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- PDB-5cte: Humanized yeast ACC carboxyltransferase domain bound to 2,2-dimet... -

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Basic information

Entry
Database: PDB / ID: 5cte
TitleHumanized yeast ACC carboxyltransferase domain bound to 2,2-dimethylpropyl (1S)-1-methyl-8-[(7-methyl-1H-indazol-5-yl)carbonyl]-2,8-diazaspiro[4.5]decane-2-carboxylate
ComponentsAcetyl-CoA carboxylase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ACC / inhibitors / 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-57L / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,3915
Polymers174,4422
Non-polymers9493
Water16,880937
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-123 kcal/mol
Surface area60500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.340, 138.120, 185.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 2
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-57L / 2,2-dimethylpropyl (1S)-1-methyl-8-[(7-methyl-1H-indazol-5-yl)carbonyl]-2,8-diazaspiro[4.5]decane-2-carboxylate


Mass: 426.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H34N4O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
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: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 94999 / % possible obs: 92 % / Redundancy: 6.8 % / Biso Wilson estimate: 46.19 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.22 / Net I/av σ(I): 21.304 / Net I/σ(I): 8.5 / Num. measured all: 650391
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.34-2.424.50.60261011.01359.6
2.42-2.525.50.61277401.01976.2
2.52-2.646.20.54988411.04686.4
2.64-2.776.70.44499191.0696.8
2.77-2.957.30.312102581.08399.9
2.95-3.187.50.196102641.106100
3.18-3.57.50.117102981.143100
3.5-47.50.072103581.227100
4-5.047.40.058104361.72100
5.04-507.10.036107841.47299.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
BUSTER-TNTBUSTER 2.11.6refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→42.05 Å / Cor.coef. Fo:Fc: 0.9239 / Cor.coef. Fo:Fc free: 0.9066 / SU R Cruickshank DPI: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.246 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.189
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 4686 4.94 %RANDOM
Rwork0.185 ---
obs0.1866 94915 92.36 %-
Displacement parametersBiso max: 182.4 Å2 / Biso mean: 61.02 Å2 / Biso min: 25.74 Å2
Baniso -1Baniso -2Baniso -3
1--19.8026 Å20 Å20 Å2
2--16.7461 Å20 Å2
3---3.0565 Å2
Refine analyzeLuzzati coordinate error obs: 0.299 Å
Refinement stepCycle: final / Resolution: 2.34→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11521 0 135 937 12593
Biso mean--55.5 63.39 -
Num. residues----1449
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4196SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes319HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1748HARMONIC5
X-RAY DIFFRACTIONt_it11905HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1519SEMIHARMONIC5
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_contact14632SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11905HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg16190HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion19.41
LS refinement shellResolution: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2354 204 4.56 %
Rwork0.2155 4267 -
all0.2164 4471 -
obs--59.66 %

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