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- PDB-2h9v: Structural basis for induced-fit binding of Rho-kinase to the inh... -

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Basic information

Entry
Database: PDB / ID: 2h9v
TitleStructural basis for induced-fit binding of Rho-kinase to the inhibitor Y27632
ComponentsRho-associated protein kinase 2
KeywordsTRANSFERASE / protein kinase-inhibitor complex
Function / homology
Function and homology information


positive regulation of centrosome duplication / Rho-dependent protein serine/threonine kinase activity / regulation of cell junction assembly / embryonic morphogenesis / actomyosin structure organization / cortical actin cytoskeleton organization / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / regulation of actin cytoskeleton organization ...positive regulation of centrosome duplication / Rho-dependent protein serine/threonine kinase activity / regulation of cell junction assembly / embryonic morphogenesis / actomyosin structure organization / cortical actin cytoskeleton organization / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / regulation of actin cytoskeleton organization / regulation of circadian rhythm / small GTPase binding / rhythmic process / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Rho-associated protein kinase 2, HR1 domain / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / : / HR1 rho-binding domain / REM-1 domain profile. / Zinc finger phorbol-ester/DAG-type profile. ...: / Rho-associated protein kinase 2, HR1 domain / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / : / HR1 rho-binding domain / REM-1 domain profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-Y27 / Rho-associated protein kinase 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsYamaguchi, H. / Miwa, Y. / Kasa, M. / Kitano, K. / Amano, M. / Kaibuchi, K. / Hakoshima, T.
CitationJournal: J.Biochem.(Tokyo) / Year: 2006
Title: Structural basis for induced-fit binding of Rho-kinase to the inhibitor Y-27632
Authors: Yamaguchi, H. / Miwa, Y. / Kasa, M. / Kitano, K. / Amano, M. / Kaibuchi, K. / Hakoshima, T.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0232
Polymers45,7761
Non-polymers2471
Water1448
1
A: Rho-associated protein kinase 2
hetero molecules

A: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0474
Polymers91,5522
Non-polymers4952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area4760 Å2
ΔGint-44 kcal/mol
Surface area35430 Å2
MethodPISA
2
A: Rho-associated protein kinase 2
hetero molecules

A: Rho-associated protein kinase 2
hetero molecules

A: Rho-associated protein kinase 2
hetero molecules

A: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,0938
Polymers183,1044
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_555-x+y,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)90.781, 90.781, 341.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Rho-associated protein kinase 2 / Rho-kinase / Rho-associated / coiled- coil-containing protein kinase 2 / p164 ROCK-2


Mass: 45776.020 Da / Num. of mol.: 1 / Fragment: PROTEIN KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pFastBac-HTa / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q28021, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-Y27 / (R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE


Mass: 247.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.5 Å3/Da / Density % sol: 72.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium Citrate, FOS-Choline-9, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 8, 2004
Details: a double-crystal monochromator and a horizontal focusing mirror
RadiationMonochromator: a double-crystal monochromator and a horizontal focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 16013 / % possible obs: 99.5 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.074 / Χ2: 1.211 / Net I/σ(I): 29.988
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsΧ2
3.1-3.2199.9130.2369.78815550.819
3.21-3.3499.713.70.20212.24515500.899
3.34-3.4999.614.40.15717.0815681.082
3.49-3.6799.7150.12721.71315421.185
3.67-3.999.615.30.10527.77715711.308
3.9-4.2199.115.20.08733.2215751.395
4.21-4.6399.115.20.07739.07815841.488
4.63-5.2999.515.50.0740.09916091.317
5.29-6.6699.516.10.06542.39716541.212
6.66-3099.115.40.0551.26818051.275

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.46 / Cor.coef. Fo:Fc: 0.501
Highest resolutionLowest resolution
Rotation3 Å29.72 Å
Translation3 Å29.72 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.749 / SU ML: 0.292 / SU R Cruickshank DPI: 0.784 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397
RfactorNum. reflection% reflectionSelection details
Rfree0.277 800 5 %RANDOM
Rwork0.232 ---
all0.234 15995 --
obs0.234 15995 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.967 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20.76 Å20 Å2
2--1.52 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 18 8 3120
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01631870.022
X-RAY DIFFRACTIONr_angle_refined_deg1.71843041.961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3093815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75515624.295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45755915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2821815
X-RAY DIFFRACTIONr_chiral_restr0.1134570.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00524310.02
X-RAY DIFFRACTIONr_nbd_refined0.26417250.2
X-RAY DIFFRACTIONr_nbtor_refined0.33522390.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1621500.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.222540.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.19820.2
X-RAY DIFFRACTIONr_mcbond_it0.77119391.5
X-RAY DIFFRACTIONr_mcangle_it1.42730752
X-RAY DIFFRACTIONr_scbond_it1.714033
X-RAY DIFFRACTIONr_scangle_it2.912294.5
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 68 -
Rwork0.279 1047 -
obs--98.24 %

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