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- PDB-4br3: Determination of potential scaffolds for human choline kinase alp... -

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Basic information

Entry
Database: PDB / ID: 4br3
TitleDetermination of potential scaffolds for human choline kinase alpha 1 by chemical deconvolution studies
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / ethanolamine kinase activity / Synthesis of PE / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / Synthesis of PE / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity / lipid transport / Synthesis of PC / cellular response to glucose starvation / lipid droplet / lipid metabolic process / protein tyrosine kinase activity / protein homodimerization activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Choline/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-benzyladenine / PHOSPHATE ION / Chem-U85 / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSahun-Roncero, M. / Rubio-Ruiz, B. / Conejo-Garcia, A. / Velazquez-Campoy, A. / Entrena, A. / Hurtado-Guerrero, R.
CitationJournal: Chembiochem / Year: 2013
Title: Determination of Potential Scaffolds for Human Choline Kinase Alpha 1 by Chemical Deconvolution Studies
Authors: Sahun-Roncero, M. / Rubio-Ruiz, B. / Conejo-Garcia, A. / Velazquez-Campoy, A. / Entrena, A. / Hurtado-Guerrero, R.
History
DepositionJun 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3Mar 25, 2015Group: Structure summary
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: CHOLINE KINASE ALPHA
B: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3297
Polymers89,9092
Non-polymers1,4215
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-17.3 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.737, 122.254, 132.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 82 - 457 / Label seq-ID: 8 - 383

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.2483, -0.8553, 0.454), (-0.8579, -0.4122, -0.3069), (0.4499, -0.3139, -0.8361)
Vector: -3.859, 12.7, 33.89)

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Components

#1: Protein CHOLINE KINASE ALPHA / CK / CHETK-ALPHA / EK / CHOLINE KINASE A1 / ETHANOLAMINE KINASE


Mass: 44954.457 Da / Num. of mol.: 2 / Fragment: RESIDUES 75-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P35790, choline kinase, ethanolamine kinase
#2: Chemical ChemComp-U85 / 1-((4'-((6-amino-3H-purin-3-yl)methyl)biphenyl-4-yl)methyl)-4-(dimethylamino)pyridinium


Mass: 436.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H26N7
#3: Chemical ChemComp-A4V / 3-benzyladenine


Mass: 226.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N5 / Comment: inhibitor*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.89 % / Description: NONE

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.872
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 46439 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G15

3g15


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.34 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25764 1189 2.6 %RANDOM
Rwork0.20778 ---
obs0.20904 45200 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.986 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20 Å2
2--3.84 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5847 0 105 181 6133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196130
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9888264
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12323.333303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.547151103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1251546
X-RAY DIFFRACTIONr_chiral_restr0.1060.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214696
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 426 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 71 -
Rwork0.307 3179 -
obs--97.22 %
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)
10.035-0.1117-0.12940.46960.15751.24630.0130.00130.0047-0.0148-0.00320.00720.0249-0.0732-0.00980.0408-0.03570.0280.1042-0.04180.0256-12.5196-6.97785.1664
20.3980.4258-0.06680.74090.31310.552-0.06130.00750.011-0.03380.01790.01420.03810.01560.04350.02290.0017-0.02860.0602-0.00810.08361.60624.528526.2753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 457
2X-RAY DIFFRACTION2B82 - 457

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