASP5AA299 - 598299 - 598
212GLYGLYASPASP5BB299 - 598299 - 598
312GLYGLYASPASP5CC299 - 598299 - 598
412GLYGLYASPASP5DD299 - 598299 - 598

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.993125, 0.095326, 0.067943), (0.051587, 0.877399, -0.47698), (-0.105081, -0.470196, -0.876284)-83.554947, -17.292629, -89.875648
3given(-0.823509, -0.185922, -0.535971), (-0.202896, -0.785755, 0.584314), (-0.529779, 0.589934, 0.609354)-104.368568, 17.675579, -39.503361
4given(0.867235, 0.129232, 0.480835), (0.108736, -0.991576, 0.070384), (0.48588, -0.008756, -0.873982)15.81744, 3.76523, -69.141167
5given(1), (1), (1)
6given(-0.990532, 0.132963, -0.034175), (0.121128, 0.729282, -0.673406), (-0.064615, -0.671169, -0.738483)-87.257637, -28.21595, -88.181519
7given(-0.872978, -0.180513, -0.453127), (-0.195351, -0.72184, 0.663916), (-0.446931, 0.668103, 0.594887)-103.091843, 20.53537, -37.70916
8given(0.871954, 0.053419, 0.486665), (0.0522, -0.998507, 0.016076), (0.486798, 0.011387, -0.873441)18.23221, -0.72018, -69.698936

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Components

#1: Protein
Glycogen [starch] synthase isoform 2


Mass: 80199.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GSY2, YLR258W, L8479.8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27472, glycogen(starch) synthase
#2: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-VMC / 2-methoxy-4-(1-{2-[(2S)-1-methylpyrrolidin-2-yl]ethyl}-4-phenyl-1H-imidazol-5-yl)phenol


Mass: 377.479 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H27N3O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris, pH 5.9 and 13-15% PEG300

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→145.52 Å / Num. obs: 95326 / % possible obs: 99.9 % / Redundancy: 6 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Χ2: 1.001 / Net I/σ(I): 20.3
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 5.7 % / Num. unique obs: 4703 / CC1/2: 0.857 / Rpim(I) all: 0.347 / Rrim(I) all: 0.843 / Χ2: 0.887 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NB0

3nb0


Resolution: 2.85→145.52 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 36.36 / SU ML: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.948 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 4888 5.1 %RANDOM
Rwork0.1988 ---
obs0.2018 90409 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.44 Å2 / Biso mean: 84.811 Å2 / Biso min: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å2-0 Å2
2---6.74 Å2-0 Å2
3---5.84 Å2
Refinement stepCycle: final / Resolution: 2.85→145.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20528 0 164 0 20692
Biso mean--88.85 --
Num. residues----2546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01921199
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219453
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.95428731
X-RAY DIFFRACTIONr_angle_other_deg0.965344989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33952541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80623.5631061
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.047153557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.32915156
X-RAY DIFFRACTIONr_chiral_restr0.080.23123
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024587
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3617MEDIUM POSITIONAL0.480.5
12B3617MEDIUM POSITIONAL0.50.5
13C3617MEDIUM POSITIONAL0.460.5
14D3617MEDIUM POSITIONAL0.490.5
11A144LOOSE POSITIONAL0.635
12B144LOOSE POSITIONAL0.595
13C144LOOSE POSITIONAL0.495
14D144LOOSE POSITIONAL0.845
11A3617MEDIUM THERMAL9.792
12B3617MEDIUM THERMAL12.312
13C3617MEDIUM THERMAL7.022
14D3617MEDIUM THERMAL18.552
11A144LOOSE THERMAL5.2310
12B144LOOSE THERMAL14.5410
13C144LOOSE THERMAL6.1310
14D144LOOSE THERMAL18.3510
21A1768MEDIUM POSITIONAL0.190.5
22B1768MEDIUM POSITIONAL0.220.5
23C1768MEDIUM POSITIONAL0.180.5
24D1768MEDIUM POSITIONAL0.180.5
21A2926LOOSE POSITIONAL0.535
22B2926LOOSE POSITIONAL0.675
23C2926LOOSE POSITIONAL0.555
24D2926LOOSE POSITIONAL0.585
21A1768MEDIUM THERMAL9.52
22B1768MEDIUM THERMAL6.632
23C1768MEDIUM THERMAL9.22
24D1768MEDIUM THERMAL6.332
21A2926LOOSE THERMAL9.8510
22B2926LOOSE THERMAL6.8210
23C2926LOOSE THERMAL9.8210
24D2926LOOSE THERMAL6.8310
LS refinement shellResolution: 2.85→2.919 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.372 374 -
Rwork0.334 6481 -
obs--98.11 %
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)
10.3147-0.20470.19470.1892-0.160.4451-0.0679-0.0981-0.03020.00850.0686-0.0095-0.0039-0.0911-0.00070.06070.0167-0.00560.0735-0.0040.0599-24.7525-23.849-21.2512
20.13120.21980.11960.73380.23110.1992-0.0272-0.02440.0471-0.08420.0190.1923-0.0077-0.00810.00830.021-0.0088-0.0270.03-0.01530.1697-66.1464-31.0305-55.4669
30.2283-0.2939-0.06530.60680.01280.0970.03450.0543-0.05580.0187-0.00290.1261-0.0064-0.0163-0.03170.0540.0177-0.05670.04790.02210.149-67.675428.2667-55.2703
40.40180.03610.00190.14580.05250.1503-0.00970.14210.103-0.01410.005-0.02580.00220.02480.00460.04930.01330.00960.08070.03630.0899-15.135220.853-63.1605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 901
2X-RAY DIFFRACTION2B2 - 901
3X-RAY DIFFRACTION3C2 - 901
4X-RAY DIFFRACTION4D2 - 901

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