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- PDB-7w7x: The crystal structure of human abl1 kinase domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 7w7x
TitleThe crystal structure of human abl1 kinase domain in complex with ABL1-A11
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE / ABL1
Function / homology
Function and homology information


: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation ...: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / regulation of hematopoietic stem cell differentiation / syntaxin binding / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / neuromuscular process controlling balance / regulation of endocytosis / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / actin monomer binding / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / BMP signaling pathway / mismatch repair / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / peptidyl-tyrosine autophosphorylation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / ruffle / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization / phosphotyrosine residue binding / positive regulation of endothelial cell migration / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / SH2 domain binding / substrate adhesion-dependent cell spreading / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / regulation of autophagy / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
Similarity search - Domain/homology
Chem-8DW / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00000937681 Å
AuthorsZhu, C. / Zhang, Z.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Cell-Active, Reversible, and Irreversible Covalent Inhibitors That Selectively Target the Catalytic Lysine of BCR-ABL Kinase.
Authors: Chen, P. / Sun, J. / Zhu, C. / Tang, G. / Wang, W. / Xu, M. / Xiang, M. / Zhang, C.J. / Zhang, Z.M. / Gao, L. / Yao, S.Q.
History
DepositionDec 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 29, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1
B: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2594
Polymers63,3182
Non-polymers9412
Water8,179454
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-6 kcal/mol
Surface area24060 Å2
Unit cell
Length a, b, c (Å)56.408, 104.878, 132.906
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-894-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRLEULEUchain 'A'AA232 - 2734 - 45
12GLUGLUTHRTHRchain 'A'AA279 - 30651 - 78
13PROPROTHRTHRchain 'A'AA309 - 39281 - 164
14THRTHRSERSERchain 'A'AA394 - 500166 - 272
25TYRTYRLEULEUchain 'B'BB232 - 2734 - 45
26GLUGLUTHRTHRchain 'B'BB279 - 30651 - 78
27PROPROTHRTHRchain 'B'BB309 - 39281 - 164
28THRTHRSERSERchain 'B'BB394 - 500166 - 272

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Components

#1: Protein Tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Abelson tyrosine-protein kinase 1


Mass: 31659.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-8DW / 5-[5-(dimethylcarbamoyl)pyridin-3-yl]-3-(5-fluorosulfonyloxy-2-methoxy-phenyl)-1H-pyrrolo[2,3-b]pyridine


Mass: 470.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19FN4O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.0 M (NH4)2SO4 and 0.1 M HEPES (pH 7.0).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9876 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9876 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 54422 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 3811 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
Cootmodel building
PHASERphasing
autoPROCdata processing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GQG

