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- PDB-4bkj: Crystal structure of the human DDR1 kinase domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 4bkj
TitleCrystal structure of the human DDR1 kinase domain in complex with imatinib
ComponentsEPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
KeywordsTRANSFERASE / RECEPTOR / RTK / COLLAGEN / DISCOIDIN DOMAIN / RECEPTOR TYROSINE KINASE
Function / homology
Function and homology information


smooth muscle cell-matrix adhesion / protein tyrosine kinase collagen receptor activity / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / neuron projection extension / peptidyl-tyrosine autophosphorylation ...smooth muscle cell-matrix adhesion / protein tyrosine kinase collagen receptor activity / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / neuron projection extension / peptidyl-tyrosine autophosphorylation / smooth muscle cell migration / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / collagen binding / lactation / transmembrane receptor protein tyrosine kinase activity / embryo implantation / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cell growth / receptor protein-tyrosine kinase / positive regulation of neuron projection development / protein autophosphorylation / cell population proliferation / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / negative regulation of cell population proliferation / extracellular space / extracellular exosome / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / : / Galactose-binding-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-STI / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCanning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Krojer, T. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural Mechanisms Determining Inhibition of the Collagen Receptor Ddr1 by Selective and Multi-Targeted Type II Kinase Inhibitors
Authors: Canning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Krojer, T. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionApr 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2May 7, 2014Group: Database references
Revision 1.3Jun 18, 2014Group: Database references
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
B: EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,67523
Polymers71,5082
Non-polymers2,16621
Water6,756375
1
A: EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,86812
Polymers35,7541
Non-polymers1,11411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,80611
Polymers35,7541
Non-polymers1,05210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.074, 60.074, 180.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 600 - 913 / Label seq-ID: 2 - 315

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.0158, 0.9999, 0.0039), (0.9996, 0.0159, -0.0226), (-0.0226, 0.0036, -0.9997)
Vector: -14.6697, 11.751, 45.5798)

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Components

#1: Protein EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 / EPITHELIAL DISCOIDIN DOMAIN RECEPTOR 1 / CD167 ANTIGEN-LIKE FAMILY MEMBER A / CELL ADHESION KINASE ...EPITHELIAL DISCOIDIN DOMAIN RECEPTOR 1 / CD167 ANTIGEN-LIKE FAMILY MEMBER A / CELL ADHESION KINASE / DISCOIDIN RECEPTOR TYROSINE KINASE / HGK2 / MAMMARY CARCINOMA KINASE 10 / MCK-10 / PROTEIN-TYROSINE KINASE 3A / PROTEIN-TYROSINE KINASE RTK-6 / TRK E / TYROSINE KINASE DDR / TYROSINE-PROTEIN KINASE CAK / CD167A


Mass: 35754.094 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESDIUES 564-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q08345, receptor protein-tyrosine kinase
#2: Chemical ChemComp-STI / 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE / STI-571 / IMATINIB


Mass: 493.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31N7O / Comment: medication, inhibitor*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.28 Å3/Da / Density % sol: 46.11 % / Description: NONE
Crystal growDetails: 0.1M BIS-TRIS PH 6.3, 34% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.712
11K, H, -L20.288
ReflectionResolution: 1.7→45.14 Å / Num. obs: 72847 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZOS

3zos


Resolution: 1.7→45.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.745 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.17556 3690 5.1 %RANDOM
Rwork0.15554 ---
obs0.15656 69069 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.117 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2---17.49 Å20 Å2
3---19.69 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 150 375 5175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194974
X-RAY DIFFRACTIONr_bond_other_d0.0030.024732
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9876733
X-RAY DIFFRACTIONr_angle_other_deg0.886310826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.195610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42423.422225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89115798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3321539
X-RAY DIFFRACTIONr_chiral_restr0.0690.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215589
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021180
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_it1.4783.3692388
X-RAY DIFFRACTIONr_mcbond_other1.4783.3682387
X-RAY DIFFRACTIONr_mcangle_it2.0755.282981
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2484.0862586
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 17287 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 236 -
Rwork0.307 5021 -
obs--99.72 %
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)
12.39850.6278-1.87471.9792-0.41994.54220.0525-0.1034-0.09360.1442-0.0887-0.02770.03910.09950.03620.023-0.0193-0.00540.1549-0.02710.0754-31.072920.675736.9633
23.82770.10861.83952.3636-1.45661.9340.0995-0.1278-0.12470.2924-0.03390.0097-0.0169-0.0127-0.06560.20420.030.00120.1532-0.00570.0589-23.869118.650837.0646
31.52140.98490.2142.45590.02481.01160.06340.03750.05760.2084-0.05840.23380.0235-0.1011-0.0050.02620.01010.01140.1847-0.00940.0378-20.172528.902938.3636
42.0988-0.4497-0.14162.1594-0.36460.8054-0.01390.2725-0.1235-0.0922-0.03490.13880.0545-0.1190.04880.0103-0.0072-0.00730.1521-0.00150.0322-10.094832.874334.9535
51.9249-0.135-0.6361.80620.25321.3453-0.00420.24260.0854-0.13520.0194-0.1715-0.08210.1323-0.01520.0285-0.0209-0.00520.17430.03530.03972.015538.172632.8196
66.3314-0.68321.3613.84320.06093.55360.0932-0.7146-0.40780.2597-0.11320.2933-0.13070.01170.01990.3063-0.124-0.03150.34620.09750.26258.7311-13.486812.313
78.0194-1.7043.23161.21260.154110.3663-0.01480.49520.0485-0.16380.085-0.1367-0.31840.3584-0.07020.3259-0.104-0.06870.237-0.00350.574714.7831-20.3128-0.1982
84.95790.97850.40942.02-0.37741.42450.2017-0.356-0.24920.2284-0.05010.36140.1956-0.3381-0.15160.2116-0.0729-00.22640.00950.14886.0267-5.77387.9647
99.77582.5184-0.65864.7287-0.85313.2559-0.01750.0425-0.5204-0.16150.0015-0.63510.29960.25440.01590.13440.0644-0.0280.16530.02120.166932.9067-3.04310.8607
101.33860.30880.11740.93370.52921.79810.0233-0.1153-0.04940.0359-0.0433-0.01710.0989-0.01440.02010.0090.0021-0.00310.1243-0.00430.006224.073311.926211.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A600 - 638
2X-RAY DIFFRACTION2A639 - 677
3X-RAY DIFFRACTION3A678 - 734
4X-RAY DIFFRACTION4A735 - 813
5X-RAY DIFFRACTION5A814 - 913
6X-RAY DIFFRACTION6B600 - 627
7X-RAY DIFFRACTION7B628 - 650
8X-RAY DIFFRACTION8B651 - 703
9X-RAY DIFFRACTION9B704 - 735
10X-RAY DIFFRACTION10B736 - 913

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