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- PDB-2f2u: crystal structure of the Rho-kinase kinase domain -

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Basic information

Entry
Database: PDB / ID: 2f2u
Titlecrystal structure of the Rho-kinase kinase domain
ComponentsRho-associated protein kinase 2
KeywordsTRANSFERASE / enzyme-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
5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE / Rho-associated protein kinase 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYamaguchi, H. / Hakoshima, T.
CitationJournal: Structure / Year: 2006
Title: Molecular mechanism for the regulation of rho-kinase by dimerization and its inhibition by fasudil
Authors: Yamaguchi, H. / Kasa, M. / Amano, M. / Kaibuchi, K. / Hakoshima, T.
History
DepositionNov 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
B: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1354
Polymers91,5522
Non-polymers5832
Water2,918162
1
A: Rho-associated protein kinase 2
hetero molecules

A: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1354
Polymers91,5522
Non-polymers5832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
2
B: Rho-associated protein kinase 2
hetero molecules

B: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1354
Polymers91,5522
Non-polymers5832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)102.531, 102.531, 257.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly for chain A is generated by the two fold axis: y-1, x+1, -z+1 / The second part of the biological assembly for chain B is generated by the two fold axis: y, x, -z+1

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Components

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


Mass: 45776.020 Da / Num. of mol.: 2 / Fragment: protein kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ROCK2 / Plasmid: pFastBac-HTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q28021, EC: 2.7.1.37
#2: Chemical ChemComp-M77 / 5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE / Fasudil / (5-ISOQUINOLINESULFONYL)HOMOPIPERAZINE


Mass: 291.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17N3O2S / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.8M Sodium Citrate, 0.1M Sodium Citrate Buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Apr 20, 2003
Details: a double-crystal monochromator and a horizontal focusing mirror
RadiationMonochromator: a double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 53814 / Num. obs: 52492 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.075
Reflection shellResolution: 2.4→2.49 Å / Rsym value: 0.347 / % possible all: 81

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1APM

1apm


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2663 5.1 %RANDOM
Rwork0.195 ---
all0.197 52481 --
obs0.197 52481 95.92 %-
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: 47.404 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6211 0 40 162 6413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226407
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9638662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3845765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59324.359312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.077151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7011534
X-RAY DIFFRACTIONr_chiral_restr0.1150.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024894
X-RAY DIFFRACTIONr_nbd_refined0.2480.23012
X-RAY DIFFRACTIONr_nbtor_refined0.3240.24527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.210
X-RAY DIFFRACTIONr_mcbond_it1.3481.53831
X-RAY DIFFRACTIONr_mcangle_it2.54726183
X-RAY DIFFRACTIONr_scbond_it3.86632576
X-RAY DIFFRACTIONr_scangle_it6.0714.52479
LS refinement shellResolution: 2.398→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 164 -
Rwork0.282 2959 -
obs-3123 78.86 %

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