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- PDB-4wz8: Crystal structure of human-yeast chimera acetyl coA carboxylase C... -

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Basic information

Entry
Database: PDB / ID: 4wz8
TitleCrystal structure of human-yeast chimera acetyl coA carboxylase CT domain bound to Compound 6
ComponentsAcetyl-CoA carboxylase
KeywordsLIGASE/LIGASE INHIBITOR / ACC / acetyl-coA / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process ...Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / 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 / protein import into nucleus / fatty acid biosynthetic process / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / metal ion binding / identical protein 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-3W7 / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.23 Å
AuthorsVajdos, F.F.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Decreasing the Rate of Metabolic Ketone Reduction in the Discovery of a Clinical Acetyl-CoA Carboxylase Inhibitor for the Treatment of Diabetes.
Authors: Griffith, D.A. / Kung, D.W. / Esler, W.P. / Amor, P.A. / Bagley, S.W. / Beysen, C. / Carvajal-Gonzalez, S. / Doran, S.D. / Limberakis, C. / Mathiowetz, A.M. / McPherson, K. / Price, D.A. / ...Authors: Griffith, D.A. / Kung, D.W. / Esler, W.P. / Amor, P.A. / Bagley, S.W. / Beysen, C. / Carvajal-Gonzalez, S. / Doran, S.D. / Limberakis, C. / Mathiowetz, A.M. / McPherson, K. / Price, D.A. / Ravussin, E. / Sonnenberg, G.E. / Southers, J.A. / Sweet, L.J. / Turner, S.M. / Vajdos, F.F.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)175,2254
Polymers174,4422
Non-polymers7832
Water27,4011521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-96 kcal/mol
Surface area56680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.520, 138.030, 184.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a dimer.

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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: Carboxyl transferase 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)
Strain: ATCC 204508 / S288c / Gene: ACC1, ABP2, FAS3, MTR7, YNR016C, N3175 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical ChemComp-3W7 / 1'-(2H-indazol-5-ylcarbonyl)-1-(propan-2-yl)-1,4-dihydrospiro[indazole-5,4'-piperidin]-7(6H)-one


Mass: 391.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1521 / 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: 64.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM NaCitrate, 12%(w/v) PEG8000, 150 mM LiSO4, 7.5% (v/v) glycerol, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.226→184.83 Å / Num. all: 116347 / Num. obs: 116347 / % possible obs: 98.1 % / Redundancy: 5 % / Biso Wilson estimate: 38.09 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.095 / Rsym value: 0.077 / Net I/av σ(I): 9.527 / Net I/σ(I): 14.4 / Num. measured all: 582564
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
2.23-2.354.90.4971.483581169670.2740.4972.999.1
2.35-2.4950.3362.380630160710.1790.3364.198.8
2.49-2.6650.2553.175948151220.1350.2555.499
2.66-2.8750.1744.470810140550.0910.1747.598.4
2.87-3.155.10.11765600129300.0570.1111.198.3
3.15-3.5250.06811.258863116730.0350.06817.998
3.52-4.0650.0431751435102780.0220.04327.797.3
4.06-4.9850.03122.84375786930.0160.03136.496.7
4.98-7.0450.031233391467580.0150.03136.496.3
7.04-184.834.70.02128.71802638000.0110.02144.594.3

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.23→110.59 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.9187 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.191 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 5766 4.99 %RANDOM
Rwork0.1773 ---
obs0.1789 115579 97.77 %-
Displacement parametersBiso max: 145.21 Å2 / Biso mean: 41.79 Å2 / Biso min: 14.23 Å2
Baniso -1Baniso -2Baniso -3
1--9.4165 Å20 Å20 Å2
2--8.473 Å20 Å2
3---0.9435 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: final / Resolution: 2.23→110.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11149 0 58 1521 12728
Biso mean--33.14 52.08 -
Num. residues----1396
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4029SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes312HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1663HARMONIC5
X-RAY DIFFRACTIONt_it11452HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1457SEMIHARMONIC5
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_contact14543SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11452HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15516HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion18.9
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2704 412 4.84 %
Rwork0.237 8098 -
all0.2386 8510 -
obs--97.77 %

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