[English] 日本語
Yorodumi
- PDB-8v6z: Crystal structure of the core catalytic domain of human inositol ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v6z
TitleCrystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with compound 4
ComponentsInositol polyphosphate multikinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structure-based inhibitor development / kinase / inhibitor / inositol polyphosphate / inositol polyphosphate kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity ...inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol trisphosphate metabolic process / inositol phosphate metabolic process / inositol phosphate biosynthetic process / phosphatidylinositol metabolic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / necroptotic process / ciliary basal body / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
: / Inositol polyphosphate multikinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsWang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046 United States
CitationJournal: To Be Published
Title: Structure-based development of IPMK kinase inhibitors.
Authors: Wang, H. / Shears, S.B.
History
DepositionDec 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1192
Polymers29,8281
Non-polymers2911
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.940, 77.940, 85.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-661-

HOH

21A-743-

HOH

31A-745-

HOH

-
Components

#1: Protein Inositol polyphosphate multikinase / Inositol 1 / 3 / 4 / 6-tetrakisphosphate 5-kinase


Mass: 29827.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPMK, IPMK, IMPK / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NFU5, inositol-tetrakisphosphate 5-kinase, inositol-polyphosphate multikinase, phosphatidylinositol-4,5-bisphosphate 3-kinase
#2: Chemical ChemComp-YHS / (5P)-3-(3,5-dimethylphenyl)-5-(1H-tetrazol-5-yl)-2,1-benzoxazole


Mass: 291.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG ...Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 2 mM compound 4 for 3 days

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 23240 / % possible obs: 99.1 % / Redundancy: 11.4 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.031 / Rrim(I) all: 0.119 / Χ2: 1.145 / Net I/σ(I): 20.39
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 1136 / CC1/2: 0.779 / CC star: 0.936 / Rpim(I) all: 0.268 / Rrim(I) all: 0.819 / Χ2: 0.636 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→46.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.037 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22942 1162 5.1 %RANDOM
Rwork0.17294 ---
obs0.17576 21483 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.625 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å2-0 Å20 Å2
2--1.49 Å2-0 Å2
3----2.97 Å2
Refinement stepCycle: 1 / Resolution: 1.85→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 22 157 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122050
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161835
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.6682783
X-RAY DIFFRACTIONr_angle_other_deg0.311.5784293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.50159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81810350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0420.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
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_it1.6462.292976
X-RAY DIFFRACTIONr_mcbond_other1.6452.292976
X-RAY DIFFRACTIONr_mcangle_it2.3483.4291225
X-RAY DIFFRACTIONr_mcangle_other2.3473.431226
X-RAY DIFFRACTIONr_scbond_it1.7522.5811074
X-RAY DIFFRACTIONr_scbond_other1.7512.5811073
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.313.7821559
X-RAY DIFFRACTIONr_long_range_B_refined3.93545.6848852
X-RAY DIFFRACTIONr_long_range_B_other3.744.8318746
X-RAY DIFFRACTIONr_rigid_bond_restr3.09633885
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 87 -
Rwork0.221 1432 -
obs--90.47 %
Refinement TLS params.Method: refined / Origin x: 3.32 Å / Origin y: 17.999 Å / Origin z: 25.682 Å
111213212223313233
T0.0013 Å20.0004 Å2-0.0005 Å2-0.0014 Å20.0001 Å2--0.0295 Å2
L0.1082 °20.0129 °2-0.0325 °2-0.0399 °2-0.0113 °2--0.0686 °2
S-0.0028 Å °0.0067 Å °0.0014 Å °0.0061 Å °0.0025 Å °0.0016 Å °0.0018 Å °-0.0014 Å °0.0004 Å °

+
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