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- PDB-5kkn: Crystal structure of human ACC2 BC domain in complex with ND-646,... -

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Basic information

Entry
Database: PDB / ID: 5kkn
TitleCrystal structure of human ACC2 BC domain in complex with ND-646, the primary amide of ND-630
ComponentsAcetyl-CoA carboxylase 2
KeywordsLYASE / biotin-dependent carboxylase / grasp fold
Function / homology
Function and homology information


positive regulation of heart growth / negative regulation of fatty acid beta-oxidation / acetyl-CoA carboxylase / malonyl-CoA biosynthetic process / Biotin transport and metabolism / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity / acetyl-CoA metabolic process / positive regulation of lipid storage / Carnitine shuttle ...positive regulation of heart growth / negative regulation of fatty acid beta-oxidation / acetyl-CoA carboxylase / malonyl-CoA biosynthetic process / Biotin transport and metabolism / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity / acetyl-CoA metabolic process / positive regulation of lipid storage / Carnitine shuttle / regulation of glucose metabolic process / fatty acid homeostasis / energy homeostasis / Activation of gene expression by SREBF (SREBP) / response to nutrient levels / fatty acid biosynthetic process / protein homotetramerization / mitochondrial outer membrane / mitochondrion / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
PreATP-grasp fold / PreATP-grasp domain / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal ...PreATP-grasp fold / PreATP-grasp domain / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Rossmann fold - #20 / 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 / ATP-grasp fold, A 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 / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6U3 / Acetyl-CoA carboxylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsWang, R. / Paul, D. / Tong, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Acetyl-CoA carboxylase inhibition by ND-630 reduces hepatic steatosis, improves insulin sensitivity, and modulates dyslipidemia in rats.
Authors: Harriman, G. / Greenwood, J. / Bhat, S. / Huang, X. / Wang, R. / Paul, D. / Tong, L. / Saha, A.K. / Westlin, W.F. / Kapeller, R. / Harwood, H.J.
History
DepositionJun 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_assembly_auth_evidence ...citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Mar 6, 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 2
C: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3234
Polymers120,1862
Non-polymers1,1372
Water46826
1
B: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6622
Polymers60,0931
Non-polymers5691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Acetyl-CoA carboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6622
Polymers60,0931
Non-polymers5691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.671, 141.671, 163.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsMonomer confirmed by gel filtration

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Components

#1: Protein Acetyl-CoA carboxylase 2 / ACC-beta


Mass: 60092.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACACB, ACC2, ACCB / Production host: Escherichia coli (E. coli)
References: UniProt: O00763, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical ChemComp-6U3 / 2-[1-[(2~{R})-2-(2-methoxyphenyl)-2-(oxan-4-yloxy)ethyl]-5-methyl-6-(1,3-oxazol-2-yl)-2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-3-yl]-2-methyl-propanamide


Mass: 568.641 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H32N4O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 7, 2.8 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 47726 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.6 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.892 / SU B: 21.497 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.43 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26563 2441 5.1 %RANDOM
Rwork0.21966 ---
obs0.22198 45207 92.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7480 0 80 26 7586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.96210571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325943
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11323.904356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.302151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7141553
X-RAY DIFFRACTIONr_chiral_restr0.1140.21163
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215924
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_it0.6651.54758
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31427673
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.10433024
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5984.52898
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.74 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.377 370 -
Rwork0.306 6553 -
obs--93.66 %
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)
10.8497-0.332-0.11770.7035-0.1590.5253-0.0403-0.0323-0.01550.01050.0425-0.02250.0496-0.0367-0.00210.1072-0.10360.01560.13710.02660.066455.497454.265539.8771
20.6944-0.110.15690.74450.33442.36660.0549-0.0733-0.08040.06370.00350.10850.2884-0.4435-0.05840.0491-0.0768-0.00640.13980.02370.123127.768982.77742.0853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B241 - 760
2X-RAY DIFFRACTION1B801 - 915
3X-RAY DIFFRACTION2C241 - 760
4X-RAY DIFFRACTION2C801 - 911

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