[English] 日本語
Yorodumi
- PDB-5ukf: Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ukf
TitleCrystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTransferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation ...histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / Cajal body / nucleosomal DNA binding / neuron projection development / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / nucleolus / protein kinase binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8E1 / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCounago, R.M. / Wells, C. / Zuercher, W. / Willson, T.M. / Bountra, C. / Edwards, A.M. / Arruda, P. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: Sci Rep / Year: 2017
Title: Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Authors: Counago, R.M. / Allerston, C.K. / Savitsky, P. / Azevedo, H. / Godoi, P.H. / Wells, C.I. / Mascarello, A. / de Souza Gama, F.H. / Massirer, K.B. / Zuercher, W.J. / Guimaraes, C.R.W. / Gileadi, O.
History
DepositionJan 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase VRK1
B: Serine/threonine-protein kinase VRK1
C: Serine/threonine-protein kinase VRK1
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,71323
Polymers164,2044
Non-polymers2,50919
Water9,926551
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5544
Polymers41,0511
Non-polymers5033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8397
Polymers41,0511
Non-polymers7886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6495
Polymers41,0511
Non-polymers5984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6717
Polymers41,0511
Non-polymers6206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.138, 96.051, 192.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine/threonine-protein kinase VRK1 / Vaccinia-related kinase 1


Mass: 41051.047 Da / Num. of mol.: 4 / Fragment: UNP residues 3-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: Q99986, non-specific serine/threonine protein kinase

-
Non-polymers , 5 types, 570 molecules

#2: Chemical
ChemComp-8E1 / 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide


Mass: 372.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H12N4O3S2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 27.5% PEG 3350; 0.3M AmSO4; 0.1M HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2016
Details: Kirkpatrick Baez (KB) bimorph mirror pair for horizontal and vertical focussing
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→29.56 Å / Num. obs: 67658 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 53.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.028 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4493 / CC1/2: 0.807 / Rpim(I) all: 0.352 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP5

