[English] 日本語
Yorodumi
- PDB-5cte: Humanized yeast ACC carboxyltransferase domain bound to 2,2-dimet... -

+
Open data


ID or keywords:

Loading...

-
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 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 biosynthetic process / acetyl-CoA carboxylase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more