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- PDB-2cke: Human death-associated DRP-1 kinase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2cke
TitleHuman death-associated DRP-1 kinase in complex with inhibitor
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 2
KeywordsTRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX / CALMODULIN-BINDING / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / APOPTOSIS
Function / homology
Function and homology information


positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / Caspase activation via Dependence Receptors in the absence of ligand / anoikis / positive regulation of neutrophil chemotaxis / protein autophosphorylation / cytoplasmic vesicle / regulation of apoptotic process ...positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / Caspase activation via Dependence Receptors in the absence of ligand / anoikis / positive regulation of neutrophil chemotaxis / protein autophosphorylation / cytoplasmic vesicle / regulation of apoptotic process / calmodulin binding / protein phosphorylation / non-specific serine/threonine protein kinase / regulation of autophagy / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-(2-AMINOETHYL)ISOQUINOLINE-5-SULFONAMIDE / Death-associated protein kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKursula, P. / Wilmanns, M.
CitationJournal: To be Published
Title: Crystal Structure of Human Drp-1 Complexed with an Inhibitor
Authors: Kursula, P. / Wilmanns, M.
History
DepositionApr 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEATH-ASSOCIATED PROTEIN KINASE 2
B: DEATH-ASSOCIATED PROTEIN KINASE 2
C: DEATH-ASSOCIATED PROTEIN KINASE 2
D: DEATH-ASSOCIATED PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,6718
Polymers148,6664
Non-polymers1,0054
Water1,08160
1
A: DEATH-ASSOCIATED PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4182
Polymers37,1671
Non-polymers2511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DEATH-ASSOCIATED PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4182
Polymers37,1671
Non-polymers2511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DEATH-ASSOCIATED PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4182
Polymers37,1671
Non-polymers2511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DEATH-ASSOCIATED PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4182
Polymers37,1671
Non-polymers2511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.210, 60.480, 99.280
Angle α, β, γ (deg.)92.09, 103.39, 94.16
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DEATH-ASSOCIATED PROTEIN KINASE 2 / HUMAN DRP-1 KINASE / DAP KINASE 2 / DAP-KINASE- RELATED PROTEIN 1 / DRP-1


Mass: 37166.504 Da / Num. of mol.: 4 / Fragment: RESIDUES 11-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDEST-15 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3) / Variant (production host): PLYSS
References: UniProt: Q9UIK4, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-IQU / N-(2-AMINOETHYL)ISOQUINOLINE-5-SULFONAMIDE


Mass: 251.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13N3O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.32 Å3/Da / Density % sol: 46.48 %
Crystal growpH: 8.5
Details: 0.2 M LI SULFATE, 0.1 M TRIS PH 8.5, 25 % PEG 4000, 15 % GLYCEROL, 10 MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.814
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.814 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 30010 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A2A

2a2a


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / SU B: 37.206 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1497 5 %RANDOM
Rwork0.203 ---
obs0.206 28431 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20.1 Å20.72 Å2
2---1.03 Å21.74 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9776 0 68 60 9904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210040
X-RAY DIFFRACTIONr_bond_other_d0.0010.026962
X-RAY DIFFRACTIONr_angle_refined_deg0.8821.9713550
X-RAY DIFFRACTIONr_angle_other_deg0.738316967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.10351197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91424.48500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.269151859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6841564
X-RAY DIFFRACTIONr_chiral_restr0.0510.21509
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022041
X-RAY DIFFRACTIONr_nbd_refined0.1890.21944
X-RAY DIFFRACTIONr_nbd_other0.1680.26865
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24871
X-RAY DIFFRACTIONr_nbtor_other0.0790.25316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.42526304
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74139720
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.55944359
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8653830
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: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 110
Rwork0.296 2087
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)
11.5228-0.75940.38541.9066-1.49692.6029-0.0847-0.03870.08830.19170.1393-0.063-0.174-0.1393-0.0546-0.0657-0.0627-0.0125-0.1082-0.0651-0.1271-0.2394-0.55621.8545
22.37691.64260.02112.78290.58061.3298-0.0082-0.0602-0.08540.0606-0.0039-0.26730.06840.17160.0121-0.12380.09730.0121-0.09090.0129-0.074-21.402911.666827.8406
32.3746-1.26510.05592.4522-0.42631.48360.0593-0.0328-0.3234-0.0313-0.13280.14820.1211-0.10540.0735-0.1717-0.04130.0114-0.0765-0.0052-0.1203-34.483-19.803953.1786
41.56730.76580.22373.08771.62752.82930.0820.090.1132-0.1349-0.13280.1581-0.281-0.00410.0508-0.1370.0080.0149-0.15240.0346-0.1245-54.3266-34.753178.3176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION1A1302
3X-RAY DIFFRACTION2B2 - 301
4X-RAY DIFFRACTION2B1302
5X-RAY DIFFRACTION3C2 - 301
6X-RAY DIFFRACTION3C1302
7X-RAY DIFFRACTION4D2 - 301
8X-RAY DIFFRACTION4D1302

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