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- PDB-5ctb: Humanized yeast ACC carboxyltransferase domain bound to 6,7-dimet... -

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Basic information

Entry
Database: PDB / ID: 5ctb
TitleHumanized yeast ACC carboxyltransferase domain bound to 6,7-dimethyl-1'-[(7-methyl-1H-indazol-5-yl)carbonyl]spiro[chromene-2,4'-piperidin]-4(3H)-one
ComponentsAcetyl-CoA carboxylase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ACC / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity ...: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / acetyl-CoA biosynthetic process / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / protein import into nucleus / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal ...ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-57J / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVajdos, F.F.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery of spirocyclic-diamine inhibitors of mammalian acetyl CoA-carboxylase.
Authors: Kung, D.W. / Griffith, D.A. / Esler, W.P. / Vajdos, F.F. / Mathiowetz, A.M. / Doran, S.D. / Amor, P.A. / Bagley, S.W. / Banks, T. / Cabral, S. / Ford, K. / Garcia-Irizarry, C.N. / Landis, M. ...Authors: Kung, D.W. / Griffith, D.A. / Esler, W.P. / Vajdos, F.F. / Mathiowetz, A.M. / Doran, S.D. / Amor, P.A. / Bagley, S.W. / Banks, T. / Cabral, S. / Ford, K. / Garcia-Irizarry, C.N. / Landis, M.S. / Loomis, K. / McPherson, K. / Niosi, M. / Rockwell, K.L. / Rose, C. / Smith, A.C. / Southers, J.A. / Tapley, S. / Tu, M. / Valentine, J.J.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,35311
Polymers261,6633
Non-polymers1,6918
Water24,6991371
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,6338
Polymers174,4422
Non-polymers1,1916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12730 Å2
ΔGint-155 kcal/mol
Surface area57460 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,5377
Polymers174,4422
Non-polymers1,0955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-140 kcal/mol
Surface area54380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.853, 124.381, 145.674
Angle α, β, γ (deg.)90.000, 94.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Acetyl-CoA carboxylase / ACC / Fatty acid synthetase 3 / mRNA transport-defective protein 7


Mass: 87220.844 Da / Num. of mol.: 3
Fragment: carboxyltransferase domain (UNP residues 1476-2233)
Mutation: E1919Q,P1920A,H1925F,P1760S,I1762L,M1765V,Q2028E,M2030T,G2032E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ACC1, ABP2, FAS3, MTR7, YNR016C, N3175 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical ChemComp-57J / 6,7-dimethyl-1'-[(7-methyl-1H-indazol-5-yl)carbonyl]spiro[chromene-2,4'-piperidin]-4(3H)-one


Mass: 403.474 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H25N3O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1371 / 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: 4.24 Å3/Da / Density % sol: 71.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium citrate, 12% w/v PEG8000, 150 mM lithium sulfate, 7.5% v/v glycerol, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2006
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→39.936 Å / Num. all: 167944 / Num. obs: 167944 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 55.87 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.053 / Rrim(I) all: 0.1 / Rsym value: 0.085 / Net I/av σ(I): 7.105 / Net I/σ(I): 12.8 / Num. measured all: 583810
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.532.90.6680.965607229680.4660.6681.792.7
2.53-2.683.60.4591.484061234300.2830.459399.7
2.68-2.873.70.272.581128221170.1640.274.8100
2.87-3.13.70.1664.175904205980.1010.1668100
3.1-3.393.70.1076.369272189460.0660.10712.5100
3.39-3.793.60.0699.661665171400.0420.06919.7100
3.79-4.383.50.0521253616151560.0320.05224.8100
4.38-5.373.50.04712.444422128380.030.04727.899.9
5.37-7.593.20.04313.33182299040.0280.0432999.5
7.59-39.9363.40.03815.41631348470.0240.03834.687.6

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Processing

Software
NameVersionClassification
SCALA3.2.19data scaling
BUSTER-TNTBUSTER 2.11.6refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.66 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9292 / SU R Cruickshank DPI: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 16730 9.98 %RANDOM
Rwork0.1723 ---
obs0.175 167709 98.45 %-
Displacement parametersBiso max: 236.38 Å2 / Biso mean: 57.03 Å2 / Biso min: 20.94 Å2
Baniso -1Baniso -2Baniso -3
1-6.0751 Å20 Å2-2.111 Å2
2---13.4378 Å20 Å2
3---7.3627 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: final / Resolution: 2.4→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16156 0 190 1371 17717
Biso mean--65.78 63.91 -
Num. residues----2040
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5797SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes433HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2492HARMONIC5
X-RAY DIFFRACTIONt_it16698HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2135SEMIHARMONIC5
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_contact20282SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16698HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg22707HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion19.97
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2574 1116 10.08 %
Rwork0.2288 9950 -
all0.2317 11066 -
obs--87.62 %

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