3op5


Resolution: 2.4→24.19 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3415 5.06 %RANDOM
Rwork0.177 ---
obs0.179 67552 100 %-
Displacement parametersBiso mean: 60.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.9223 Å20 Å20 Å2
2---9.5099 Å20 Å2
3---7.5875 Å2
Refinement stepCycle: 1 / Resolution: 2.4→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9154 0 149 551 9854
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019517HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0812926HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3196SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes211HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1388HARMONIC5
X-RAY DIFFRACTIONt_it9517HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion17.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1198SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10996SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2136 226 4.57 %
Rwork0.2003 4716 -
all0.201 4942 -
obs--100 %
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)
17.1230.2686-2.04144.55181.51710.83870.04030.4599-0.439-0.23310.4105-0.62580.72260.8567-0.4508-0.13340.0715-0.09060.1156-0.1107-0.163480.80752.52791.3548
22.1958-0.35680.29582.18061.75013.44430.1529-0.1303-0.0590.2326-0.0366-0.22810.390.0548-0.1163-0.11220.0005-0.0452-0.0697-0.0153-0.24868.31113.883788.0726
32.67720.03341.3151.69630.54222.6910.31390.0752-0.18050.21190.0341-0.56480.77160.5021-0.3480.0430.1345-0.0766-0.011-0.0058-0.156273.8428-5.971679.4281
41.43430.41660.85414.06762.14415.31380.1435-0.2404-0.12010.2797-0.0945-0.12320.5658-0.1902-0.049-0.0286-0.0289-0.0586-0.0299-0.0345-0.210261.4249-3.546777.755
51.7472-0.8358-0.12652.81051.4645.0144-0.002-0.03650.1252-0.26480.0158-0.1625-0.3887-0.0284-0.0138-0.0486-0.0211-0.0333-0.0702-0.04-0.247660.84182.501665.5235
62.28721.4411.10834.5827-0.3586.117-0.08890.1818-0.0307-0.37820.2364-0.48050.12570.6075-0.14750.0505-0.00180.0329-0.144-0.0876-0.301664.6033-5.146454.0854
70.4124-0.17770.64954.9091.74066.08350.0095-0.1518-0.20190.1441-0.34680.43380.9314-0.78620.3373-0.0184-0.1734-0.04440.0584-0.0937-0.160851.8145-10.921866.9945
87.9778-0.18-2.33896.99480.40792.9526-0.2107-0.4674-0.50760.58320.52430.7920.5727-0.521-0.3136-0.1326-0.09780.06680.00810.2204-0.195427.9477-11.404652.9311
90.0057-2.43630.28583.3855-0.69490-0.1602-0.7046-0.19370.55430.38380.4610.2777-0.5237-0.22360.0114-0.02720.15580.1290.0719-0.147324.5398-9.023354.8845
102.5138-1.1979-2.19264.5523-1.18670.5245-0.0803-0.44410.23380.0666-0.20390.5951-0.3603-0.69540.2843-0.10360.147-0.03950.1009-0.09510.032121.34798.037541.7002
112.0909-0.43420.34411.9089-0.22242.5759-0.0189-0.18710.01860.0417-0.02620.33160.0366-0.40640.0451-0.114-0.0115-0.0261-0.1079-0.0175-0.189234.3746-3.317241.2311
124.08780.6440.69211.77061.45043.4474-0.1760.65150.3889-0.31050.02280.1828-0.3638-0.07810.15320.02950.0453-0.0598-0.12190.0658-0.175934.79732.40423.8275
131.757-0.23840.75881.38870.06363.2594-0.1618-0.03690.53380.0148-0.0160.0638-0.6039-0.13510.17780.03980.0042-0.0443-0.1108-0.0292-0.066241.69679.46740.8151
142.58781.0482-0.8127.4844.35593.8246-0.0253-0.01680.8730.3428-0.07270.472-0.9843-0.22160.09790.34260.16990.0424-0.25640.0544-0.199527.415862.087151.8561
152.9107-0.3027-1.94760.436-0.27763.80430.11580.15710.2486-0.2087-0.01860.137-0.4774-0.5214-0.0972-0.03830.0777-0.0161-0.09350.0279-0.230322.136948.324561.7207
164.5595-0.86793.04150-2.17536.04010.02120.02260.58670.23220.053-0.4178-0.12920.5444-0.0742-0.1010.00820.14880.09840.0979-0.142835.294240.865176.919
171.8002-0.0453-0.88331.1192-0.20693.6969-0.1174-0.044-0.01830.0084-0.00330.28020.0088-0.57350.1208-0.1987-0.01060.0374-0.03170.0056-0.212214.123339.021679.8654
186.79020.40950.20833.56131.65110.5923-0.05830.6034-0.7022-0.5340.31740.50580.3136-0.2804-0.2591-0.1006-0.1116-0.1223-0.0812-0.0735-0.067510.52255.043989.2316
193.4362-0.71860.05963.4017-0.01863.95880.28210.9701-0.529-0.7534-0.03970.10040.1129-0.2955-0.2424-0.0965-0.0031-0.09730.0075-0.1385-0.033514.50526.682886.4225
200.40833.5734-0.32913.7123.10620.5896-0.10480.167-0.6689-0.1992-0.0687-0.26920.44650.27010.1735-0.1240.10370.011-0.0257-0.04270.049831.04821.378298.8395
212.34320.78810.13110.5046-0.41081.581-0.06480.0803-0.1516-0.17170.0823-0.0544-0.15570.2444-0.0176-0.1168-0.03810.00810.0503-0.0279-0.102125.292415.877193.7575
222.082-0.32580.02481.6560.04821.8046-0.0397-0.0437-0.29820.01760.05460.14850.1384-0.0141-0.0149-0.1729-0.01370.0087-0.04850.0167-0.118317.137113.1428102.936
234.1742.051-0.96670.0009-1.38831.8337-0.0247-0.5414-0.2470.5763-0.097-0.23050.02080.2360.1218-0.05850.0575-0.02910.1550.0502-0.048626.151913.8533118.005
242.2223-2.33020.46255.0020.0532.1888-0.0551-0.06690.2362-0.0012-0.1421-0.4586-0.16160.24410.1972-0.0772-0.0008-0.10010.2452-0.01570.095737.932719.9352111.363
255.16491.6796-0.19392.8921-0.44861.5347-0.05460.0650.33320.14930.0734-0.06890.0444-0.0276-0.0188-0.128-0.0238-0.0202-0.0624-0.0161-0.167123.663926.0216103.682
265.2209-0.407-0.78734.62432.51595.34260.07920.22260.0398-0.25780.129-0.5343-0.34450.6633-0.2082-0.1852-0.08520.0630.0988-0.0266-0.135833.525919.780592.2526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|20 - 56}
2X-RAY DIFFRACTION2{A|57 - 121}
3X-RAY DIFFRACTION3{A|122 - 150}
4X-RAY DIFFRACTION4{A|151 - 205}
5X-RAY DIFFRACTION5{A|206 - 256}
6X-RAY DIFFRACTION6{A|257 - 280}
7X-RAY DIFFRACTION7{A|281 - 341}
8X-RAY DIFFRACTION8{B|51 - 103}
9X-RAY DIFFRACTION9{B|104 - 131}
10X-RAY DIFFRACTION10{B|132 - 150}
11X-RAY DIFFRACTION11{B|151 - 256}
12X-RAY DIFFRACTION12{B|257 - 280}
13X-RAY DIFFRACTION13{B|281 - 341}
14X-RAY DIFFRACTION14{C|21 - 56}
15X-RAY DIFFRACTION15{C|57 - 205}
16X-RAY DIFFRACTION16{C|206 - 223}
17X-RAY DIFFRACTION17{C|224 - 341}
18X-RAY DIFFRACTION18{D|39 - 102}
19X-RAY DIFFRACTION19{D|103 - 132}
20X-RAY DIFFRACTION20{D|133 - 150}
21X-RAY DIFFRACTION21{D|151 - 170}
22X-RAY DIFFRACTION22{D|171 - 256}
23X-RAY DIFFRACTION23{D|257 - 280}
24X-RAY DIFFRACTION24{D|281 - 296}
25X-RAY DIFFRACTION25{D|297 - 316}
26X-RAY DIFFRACTION26{D|317 - 341}

+
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