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- PDB-3d9v: CRYSTAL STRUCTURE OF ROCK I BOUND TO H-1152P A DI-METHYLATED VARI... -

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Basic information

Entry
Database: PDB / ID: 3d9v
TitleCRYSTAL STRUCTURE OF ROCK I BOUND TO H-1152P A DI-METHYLATED VARIANT OF FASUDIL
ComponentsRho-associated protein kinase 1
KeywordsTRANSFERASE / DIMER / DIMERIZATION / KINASE / PHOSPHORYLATION / FASUDIL / Apoptosis / ATP-binding / Coiled coil / Cytoplasm / Golgi apparatus / Membrane / Metal-binding / Nucleotide-binding / Phorbol-ester binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Zinc / Zinc-finger
Function / homology
Function and homology information


regulation of amyloid-beta formation / regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / regulation of keratinocyte differentiation / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking ...regulation of amyloid-beta formation / regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / regulation of keratinocyte differentiation / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis / response to transforming growth factor beta / negative regulation of myosin-light-chain-phosphatase activity / regulation of cell junction assembly / positive regulation of dephosphorylation / negative regulation of bicellular tight junction assembly / regulation of synapse maturation / bleb / positive regulation of amyloid-beta clearance / negative regulation of amyloid precursor protein catabolic process / neuron projection arborization / bleb assembly / embryonic morphogenesis / leukocyte tethering or rolling / negative regulation of biomineral tissue development / negative regulation of phosphorylation / actomyosin structure organization / aspartic-type endopeptidase inhibitor activity / regulation of establishment of endothelial barrier / RHO GTPases Activate ROCKs / negative regulation of motor neuron apoptotic process / regulation of stress fiber assembly / regulation of cell motility / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / response to angiotensin / regulation of establishment of cell polarity / motor neuron apoptotic process / RHOBTB1 GTPase cycle / RND3 GTPase cycle / regulation of synaptic vesicle endocytosis / cortical actin cytoskeleton organization / regulation of neuron differentiation / regulation of focal adhesion assembly / leukocyte cell-cell adhesion / RHOB GTPase cycle / tau-protein kinase activity / leukocyte migration / negative regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / Apoptotic cleavage of cellular proteins / positive regulation of focal adhesion assembly / RHOH GTPase cycle / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / RHOA GTPase cycle / epithelial to mesenchymal transition / canonical NF-kappaB signal transduction / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / regulation of cell adhesion / regulation of cell migration / ruffle / EPHB-mediated forward signaling / centriole / blood vessel diameter maintenance / negative regulation of angiogenesis / negative regulation of protein binding / regulation of autophagy / protein localization to plasma membrane / regulation of actin cytoskeleton organization / tau protein binding / Schaffer collateral - CA1 synapse / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic stress granule / neuron projection development / G alpha (12/13) signalling events / lamellipodium / actin cytoskeleton organization / peptidyl-serine phosphorylation / secretory granule lumen / Potential therapeutics for SARS / positive regulation of MAPK cascade / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular region / ATP binding
Similarity search - Function
Rho-associated protein kinase 1, HR1 / 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 ...Rho-associated protein kinase 1, HR1 / 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-H52 / Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsJacobs, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The structure of dimeric ROCK I reveals the mechanism for ligand selectivity.
Authors: Jacobs, M. / Hayakawa, K. / Swenson, L. / Bellon, S. / Fleming, M. / Taslimi, P. / Doran, J.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionJun 10, 2008ID: 2ETO
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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 1
B: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6634
Polymers96,0252
Non-polymers6392
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-30 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.625, 183.625, 91.666
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Rho-associated protein kinase 1 / Rho-associated / coiled-coil-containing protein kinase 1 / p160 ROCK-1 / p160ROCK / Renal carcinoma ...Rho-associated / coiled-coil-containing protein kinase 1 / p160 ROCK-1 / p160ROCK / Renal carcinoma antigen NY-REN-35


Mass: 48012.285 Da / Num. of mol.: 2 / Fragment: N-terminal and kinase domain, residues 6-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Plasmid: PBEV10 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-H52 / (S)-2-METHYL-1-[(4-METHYL-5-ISOQUINOLINE)SULFONYL]-HOMOPIPERAZINE


Mass: 319.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O2S

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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: 4.65 Å3/Da / Density % sol: 73.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 4.5% PEG3350, 100mM MES, PH 5.5,0.45mM PROTEIN, 50mM CACL2, 10mM DTT, pH 5.50, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2003
RadiationMonochromator: DOUBLE-CRYSTAL SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→28.99 Å / Num. obs: 26858 / % possible obs: 99.4 % / Redundancy: 6.11 % / Rmerge(I) obs: 0.121 / Χ2: 0.9 / Net I/σ(I): 11.7 / Scaling rejects: 8643
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
3.3-3.426.170.36951728027021.04100
3.42-3.555.840.3526.81705526531.199.9
3.55-3.726.230.296.91729026721.01100
3.72-3.916.20.2068.11729026590.99100
3.91-4.166.020.2029.6174022682199.9
4.16-4.486.210.12711.11759427030.999.6
4.48-4.926.170.097131718226380.8499.4
4.92-5.636.230.09513.91756027120.7799.4
5.63-7.086.170.08214.81742527200.7199.1
7.08-28.995.890.03827.81675727170.6697

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
RefinementResolution: 3.3→28.99 Å / FOM work R set: 0.802 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.28 1344 5 %
Rwork0.262 --
obs-26470 98 %
Displacement parametersBiso mean: 64.548 Å2
Baniso -1Baniso -2Baniso -3
1-0.038 Å20.111 Å20 Å2
2--0.038 Å20 Å2
3----0.076 Å2
Refinement stepCycle: LAST / Resolution: 3.3→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 44 0 6517
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5151.5
X-RAY DIFFRACTIONc_scbond_it1.6912
X-RAY DIFFRACTIONc_mcangle_it2.7142
X-RAY DIFFRACTIONc_scangle_it2.8882.5
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angle_d1.17
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5inhib.par

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