[English] 日本語
Yorodumi
- PDB-8bem: STE20-like serine/threonine-protein kinase (SLK) in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bem
TitleSTE20-like serine/threonine-protein kinase (SLK) in complex with Tivozanib
ComponentsSTE20-like serine/threonine-protein kinase
KeywordsTRANSFERASE / Kinase / Typ II inhibitor / SLK / Tivozanib
Function / homology
Function and homology information


regulation of focal adhesion assembly / RHOB GTPase cycle / RHOC GTPase cycle / cell leading edge / RHOA GTPase cycle / cytoplasmic microtubule organization / regulation of cell migration / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase ...regulation of focal adhesion assembly / RHOB GTPase cycle / RHOC GTPase cycle / cell leading edge / RHOA GTPase cycle / cytoplasmic microtubule organization / regulation of cell migration / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Polo kinase kinase / : / Polo kinase kinase / UVR domain / UVR domain profile. / 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 ...Polo kinase kinase / : / Polo kinase kinase / UVR domain / UVR domain profile. / 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
Similarity search - Domain/homology
TIVOZANIB / STE20-like serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKraemer, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: STE20-like serine/threonine-protein kinase (SLK) in complex with Tivozanib
Authors: Kraemer, A. / Doelle, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STE20-like serine/threonine-protein kinase
B: STE20-like serine/threonine-protein kinase
D: STE20-like serine/threonine-protein kinase
G: STE20-like serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,46511
Polymers138,3574
Non-polymers2,1087
Water54030
1
A: STE20-like serine/threonine-protein kinase
G: STE20-like serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2816
Polymers69,1792
Non-polymers1,1024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-34 kcal/mol
Surface area26220 Å2
MethodPISA
2
B: STE20-like serine/threonine-protein kinase
D: STE20-like serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1855
Polymers69,1792
Non-polymers1,0063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-26 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.012, 107.280, 129.400
Angle α, β, γ (deg.)90.000, 95.320, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
STE20-like serine/threonine-protein kinase / STE20-like kinase / hSLK / CTCL tumor antigen se20-9 / STE20-related serine/threonine-protein ...STE20-like kinase / hSLK / CTCL tumor antigen se20-9 / STE20-related serine/threonine-protein kinase / STE20-related kinase / Serine/threonine-protein kinase 2


Mass: 34589.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLK, KIAA0204, STK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2G2, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-AV9 / TIVOZANIB / 1-{2-chloro-4-[(6,7-dimethoxyquinolin-4-yl)oxy]phenyl}-3-[(3E)-5-methylisoxazol-3(2H)-ylidene]urea


Mass: 454.863 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H19ClN4O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350 0.2M Na2SO4 10% Ethylene Glycol 0.1M bis-tris propane 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000031 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.6→49.52 Å / Num. obs: 48206 / % possible obs: 99.2 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.054 / Rrim(I) all: 0.145 / Net I/σ(I): 11 / Num. measured all: 341607 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.697.31.0253229544360.7690.4051.1032.299.6
10.4-49.5270.04455857980.9990.0180.0473199

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.608
Highest resolutionLowest resolution
Rotation48.68 Å2.87 Å

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0352refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HVD

6hvd


Resolution: 2.6→48.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2449 / WRfactor Rwork: 0.213 / FOM work R set: 0.7906 / SU B: 24.644 / SU ML: 0.244 / SU R Cruickshank DPI: 0.5243 / SU Rfree: 0.2927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.524 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 2391 5 %RANDOM
Rwork0.2219 ---
obs0.2236 45795 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.71 Å2 / Biso mean: 53.733 Å2 / Biso min: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-0.43 Å2
2--1.41 Å20 Å2
3---0.45 Å2
Refinement stepCycle: final / Resolution: 2.6→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8477 0 143 30 8650
Biso mean--58.86 39.48 -
Num. residues----1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128878
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168038
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.64112112
X-RAY DIFFRACTIONr_angle_other_deg0.4781.56318641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10251103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.705525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.293101393
X-RAY DIFFRACTIONr_chiral_restr0.0650.21378
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021666
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 150 -
Rwork0.3 3412 -
all-3562 -
obs--99.58 %
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)
12.7202-0.8569-0.32952.43780.74111.50240.0604-0.3546-0.19330.4521-0.05810.15350.14840.017-0.00220.2476-0.0624-0.0580.06210.02610.05725.24449.7483-15.8138
22.65030.90010.82062.49660.49391.2955-0.01940.30510.2018-0.4-0.02090.3137-0.2682-0.12340.04030.25970.0529-0.09120.08970.01860.07191.769822.067-49.3197
32.48581.30530.7942.05950.68371.436-0.06780.0464-0.1519-0.08250.0053-0.13440.21540.09530.06250.20080.0492-0.05580.0595-0.04470.1017-5.4809-15.0204-49.8509
42.3652-1.4056-0.59463.01540.8732.3643-0.0105-0.01640.1558-0.0734-0.0572-0.2269-0.30090.1150.06770.2424-0.0537-0.10530.1058-0.03270.111817.306246.5646-14.0883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 309
2X-RAY DIFFRACTION2B17 - 310
3X-RAY DIFFRACTION3D17 - 310
4X-RAY DIFFRACTION4G17 - 309

+
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