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- PDB-5fut: Human choline kinase a1 in complex with compound 4-(dimethylamino... -

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Basic information

Entry
Database: PDB / ID: 5fut
TitleHuman choline kinase a1 in complex with compound 4-(dimethylamino)-1-{4-[4-(4-{[4-(pyrrolidin- 1-yl)pyridinium-1-yl]methyl}phenyl)butyl]benzyl}pyridinium (compound BR25)
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE / CHOLINE KINASE / PHOSPHATIDYLETANOLAMINE / INHIBITORS
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
Chem-PQ7 / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSerran-Aguilera, L. / Denton, H. / Rubio-Ruiz, B. / Lopez-Gutierrez, B. / Entrena, A. / Izquierdo, L. / Smith, T.K. / Conejo-Garcia, A. / Hurtado-Guerrero, R.
CitationJournal: Sci.Rep. / Year: 2016
Title: Plasmodium Falciparum Choline Kinase Inhibition Leads to a Major Decrease in Phosphatidylethanolamine Causing Parasite Death.
Authors: Serran-Aguilera, L. / Denton, H. / Rubio-Ruiz, B. / Lopez-Gutierrez, B. / Entrena, A. / Izquierdo, L. / Smith, T.K. / Conejo-Garcia, A. / Hurtado-Guerrero, R.
History
DepositionJan 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Data collection / Structure summary
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Jan 10, 2024Group: 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52911
Polymers44,4641
Non-polymers1,06510
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.364, 61.364, 219.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CHOLINE KINASE ALPHA


Mass: 44463.902 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMALC2X / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PQ7 / 4-(dimethylamino)-1-{4-[4-(4-{[4-(pyrrolidin-1-yl)pyridinium-1-yl]methyl}phenyl)butyl]benzyl}pyridinium


Mass: 506.724 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H42N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.33 Å3/Da / Density % sol: 47.11 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: HSCKALPHA1 AT 20 MG/ML WAS PREINCUBATED AT ROOM TEMPERATURE WITH 12 MM OF COMPOUND BR25 IN BUFFER 25 MM TRIS/HCL, 150 MM NACL PH 7.5 (DMSO IS AT 5% FINAL CONCENTRATION IN THE MIX). THE ...Details: HSCKALPHA1 AT 20 MG/ML WAS PREINCUBATED AT ROOM TEMPERATURE WITH 12 MM OF COMPOUND BR25 IN BUFFER 25 MM TRIS/HCL, 150 MM NACL PH 7.5 (DMSO IS AT 5% FINAL CONCENTRATION IN THE MIX). THE SITTING-DROP VAPOUR DIFFUSION METHOD WAS USED TO PRODUCE CRYSTALS BY MIXING 0.5 MICROL OF THE PROTEIN SOLUTION AND AN EQUAL VOLUME OF MOTHER LIQUOR (20% PEG 5000 MME AND 0.2 M KSCN). TETRAGONAL CRYSTALS (SPACE GROUP P43212) GREW WITHIN 2-4 DAYS AND THEN WERE SOAKED FOR ONE DAY WITH 20 MM COMPOUND BR25 SOLVED IN 100% DMSO. THE CRYSTALS USED IN THIS STUDY WERE CRYOPROTECTED IN MOTHER LIQUOR SOLUTIONS CONTAINING 20 % ETHYLENGLYCOL AND FROZEN IN A NITROGEN GAS STREAM COOLED TO 100 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0507
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0507 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 56719 / % possible obs: 99.9 % / Observed criterion σ(I): 44.2 / Redundancy: 25.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 44.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 26.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 6.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_743: ???)refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G15

3g15


Resolution: 1.6→19.701 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 1600 2.8 %
Rwork0.1809 --
obs0.1815 56602 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→19.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 74 278 3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073147
X-RAY DIFFRACTIONf_angle_d1.0654231
X-RAY DIFFRACTIONf_dihedral_angle_d17.2711895
X-RAY DIFFRACTIONf_chiral_restr0.051430
X-RAY DIFFRACTIONf_plane_restr0.006543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65160.23571280.20014916X-RAY DIFFRACTION100
1.6516-1.71060.22361300.19724920X-RAY DIFFRACTION100
1.7106-1.77910.22681400.19344913X-RAY DIFFRACTION100
1.7791-1.860.21561310.19684958X-RAY DIFFRACTION100
1.86-1.9580.20551610.19064884X-RAY DIFFRACTION100
1.958-2.08050.22671510.19444948X-RAY DIFFRACTION100
2.0805-2.24090.20941350.18614973X-RAY DIFFRACTION100
2.2409-2.46610.25191570.19124997X-RAY DIFFRACTION100
2.4661-2.8220.2121550.18495012X-RAY DIFFRACTION100
2.822-3.5520.20491580.18045093X-RAY DIFFRACTION100
3.552-19.70220.17341540.16465388X-RAY DIFFRACTION100
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)
10.9694-0.4209-0.73241.05230.27121.4947-0.07330.0933-0.16290.0437-0.04990.0690.35470.0050.00020.1842-0.00450.01340.1807-0.0310.18446.8793-8.1749-13.5273
20.47360.1662-0.24010.658-0.55260.8395-0.01420.079-0.0390.04530.0193-0.0307-0.011-0.0133-00.174-0.0095-0.00450.1232-0.01190.15413.8491-14.27312.3016
31.48970.7950.04320.8614-0.50580.6167-0.0985-0.0177-0.13360.07140.0728-0.15070.04450.0025-0.0060.19110.0059-0.0140.1177-0.01530.14520.1347-16.478317.1745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 80 THROUGH 207 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 208 THROUGH 351 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 352 THROUGH 457 )

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