[English] 日本語
Yorodumi
- PDB-6myn: Crystal structure of murine NF-kappaB inducing kinase (NIK) bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6myn
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) bound to inhibitor R7
ComponentsMitogen-activated protein kinase kinase kinase 14
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / NIK / kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center ...CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / : / 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 ...Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / : / 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-K6Y / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.744 Å
AuthorsHarris, S.F. / Smith, M. / Barker, J.
Citation
Journal: Acs Med.Chem.Lett. / Year: 2019
Title: Structure Based Design of Potent Selective Inhibitors of Protein Kinase D1 (PKD1).
Authors: Feng, J.A. / Lee, P. / Alaoui, M.H. / Barrett, K. / Castanedo, G. / Godemann, R. / McEwan, P. / Wang, X. / Wu, P. / Zhang, Y. / Harris, S.F. / Staben, S.T.
#1: Journal: Acs Med.Chem.Lett. / Year: 2019
Title: Structure based design of potent selective inhibitors of protein kinase D1 (PKD1)
Authors: Feng, J.W. / Lee, P. / Alaoui, M.H. / Barrett, K. / Castaneda, G.M. / Godemann, R. / McEwan, P. / Wang, X. / Wu, P. / Zhang, Y. / Harris, S.F. / Staben, S.T.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation_author
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 14
B: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2069
Polymers76,7992
Non-polymers1,4077
Water1,892105
1
A: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0554
Polymers38,3991
Non-polymers6563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1515
Polymers38,3991
Non-polymers7524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.220, 143.220, 46.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Mitogen-activated protein kinase kinase kinase 14 / NF-kappa-beta-inducing kinase / Serine/threonine-protein kinase NIK


Mass: 38399.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map3k14, Nik / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WUL6, mitogen-activated protein kinase kinase kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K6Y / (5s,7s)-9-fluoro-10-[(3R)-3-hydroxy-3-(5-methyl-1,2-oxazol-3-yl)but-1-yn-1-yl]-N~3~-methyl-6,7-dihydro-5H-5,7-methanoimidazo[2,1-a][2]benzazepine-2,3-dicarboxamide


Mass: 463.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22FN5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM sodium citrate tribasic dihydrate (pH 6.2), 0.5 M ammonium sulfate, 0.9 M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.744→44.15 Å / Num. obs: 25142 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 58.27 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Rsym value: 0.086 / Net I/av σ(I): 8.4 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.744-2.826.90.691.118280.310.8160.69100
2.82-2.896.90.6411.218320.2850.7540.641100
2.89-2.986.70.4841.616900.2210.5750.48499.8
2.98-3.076.60.3652.117050.1690.4350.36599.8
3.07-3.176.20.2912.616360.140.3510.29199.8
3.17-3.285.50.2233.416030.1170.2810.22399.7
3.28-3.46.90.1624.715300.0730.1930.162100
3.4-3.5470.1295.914920.0590.1570.12999.9
3.54-3.76.90.0977.814080.0450.1190.09799.9
3.7-3.886.90.0888.713840.0410.1080.08899.9
3.88-4.096.70.0671112720.0320.0830.06799.8
4.09-4.346.80.05612.712400.0270.070.05699.9
4.34-4.646.60.0461511720.0230.060.046100
4.64-5.016.50.04615.210760.0240.0620.04699.9
5.01-5.496.30.04814.99990.0250.0640.048100
5.49-6.145.90.04615.39010.0250.0610.04699.6
6.14-7.096.10.03818.48140.0190.0470.038100
7.09-8.686.90.02922.16880.0130.0350.029100
8.68-12.276.70.02524.85560.0120.030.025100
12.27-44.156.10.024273160.0120.0290.02498.2

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.12-2829_finalrefinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.744→42.191 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.3
RfactorNum. reflection% reflection
Rfree0.255 2603 10.36 %
Rwork0.1795 --
obs0.1871 25125 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.73 Å2 / Biso mean: 55.4264 Å2 / Biso min: 26.57 Å2
Refinement stepCycle: final / Resolution: 2.744→42.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 93 105 5251
Biso mean--63.89 51.2 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015301
X-RAY DIFFRACTIONf_angle_d1.1287190
X-RAY DIFFRACTIONf_chiral_restr0.057764
X-RAY DIFFRACTIONf_plane_restr0.007976
X-RAY DIFFRACTIONf_dihedral_angle_d16.5673214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7444-2.79430.35511530.290211451298
2.7943-2.8480.38531400.277611701310
2.848-2.90610.36431410.284811771318
2.9061-2.96930.36631640.273111201284
2.9693-3.03840.36511200.230911811301
3.0384-3.11430.33941300.227712071337
3.1143-3.19850.27751310.218611581289
3.1985-3.29260.30361190.209411951314
3.2926-3.39880.27291450.207511651310
3.3988-3.52020.29531370.204911831320
3.5202-3.66110.26191480.175611671315
3.6611-3.82760.26311300.171611871317
3.8276-4.02930.23821300.160511701300
4.0293-4.28150.21721690.146911731342
4.2815-4.61170.20371250.132212181343
4.6117-5.07510.23591250.14211961321
5.0751-5.80790.24311190.162712251344
5.8079-7.31110.20881430.162512011344
7.3111-42.19570.19671340.165312841418

+
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