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- PDB-5wnh: X-RAY CO-STRUCTURE OF RHO-ASSOCIATED PROTEIN KINASE (ROCK1) WITH ... -

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Basic information

Entry
Database: PDB / ID: 5wnh
TitleX-RAY CO-STRUCTURE OF RHO-ASSOCIATED PROTEIN KINASE (ROCK1) WITH A HIGHLY SELECTIVE INHIBITOR
ComponentsRho-associated protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE inhibitor / RHO KINASE / KINASE INHIBITOR / PHOSPHORYLATION / TRANSFERASE-INHIBITOR COMPLEX / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / myoblast migration / membrane to membrane docking / regulation of keratinocyte differentiation / negative regulation of membrane protein ectodomain proteolysis / positive regulation of connective tissue replacement / response to transforming growth factor beta / regulation of cell junction assembly ...apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / myoblast migration / membrane to membrane docking / regulation of keratinocyte differentiation / negative regulation of membrane protein ectodomain proteolysis / positive regulation of connective tissue replacement / response to transforming growth factor beta / regulation of cell junction assembly / bleb / negative regulation of amyloid precursor protein catabolic process / embryonic morphogenesis / bleb assembly / neuron projection arborization / leukocyte tethering or rolling / negative regulation of biomineral tissue development / regulation of cell motility / positive regulation of amyloid-beta clearance / regulation of establishment of endothelial barrier / response to angiotensin / regulation of synapse maturation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of stress fiber assembly / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / cortical actin cytoskeleton organization / RHOBTB1 GTPase cycle / regulation of neuron differentiation / motor neuron apoptotic process / RND3 GTPase cycle / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / tau-protein kinase activity / regulation of focal adhesion assembly / leukocyte migration / leukocyte cell-cell adhesion / RHOB GTPase cycle / EPHA-mediated growth cone collapse / positive regulation of cardiac muscle hypertrophy / Apoptotic cleavage of cellular proteins / RHOC GTPase cycle / mRNA destabilization / negative regulation of amyloid-beta formation / mitotic cytokinesis / RHOH GTPase cycle / smooth muscle contraction / epithelial to mesenchymal transition / RHOA GTPase cycle / positive regulation of focal adhesion assembly / regulation of synaptic vesicle endocytosis / Rho protein signal transduction / regulation of cell adhesion / negative regulation of protein binding / ruffle / EPHB-mediated forward signaling / positive regulation of autophagy / centriole / regulation of microtubule cytoskeleton organization / regulation of cell migration / negative regulation of angiogenesis / blood vessel diameter maintenance / protein localization to plasma membrane / Rho-dependent protein serine/threonine kinase activity / regulation of actin cytoskeleton organization / small GTPase binding / tau protein binding / Schaffer collateral - CA1 synapse / VEGFA-VEGFR2 Pathway / cytoplasmic stress granule / neuron projection development / peptidyl-serine phosphorylation / G alpha (12/13) signalling events / lamellipodium / actin cytoskeleton organization / secretory granule lumen / Potential therapeutics for SARS / cytoskeleton / non-specific serine/threonine protein kinase / positive regulation of MAPK cascade / intracellular signal transduction / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular region / zinc ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
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. / MRCK kinase PH domain / : / HR1 rho-binding domain / REM-1 domain profile. / Zinc finger phorbol-ester/DAG-type profile. ...Rho-associated protein kinase 1, HR1 / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / MRCK kinase PH domain / : / 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 / 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
Chem-B5G / Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLi, X.
CitationJournal: To Be Published
Title: Novel mechanism of Rho kinase selectivity: beyond the ATP pocket
Authors: Li, X. / Marshall, D. / Sibley, R. / Bosanac, T. / Ginn, J. / Kugler, S. / Gautschi, E. / Molinaro, T. / Soleymanzadeh, L. / Shih, C.K. / Young, E.R.R.
History
DepositionJul 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,9958
Polymers192,0494
Non-polymers1,9464
Water1,42379
1
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9984
Polymers96,0252
Non-polymers9732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-31 kcal/mol
Surface area35730 Å2
MethodPISA
2
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9984
Polymers96,0252
Non-polymers9732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-27 kcal/mol
Surface area35960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.923, 81.975, 167.476
Angle α, β, γ (deg.)90.00, 115.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 48012.285 Da / Num. of mol.: 4 / Fragment: UNP residues 6-415
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL AND KINASE DOMAIN, RESIDUES 6-415 / Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-B5G / (2R)-N-(3-cyanophenyl)-2-{3-[(5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridin-2-yl)carbamoyl]phenyl}pyrrolidine-1-carboxamide


Mass: 486.589 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H26N6O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8.5% PEG3350, 0.1M MES, 50 MM CACL2, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→47.19 Å / Num. obs: 36017 / % possible obs: 98.9 % / Redundancy: 3.48 % / Biso Wilson estimate: 115.1 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 5
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→40 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.921 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.418
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1619 4.5 %RANDOM
Rwork0.227 ---
obs0.227 36012 98.9 %-
Displacement parametersBiso mean: 129.2 Å2
Baniso -1Baniso -2Baniso -3
1-9.4901 Å20 Å2-6.2931 Å2
2---8.2562 Å20 Å2
3----1.2339 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12574 0 140 79 12793
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813028HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9417604HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4570SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes350HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1856HARMONIC5
X-RAY DIFFRACTIONt_it13028HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion21.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1588SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14323SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.212 118 4.06 %
Rwork0.231 2787 -
all0.23 2905 -
obs--98.21 %
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)
11.3767-0.11220.16642.39870.95943.3589-0.1246-0.09420.2715-0.18580.0587-0.3314-0.40550.38850.0659-0.0317-0.0796-0.0944-0.33580.0145-0.1493-19.0327-1.161139.8733
21.2516-0.5034-0.36480.9431-0.55376.95670.19570.3564-0.0492-0.3164-0.33570.16790.1351-0.3980.140.18490.0921-0.0505-0.2881-0.089-0.3505-23.7654-14.8771-12.8347
31.28150.0199-0.27530.97510.22973.53310.04490.3494-0.0796-0.38330.05910.40620.1492-0.1074-0.1040.053-0.0377-0.2166-0.2607-0.0619-0.094-61.8692-18.521227.7504
41.33110.14330.53531.5432-0.57552.9270.1903-0.0751-0.33860.18720.0707-0.18010.28330.0528-0.2610.0415-0.0291-0.1064-0.3349-0.066-0.1147-60.49-27.926881.4296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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