2gqg


Resolution: 2.00000937681→27.2363369586 Å / SU ML: 0.167729856885 / Cross valid method: FREE R-VALUE / σ(F): 1.36397557522 / Phase error: 18.052788541
RfactorNum. reflection% reflection
Rfree0.194598028559 1987 3.6772462293 %
Rwork0.168323023125 52048 -
obs0.16930251585 54035 99.8761598462 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.8330415441 Å2
Refinement stepCycle: LAST / Resolution: 2.00000937681→27.2363369586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4246 0 66 454 4766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007742680913484427
X-RAY DIFFRACTIONf_angle_d1.167667350556017
X-RAY DIFFRACTIONf_chiral_restr0.0548196255868636
X-RAY DIFFRACTIONf_plane_restr0.00582095924783755
X-RAY DIFFRACTIONf_dihedral_angle_d17.19477776681607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.00001-2.050.2442349135981400.2009614796393671X-RAY DIFFRACTION100
2.05-2.10540.2890681465891400.1984569472663660X-RAY DIFFRACTION100
2.1054-2.16730.2031452393891400.1780958106283689X-RAY DIFFRACTION99.9477943096
2.1673-2.23730.2309380480131400.1746807961173678X-RAY DIFFRACTION100
2.2373-2.31720.2189263146551400.1736008668743649X-RAY DIFFRACTION99.9736147757
2.3172-2.40990.190291235541410.1738653592913687X-RAY DIFFRACTION100
2.4099-2.51950.2083144974961410.1726755773073690X-RAY DIFFRACTION99.9739039666
2.5195-2.65220.1983214146171410.1786924581463704X-RAY DIFFRACTION100
2.6522-2.81830.2090422016251410.1739766971723723X-RAY DIFFRACTION99.9741267788
2.8183-3.03560.2027473959971420.1771802277043700X-RAY DIFFRACTION99.9739786625
3.0356-3.34060.2112540878781420.1750549331983736X-RAY DIFFRACTION99.9484536082
3.3406-3.82290.1711429327561440.1517471350813749X-RAY DIFFRACTION99.9743194658
3.8229-4.81210.1572918124971450.1447754227683802X-RAY DIFFRACTION99.9746707194
4.8121-27.2360.1920394884141500.1751955935733910X-RAY DIFFRACTION98.6634264885
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)
16.547618028381.61421529971-1.129889613283.07608186611-1.794973060274.965230940520.290362647819-0.417807273270.3665639917110.635771065022-0.5573205106450.470461513396-0.167364432297-0.4850083375720.2601095737130.3074674364580.02654544222170.04910719801030.39934939776-0.1503668740450.56200685114648.89123.41720.547
25.53863195083-1.017718725730.9390001307524.03600511687-0.8118472621354.552830350890.2404438004880.0211755302315-0.3638564294910.131490505715-0.08245388195530.2669759943310.346567144593-0.0410332540286-0.1058506524930.266821294368-0.005010391693540.03340972128830.432644281759-0.09862784442030.35731752418453.62915.61517.517
34.082969211162.528315060250.7974142874574.497912710151.981328367783.949096321060.222492494518-0.249702485368-0.1284772584520.339305461698-0.157342825893-0.0787299555472-0.0823687303523-0.28523586448-0.09450158727310.2170913668180.030824888510.02139590278290.272739873046-0.07690123951190.23166431235759.7624.55922.857
41.462553148710.118996486195-0.1109256636731.856061221320.8023454779141.751903309150.0437010781318-0.06173706501690.223595041054-0.0336903891244-0.1227302801970.186542358564-0.102354842545-0.2196278523450.07436555271420.1520623679580.0162434479448-0.01342183009670.172486479009-0.03057026412250.18964383490465.6518.8868.502
52.23943443994-0.8005776639410.1505777474632.071127148010.2736028795232.15999815881-0.00219187550398-0.2578712517560.2522423871590.2829345400690.0136296796624-0.1667737256510.002656216297180.138819373349-0.02101596931580.185188448091-0.01283308994250.00323198171020.203308402539-0.03153390720690.18897851971681.56917.80616.909
63.31386716143-0.1419570332691.125602827433.758349660131.041297518913.39543532332-0.01506524398390.2863129315060.109861808575-0.2551911965480.124855804554-0.280721017930.01265465721720.443247179203-0.1453206901860.2018953894450.007649177293630.08526322553970.277817187714-0.01793159409140.24609532472188.216.0015.13
77.895003120460.43793546361.002410721468.337324522813.140861268218.81778725528-0.1008491253210.8913079102840.320122640229-1.305664746960.0698341735085-0.3006398037-0.877358468918-0.181481661305-0.05383751110590.349176007599-0.001684190015310.03316665969640.2803886927120.07559816799250.26311843120877.13223.694-4.329
