[English] 日本語
Yorodumi
- PDB-5zxb: Crystal structure of ACK1 with compound 10d -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zxb
TitleCrystal structure of ACK1 with compound 10d
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE / inhibitor / Kinase
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity ...regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / adherens junction / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytoplasmic vesicle membrane / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / Cdc42 binding domain-like / Mig-6 domain / GTPase binding / EGFR receptor inhibitor Mig-6 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / Cdc42 binding domain-like / Mig-6 domain / GTPase binding / EGFR receptor inhibitor Mig-6 / Variant SH3 domain / Src homology 3 domains / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-9KO / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.198 Å
AuthorsHong, E.M. / Kim, H.L. / Sim, T.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
NRF-2016M3A9B5940991 Korea, Republic Of
CitationJournal: J. Med. Chem. / Year: 2018
Title: First SAR Study for Overriding NRAS Mutant Driven Acute Myeloid Leukemia.
Authors: Cho, H. / Shin, I. / Ju, E. / Choi, S. / Hur, W. / Kim, H. / Hong, E. / Kim, N.D. / Choi, H.G. / Gray, N.S. / Sim, T.
History
DepositionMay 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Activated CDC42 kinase 1
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1664
Polymers62,8472
Non-polymers1,3192
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-10 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.182, 43.120, 93.891
Angle α, β, γ (deg.)90.000, 98.340, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 117 through 119 or resid 121...
21(chain B and (resid 117 through 119 or resid 121...

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
11LEULEUCYSCYS(chain A and (resid 117 through 119 or resid 121...AA117 - 1191 - 3
12ILEILEASPASP(chain A and (resid 117 through 119 or resid 121...AA121 - 1345 - 18
13VALVALLEULEU(chain A and (resid 117 through 119 or resid 121...AA139 - 22523 - 109
14GLYGLYTHRTHR(chain A and (resid 117 through 119 or resid 121...AA227 - 319111 - 203
15TRPTRPPHEPHE(chain A and (resid 117 through 119 or resid 121...AA321 - 378205 - 262
16ALAALAALAALA(chain A and (resid 117 through 119 or resid 121...AA380 - 388264 - 272
17GLNGLNGLNGLN(chain A and (resid 117 through 119 or resid 121...AA389273
18LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
19LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
110LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
111LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
112LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
113LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
114LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
115LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
21LEULEUCYSCYS(chain B and (resid 117 through 119 or resid 121...BB117 - 1191 - 3
22ILEILELEULEU(chain B and (resid 117 through 119 or resid 121...BB121 - 1605 - 44
23ALAALATHRTHR(chain B and (resid 117 through 119 or resid 121...BB170 - 31954 - 203
24TRPTRPPHEPHE(chain B and (resid 117 through 119 or resid 121...BB321 - 378205 - 262
25ALAALAGLNGLN(chain B and (resid 117 through 119 or resid 121...BB380 - 389264 - 273

-
Components

#1: Protein Activated CDC42 kinase 1 / ACK-1 / Tyrosine kinase non-receptor protein 2


Mass: 31423.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNK2, ACK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-9KO / N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide


Mass: 659.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H32F3N9O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.3
Details: 0.1M Bis-Tris pH6.3 0.2M AmSO4 28% PEG3350 10mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.198→36.775 Å / Num. obs: 28669 / % possible obs: 98.1 % / Redundancy: 3.8 % / Net I/σ(I): 12.2
Reflection shellResolution: 2.198→2.277 Å

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.198→36.775 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.32
RfactorNum. reflection% reflection
Rfree0.2566 1398 4.88 %
Rwork0.2061 --
obs0.2087 28647 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.57 Å2 / Biso mean: 50.7222 Å2 / Biso min: 26.03 Å2
Refinement stepCycle: final / Resolution: 2.198→36.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 96 93 4051
Biso mean--50.62 46.99 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094080
X-RAY DIFFRACTIONf_angle_d1.4685530
X-RAY DIFFRACTIONf_chiral_restr0.067593
X-RAY DIFFRACTIONf_plane_restr0.008696
X-RAY DIFFRACTIONf_dihedral_angle_d10.6643359
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2188X-RAY DIFFRACTION14.329TORSIONAL
12B2188X-RAY DIFFRACTION14.329TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1976-2.27620.32181210.29982456257789
2.2762-2.36730.33891360.29082661279797
2.3673-2.4750.34831430.27042707285099
2.475-2.60550.31511510.23842728287999
2.6055-2.76870.27561270.22422754288199
2.7687-2.98230.23761280.21512741286999
2.9823-3.28230.28011450.208927622907100
3.2823-3.75680.24091350.18962788292399
3.7568-4.73160.20591520.178427942946100
4.7316-36.780.25361600.19012858301899

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more