[English] 日本語
Yorodumi
- PDB-5owq: Human STK10 bound to dovitinib -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5owq
TitleHuman STK10 bound to dovitinib
ComponentsSerine/threonine-protein kinase 10Serine/threonine-specific protein kinase
KeywordsTRANSFERASE / Kinase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation ...lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / Polo kinase kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / Polo kinase kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-38O / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSzklarz, M. / von Delft, F. / Bountra, C. / Knapp, S. / Edwards, A.M. / Arrowsmith, C. / Elkins, J.M.
CitationJournal: To Be Published
Title: Human STK10 bound to dovitinib
Authors: Elkins, J.M.
History
DepositionSep 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase 10
B: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3824
Polymers68,5972
Non-polymers7852
Water0
1
A: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6912
Polymers34,2991
Non-polymers3921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6912
Polymers34,2991
Non-polymers3921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-26 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.570, 50.400, 114.570
Angle α, β, γ (deg.)90.00, 96.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A32 - 316
2010B32 - 316

-
Components

#1: Protein Serine/threonine-protein kinase 10 / Serine/threonine-specific protein kinase / Lymphocyte-oriented kinase


Mass: 34298.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK10, LOK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3)
References: UniProt: O94804, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-38O / 4-amino-5-fluoro-3-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one / Dovitinib / Fibroblast growth factor receptor 1


Mass: 392.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21FN6O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium formate, 15%(w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.7→57.19 Å / Num. obs: 16619 / % possible obs: 91.4 % / Redundancy: 2.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.7
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2672 / CC1/2: 0.692 / % possible all: 91.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STK10

Resolution: 2.7→57.19 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.879 / SU B: 50.88 / SU ML: 0.443 / Cross valid method: THROUGHOUT / ESU R: 6.612 / ESU R Free: 0.433 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30495 838 5.1 %RANDOM
Rwork0.26322 ---
obs0.26535 15674 90.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.895 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å21.36 Å2
2---0.89 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.7→57.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 58 0 3901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193990
X-RAY DIFFRACTIONr_bond_other_d0.0020.023690
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9635440
X-RAY DIFFRACTIONr_angle_other_deg1.062.9818525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96425.166151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04415638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7141514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02732
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_it0.8171.7682026
X-RAY DIFFRACTIONr_mcbond_other0.8171.7682025
X-RAY DIFFRACTIONr_mcangle_it1.4952.6472515
X-RAY DIFFRACTIONr_mcangle_other1.4952.6482516
X-RAY DIFFRACTIONr_scbond_it0.8582.051964
X-RAY DIFFRACTIONr_scbond_other0.8592.0541965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5353.0552926
X-RAY DIFFRACTIONr_long_range_B_refined3.86922.4944387
X-RAY DIFFRACTIONr_long_range_B_other3.86922.5234388
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14820 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 43 -
Rwork0.409 1153 -
obs--89.59 %
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)
17.2907-0.69881.13826.4747-1.95450.82120.0523-0.0561-0.5269-0.1832-0.4305-1.70.04890.35690.37820.76690.06730.21260.5510.04090.601214.0939.51853.047
22.0970.8059-0.96152.8066-1.60793.5116-0.03280.36450.2332-0.24380.11520.0165-0.0336-0.1558-0.08240.46620.00870.23290.06390.04760.1491-5.26511.07439.575
32.57054.26361.44168.96750.05097.23960.4972-0.5835-0.31661.5981-0.6601-0.9777-0.41450.62120.16290.71560.09960.02440.7246-0.08050.446734.49238.02820.018
42.04271.1124-1.02943.4038-1.62623.5407-0.11150.0069-0.0522-0.0860.23460.20980.2575-0.4365-0.12310.4355-0.03420.22710.11250.02430.151213.85335.8768.865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 112
2X-RAY DIFFRACTION2A113 - 317
3X-RAY DIFFRACTION3B1 - 112
4X-RAY DIFFRACTION4B113 - 317

+
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