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- PDB-5ar3: RIP2 Kinase Catalytic Domain (1 - 310) complex with AMP-PCP -

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Basic information

Entry
Database: PDB / ID: 5ar3
TitleRIP2 Kinase Catalytic Domain (1 - 310) complex with AMP-PCP
ComponentsRECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
KeywordsTRANSFERASE / KINASE INHIBITOR / STRUCTURE-BASED DRUG DESIGN / INHIBITOR SELECTIVITY
Function / homology
Function and homology information


toll-like receptor 2 signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / caspase binding / LIM domain binding / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / CARD domain binding / JUN kinase kinase kinase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of interferon-alpha production ...toll-like receptor 2 signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / caspase binding / LIM domain binding / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / CARD domain binding / JUN kinase kinase kinase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of interferon-alpha production / positive regulation of interleukin-12 production / canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of interferon-beta production / positive regulation of protein ubiquitination / p75NTR recruits signalling complexes / positive regulation of interleukin-1 beta production / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / non-specific protein-tyrosine kinase / activated TAK1 mediates p38 MAPK activation / non-membrane spanning protein tyrosine kinase activity / NOD1/2 Signaling Pathway / positive regulation of interleukin-6 production / protein homooligomerization / TAK1-dependent IKK and NF-kappa-B activation / T cell receptor signaling pathway / Interleukin-1 signaling / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / Downstream TCR signaling / adaptive immune response / vesicle / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / non-specific serine/threonine protein kinase / positive regulation of apoptotic process / inflammatory response / innate immune response / signaling receptor binding / protein serine kinase activity / apoptotic process / protein serine/threonine kinase activity / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 ...Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Receptor-interacting serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsCharnley, A.K. / Convery, M.A. / Lakdawala Shah, A. / Jones, E. / Hardwicke, P. / Bridges, A. / Votta, B.J. / Gough, P.J. / Marquis, R.W. / Bertin, J. / Casillas, L.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: Crystal Structures of Human Rip2 Kinase Catalytic Domain Complexed with ATP-Competitive Inhibitors: Foundations for Understanding Inhibitor Selectivity.
Authors: Charnley, A.K. / Convery, M.A. / Lakdawala Shah, A. / Jones, E. / Hardwicke, P. / Bridges, A. / Ouellette, M. / Totoritis, R. / Schwartz, B. / King, B.W. / Wisnoski, D.D. / Kang, J. / Eidam, ...Authors: Charnley, A.K. / Convery, M.A. / Lakdawala Shah, A. / Jones, E. / Hardwicke, P. / Bridges, A. / Ouellette, M. / Totoritis, R. / Schwartz, B. / King, B.W. / Wisnoski, D.D. / Kang, J. / Eidam, P.M. / Votta, B.J. / Gough, P.J. / Marquis, R.W. / Bertin, J. / Casillas, L.
History
DepositionSep 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
B: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2716
Polymers75,2122
Non-polymers1,0594
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-45.9 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.566, 131.566, 106.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2 / CARD-CONTAINING INTERLEUKIN-1 BETA-CONVERTING ENZYME-ASSOCIATED KINASE / CARD-CONTAINING IL-1 BETA ...CARD-CONTAINING INTERLEUKIN-1 BETA-CONVERTING ENZYME-ASSOCIATED KINASE / CARD-CONTAINING IL-1 BETA ICE-KINASE / RIP-LIKE-INTERACTING CLARP KINASE / RECEPTOR-INTERACTING PROTEIN 2 / RIP-2 / TYROSINE-PROTEIN KINASE RIPK2 / RECEPTOR-INTERACTING SERINE THREONINE- PROTEIN KINASE 2


Mass: 37605.980 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, UNP RESIDUES 1-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O43353, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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: 3.54 Å3/Da / Density % sol: 65.26 % / Description: NONE
Crystal growDetails: 20% PEG3350, 0.2M NAKTARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Mar 9, 2009 / Details: OSMICS HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.23→40 Å / Num. obs: 72012 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.3
Reflection shellResolution: 3.23→3.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 3.23→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 19.007 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25426 712 4.1 %RANDOM
Rwork0.1896 ---
obs0.19218 16629 99.48 %-
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: 66.104 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å21.56 Å20 Å2
2--1.56 Å20 Å2
3----5.05 Å2
Refinement stepCycle: LAST / Resolution: 3.23→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 64 79 4619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194678
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9796374
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5085549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26923.365211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07115764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0241531
X-RAY DIFFRACTIONr_chiral_restr0.0920.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213549
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4448.7692217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.33719.6642759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1919.0332459
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.233→3.316 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 49 -
Rwork0.263 1226 -
obs--99.45 %

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