84.46624161539-0.567699192949-0.1234839068944.6658118963-1.077967964051.9869796645-0.409977356454-1.05250464319-1.283543883570.1357435198170.1557942488240.2246541573481.088520512550.1780803428220.4184950994420.8320948691810.05586548830390.102596793960.4525360992470.1976219169090.84693062795867.09911.05556.628
94.792745062041.61102176892-1.558809309298.70381805871-0.00304704895133.38143330781-0.355736684395-0.387275069462-0.8393677696230.233153667295-0.1010036291610.2800860239640.7917944580110.3138871001590.3620537224520.7011359800260.144811256476-0.02797337988190.443025123943-0.001233098249710.55766993098573.75815.48853.638
107.54160967686-1.701289576211.937167552554.22524467115-0.1406036874854.19772127618-0.43047178951-1.07199307711-0.4674092978590.732427467190.2873809052390.1559143921280.361546722065-0.3202814931540.194119984130.6533997854730.06043915816840.1084595897550.3675953429730.09773591097190.40337950071963.15420.69758.571
113.317401282020.690354939346-0.9806288624773.20050475614-0.9527618897292.36172922992-0.218402483175-0.359686787198-0.4335913449610.2893160714690.111144880054-0.1512173040080.5852888622240.2328433893130.08557748276130.4496530508120.03709428894290.000947100674480.316607799322-0.06904328609840.35281458121271.56923.28146.884
125.398762224550.298520098036-4.304122255492.086638817190.284584435015.48566968998-0.1262814332350.0113621378529-0.1903042567270.0100728530629-0.07348703910060.1755907915020.306797221602-0.2474958573960.1024249795480.274897769159-0.06910871412040.0001179920762140.271322314317-0.09679424710560.30178996352664.36633.24938.791
137.93243074944-1.07308949199-2.278546768363.128835772410.4652268444073.83442583486-0.180581379922-0.32633567478-0.2622211135070.2493638671690.07731240623260.1058891043960.3091703331930.05846533970630.1237034373610.326437079878-0.0238176880586-0.002824037864670.244256747837-0.04672390042070.24514129554267.27929.92346.366
146.3908577641-2.64256994599-1.424645306543.962363918220.809756527810.365561935017-0.273864281548-0.588006500669-0.3507211956330.5698366548660.1170117533250.03186553167740.4560760499040.160323998690.06255963165860.353404047920.01214933209570.08598394646980.36339212917-0.0003305454172620.2464634488357.9535.12558.748
153.58963595730.298476802021-0.5266721907752.34895841955-0.4435054467061.337508980680.146192787132-0.45158384364-0.05004505044180.283801267418-0.09555285555540.118093514375-4.99244181411E-50.0280182493596-0.024345685360.246573808494-0.07058809384960.0377229071360.325896485915-0.1210055025880.2390346279367.09943.31251.68
161.91968711139-1.56230364475-1.782945632717.637577484914.20308892874.730441514080.155569710824-0.2563230310060.0528343625350.843180168814-0.235658807983-0.07302412980570.1835760184830.195611293591-0.03263285185280.328198246312-0.1621617042620.042325741970.38638444025-0.09106530926650.27400280559876.94149.13951.881
171.116646869551.235479739841.007595919892.997828397591.193932769722.53397200940.04733236541890.01321402739910.245766522432-0.162865120121-0.1114950941590.218195585063-0.03315083995030.01356883392790.05333247193680.204612889001-0.025859729460.02271429465590.254289118896-0.06889349862310.28903957655266.8246.28138.923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 232:247 )A232 - 247
2X-RAY DIFFRACTION2( CHAIN A AND RESID 248:264 )A248 - 264
3X-RAY DIFFRACTION3( CHAIN A AND RESID 265:292 )A265 - 292
4X-RAY DIFFRACTION4( CHAIN A AND RESID 293:379 )A293 - 379
5X-RAY DIFFRACTION5( CHAIN A AND RESID 380:453 )A380 - 453
6X-RAY DIFFRACTION6( CHAIN A AND RESID 454:485 )A454 - 485
7X-RAY DIFFRACTION7( CHAIN A AND RESID 486:500 )A486 - 500
8X-RAY DIFFRACTION8( CHAIN B AND RESID 232:248 )B232 - 248
9X-RAY DIFFRACTION9( CHAIN B AND RESID 249:265 )B249 - 265
10X-RAY DIFFRACTION10( CHAIN B AND RESID 266:292 )B266 - 292
11X-RAY DIFFRACTION11( CHAIN B AND RESID 293:336 )B293 - 336
12X-RAY DIFFRACTION12( CHAIN B AND RESID 337:356 )B337 - 356
13X-RAY DIFFRACTION13( CHAIN B AND RESID 357:379 )B357 - 379
14X-RAY DIFFRACTION14( CHAIN B AND RESID 380:400 )B380 - 400
15X-RAY DIFFRACTION15( CHAIN B AND RESID 401:433 )B401 - 433
16X-RAY DIFFRACTION16( CHAIN B AND RESID 434:453 )B434 - 453
17X-RAY DIFFRACTION17( CHAIN B AND RESID 454:500 )B454 - 500

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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