[English] 日本語
Yorodumi
- PDB-7uey: PANK3 complex structure with compound PZ-4128 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uey
TitlePANK3 complex structure with compound PZ-4128
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PANK / Transferase / Inhibitor / Activator / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Coenzyme A biosynthesis / acetyl-CoA binding / vitamin binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-N0R / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWhite, S.W. / Yun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of hPANK Activators with Improved Pharmacological Properties
Authors: Tangallapally, R. / Edwards, A. / Subramanian, C. / Sharma, L.K. / Yun, M. / White, S.W. / Jackowski, S. / Rock, C.O. / Lee, R.E.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,82510
Polymers42,1261
Non-polymers1,6999
Water3,477193
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,65020
Polymers84,2522
Non-polymers3,39818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area10910 Å2
ΔGint-37 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.545, 98.545, 68.939
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Pantothenate kinase 3 / hPanK3 / Pantothenic acid kinase 3


Mass: 42125.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H999, pantothenate kinase

-
Non-polymers , 5 types, 202 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-N0R / N-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}phenyl)-2-hydroxyacetamide


Mass: 389.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, ammonium acetate, citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 42759 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 20.37 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Net I/σ(I): 26.8
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2627 / CC1/2: 0.88 / CC star: 0.968 / Rpim(I) all: 0.248 / Rrim(I) all: 0.765 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 6B3V

6b3v


Resolution: 1.7→36.28 Å / SU ML: 0.1703 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.3356 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1883 1993 4.66 %
Rwork0.1682 40740 -
obs0.1691 42733 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.39 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 107 193 3017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612882
X-RAY DIFFRACTIONf_angle_d0.97843902
X-RAY DIFFRACTIONf_chiral_restr0.0541427
X-RAY DIFFRACTIONf_plane_restr0.0045487
X-RAY DIFFRACTIONf_dihedral_angle_d10.93831659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.22151440.23052886X-RAY DIFFRACTION99.87
1.74-1.790.23331400.19972866X-RAY DIFFRACTION99.97
1.79-1.840.21871370.19122880X-RAY DIFFRACTION100
1.84-1.90.19791420.18032882X-RAY DIFFRACTION100
1.9-1.970.18381410.1692916X-RAY DIFFRACTION100
1.97-2.050.1831430.16292844X-RAY DIFFRACTION100
2.05-2.140.22421440.17072903X-RAY DIFFRACTION100
2.14-2.260.17741400.16312867X-RAY DIFFRACTION100
2.26-2.40.16591420.16662923X-RAY DIFFRACTION100
2.4-2.580.20721410.17012911X-RAY DIFFRACTION100
2.58-2.840.21041450.16522911X-RAY DIFFRACTION100
2.84-3.250.19021390.16322940X-RAY DIFFRACTION100
3.25-4.10.16481480.15312953X-RAY DIFFRACTION100
4.1-36.280.18141470.17133058X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: -21.9196075477 Å / Origin y: 22.0782801083 Å / Origin z: -6.19635915823 Å
111213212223313233
T0.124712649019 Å2-0.0137815149052 Å2-0.00751518915608 Å2-0.122760605056 Å2-0.00357636107747 Å2--0.106958011346 Å2
L1.55930886388 °20.276859930599 °2-0.813839299836 °2-0.7311169869 °2-0.19590317694 °2--1.42420917345 °2
S0.0671935927019 Å °-0.259412322872 Å °-0.0179779554466 Å °0.114905240919 Å °-0.0896004148733 Å °0.084135297731 Å °-0.0903864190998 Å °0.0702903481825 Å °0.0193717527853 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 369)

+
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