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- PDB-2x24: bovine ACC2 CT domain in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2x24
Titlebovine ACC2 CT domain in complex with inhibitor
ComponentsACETYL-COA CARBOXYLASE
KeywordsLIGASE / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS
Function / homologyClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta / Chem-X24
Function and homology information
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOster, L. / Folmer, R. / Blaho, S. / Wiberg, F. / Hallberg, K.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Design of Small Molecule Inhibitors of Acetyl-Coa Carboxylase 1 and 2 Showing Reduction of Hepatic Malonyl-Coa Levels in Vivo in Obese Zucker Rats.
Authors: Bengtsson, C. / Blaho, S. / Saitton, D.B. / Brickmann, K. / Broddefalk, J. / Davidsson, O. / Drmota, T. / Folmer, R. / Hallberg, K. / Hallen, S. / Hovland, R. / Isin, E. / Johannesson, P. / ...Authors: Bengtsson, C. / Blaho, S. / Saitton, D.B. / Brickmann, K. / Broddefalk, J. / Davidsson, O. / Drmota, T. / Folmer, R. / Hallberg, K. / Hallen, S. / Hovland, R. / Isin, E. / Johannesson, P. / Kull, B. / Larsson, L. / Lofgren, L. / Nilsson, K.E. / Noeske, T. / Oakes, N. / Plowright, A.T. / Schnecke, V. / Stahlberg, P. / Sorme, P. / Wan, H. / Wellner, E. / Oster, L.
History
DepositionJan 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ACETYL-COA CARBOXYLASE
B: ACETYL-COA CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,7674
Polymers178,7622
Non-polymers1,0052
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12670 Å2
ΔGint-85.2 kcal/mol
Surface area52780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.193, 104.867, 85.078
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2014-

HOH

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Components

#1: Protein ACETYL-COA CARBOXYLASE


Mass: 89381.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical ChemComp-X24 / TERT-BUTYL [(TRANS-4-{[({2-[4-(AMINOMETHYL)PHENYL]QUINOLIN-4-YL}CARBONYL)AMINO]METHYL}CYCLOHEXYL)METHYL]CARBAMATE


Mass: 502.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H38N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.79 Å3/Da / Density % sol: 56 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→49 Å / Num. obs: 76174 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 41.04 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2 % / Rmerge(I) obs: 0.63 / % possible all: 98

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.7 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.817 / SU R Cruickshank DPI: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.3 / SU Rfree Blow DPI: 0.25 / SU Rfree Cruickshank DPI: 0.26
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3643 5.04 %RANDOM
Rwork0.232 ---
obs0.234 72306 --
Displacement parametersBiso mean: 38.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.8572 Å20 Å20.6332 Å2
2---2.4612 Å20 Å2
3---3.3184 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10543 0 74 146 10763
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110873HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2114752HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3759SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes278HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1575HARMONIC5
X-RAY DIFFRACTIONt_it10873HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion21.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1372SEMIHARMONIC5
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_contact12351SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3724 259 5.28 %
Rwork0.3008 4645 -
all0.3045 4904 -

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