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- PDB-3tdc: Crystal Structure of Human Acetyl-CoA carboxylase 2 -

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Basic information

Entry
Database: PDB / ID: 3tdc
TitleCrystal Structure of Human Acetyl-CoA carboxylase 2
ComponentsAcetyl-CoA carboxylase 2 variant
KeywordsLIGASE/LIGASE INHIBITOR / biotin / malonyl-CoA / carboxylase / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


intracellular aspartate homeostasis / lactic acid secretion / mitochondrial fatty acid beta-oxidation multienzyme complex / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of heart growth / Biotin transport and metabolism / acetyl-CoA carboxylase / negative regulation of fatty acid beta-oxidation / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process ...intracellular aspartate homeostasis / lactic acid secretion / mitochondrial fatty acid beta-oxidation multienzyme complex / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of heart growth / Biotin transport and metabolism / acetyl-CoA carboxylase / negative regulation of fatty acid beta-oxidation / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / tricarboxylic acid metabolic process / acetyl-CoA carboxylase activity / ChREBP activates metabolic gene expression / intracellular glutamate homeostasis / positive regulation of lipid storage / Carnitine metabolism / pentose-phosphate shunt / biotin binding / glucose import / fatty acid oxidation / regulation of glucose metabolic process / energy homeostasis / response to nutrient / Activation of gene expression by SREBF (SREBP) / response to organic cyclic compound / fatty acid biosynthetic process / protein homotetramerization / mitochondrial outer membrane / response to xenobiotic stimulus / negative regulation of gene expression / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / 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 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 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / 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-0EU / Acetyl-CoA carboxylase 2 / Acetyl-CoA carboxylase 2 variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsDougan, D.R. / Mol, C.D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Design, synthesis, and structure-activity relationships of spirolactones bearing 2-ureidobenzothiophene as acetyl-CoA carboxylases inhibitors.
Authors: Yamashita, T. / Kamata, M. / Endo, S. / Yamamoto, M. / Kakegawa, K. / Watanabe, H. / Miwa, K. / Yamano, T. / Funata, M. / Sakamoto, J. / Tani, A. / Mol, C.D. / Zou, H. / Dougan, D.R. / Sang, ...Authors: Yamashita, T. / Kamata, M. / Endo, S. / Yamamoto, M. / Kakegawa, K. / Watanabe, H. / Miwa, K. / Yamano, T. / Funata, M. / Sakamoto, J. / Tani, A. / Mol, C.D. / Zou, H. / Dougan, D.R. / Sang, B. / Snell, G. / Fukatsu, K.
History
DepositionAug 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 2 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1042
Polymers86,5911
Non-polymers5131
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Acetyl-CoA carboxylase 2 variant
hetero molecules

A: Acetyl-CoA carboxylase 2 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,2074
Polymers173,1822
Non-polymers1,0252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area14100 Å2
ΔGint-105 kcal/mol
Surface area61740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.921, 119.756, 146.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acetyl-CoA carboxylase 2 variant


Mass: 86591.008 Da / Num. of mol.: 1 / Fragment: UNP residues 921-1676
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q59GJ9, UniProt: O00763*PLUS, acetyl-CoA carboxylase
#2: Chemical ChemComp-0EU / 1-[3-({4-[(5S)-3,3-dimethyl-1-oxo-2-oxa-7-azaspiro[4.5]dec-7-yl]piperidin-1-yl}carbonyl)-1-benzothiophen-2-yl]-3-ethylurea


Mass: 512.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36N4O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6.8% PEG MME 2000, 0.0175M Ammonium Sulfate, 0.1M MES , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 39078 / Num. obs: 37827 / % possible obs: 96.81 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.2

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UYT

1uyt


Resolution: 2.41→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.949 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21788 1874 5 %RANDOM
Rwork0.16918 ---
obs0.17163 35745 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2--1.73 Å20 Å2
3----2.62 Å2
Refinement stepCycle: LAST / Resolution: 2.41→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 36 456 6254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9678103
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08323.799279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.367151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9451542
X-RAY DIFFRACTIONr_chiral_restr0.0840.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1921.53584
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1425809
X-RAY DIFFRACTIONr_scbond_it3.60932388
X-RAY DIFFRACTIONr_scangle_it5.4524.52294
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 130 -
Rwork0.237 2055 -
obs--77.37 %
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)
10.5428-0.0501-0.20940.9688-0.08351.25430.02740.1459-0.09-0.25390.03570.12790.3175-0.0672-0.06310.1516-0.0102-0.06320.0622-0.03420.059813.858938.183450.5838
21.82050.7088-1.17152.3289-0.54272.3476-0.04280.17490.1131-0.360.1315-0.1469-0.0116-0.0581-0.08880.0676-0.01480.02490.04670.01550.035127.054272.153427.8607
30.2197-0.08080.15420.2875-0.09270.99350.0184-0.0176-0.03060.0069-0.015-0.05720.11550.1648-0.00340.01490.0165-0.0070.06930.0110.056427.754646.967685.1999
44.1117-1.99371.47011.1467-1.26182.2385-0.2217-0.05550.32350.14130.1659-0.1364-0.1493-0.48620.05580.0573-0.00430.01590.15720.01750.0966-7.851144.941587.6348
512.92963.429-1.56126.303110.955624.18270.17280.10010.62460.10050.3754-0.05660.09840.8907-0.54820.09940.12180.02480.25310.07580.12636.455463.548850.009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1719 - 1862
2X-RAY DIFFRACTION2A1863 - 1935
3X-RAY DIFFRACTION3A1936 - 2351
4X-RAY DIFFRACTION4A2352 - 2451
5X-RAY DIFFRACTION5A3000

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