[English] 日本語
Yorodumi
- PDB-9ecg: PANK3 complex structure with compound PZ-5588 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ecg
TitlePANK3 complex structure with compound PZ-5588
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase / Inhibitor / Activator
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 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsYun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Isoform Selectivity Driven Pantothenate Kinases Activation by Novel Sulfonamide Analogues of Pantazines
Authors: Tangallapally, R. / Coker, A. / Edwards, A. / Subramanian, C. / Jayasinghe, T. / Yun, M. / Jackowski, S. / Rock, C.O. / White, S.W. / Lee, R.E.
History
DepositionNov 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2587
Polymers42,1261
Non-polymers1,1326
Water1,45981
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,51514
Polymers84,2522
Non-polymers2,26412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9780 Å2
ΔGint-60 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.431, 98.431, 68.795
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 , 6 types, 87 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1BHG / N-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}-2-fluorophenyl)ethanesulfonamide


Mass: 441.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21ClFN5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.092→32.219 Å / Num. obs: 23058 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 44.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.4
Reflection shellResolution: 2.092→2.128 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1114 / CC1/2: 0.404 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
autoPROC1.0.5data processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.092→32.219 Å / SU ML: 0.2624 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.2794 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2372 1238 5.37 %
Rwork0.1943 21816 -
obs0.1965 23054 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.34 Å2
Refinement stepCycle: LAST / Resolution: 2.092→32.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 70 81 2858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182860
X-RAY DIFFRACTIONf_angle_d0.50863877
X-RAY DIFFRACTIONf_chiral_restr0.0391425
X-RAY DIFFRACTIONf_plane_restr0.0027484
X-RAY DIFFRACTIONf_dihedral_angle_d9.9581643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.092-2.180.31331370.29672372X-RAY DIFFRACTION99.92
2.18-2.270.28931390.26532378X-RAY DIFFRACTION100
2.27-2.390.29311430.24192403X-RAY DIFFRACTION100
2.39-2.540.24451440.2222396X-RAY DIFFRACTION100
2.54-2.740.25731420.20452417X-RAY DIFFRACTION100
2.74-3.020.24411300.19632409X-RAY DIFFRACTION100
3.02-3.450.2071340.18162434X-RAY DIFFRACTION99.96
3.45-4.350.20061330.16942452X-RAY DIFFRACTION100
4.35-32.2190.24581360.18682555X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: 29.9043629596 Å / Origin y: 7.96302344957 Å / Origin z: 4.88795728104 Å
111213212223313233
T0.341991582066 Å20.0171190291585 Å20.00655777755764 Å2-0.27365015895 Å20.0125832740185 Å2--0.243485100187 Å2
L1.6566497994 °20.366420089036 °20.431589884787 °2-3.45441976481 °21.54252085364 °2--2.36436684826 °2
S-1.48749348773E-5 Å °-0.181408646744 Å °0.089021867476 Å °0.645766851745 Å °-0.0139215206859 Å °-0.0650622356949 Å °0.253195410281 Å °0.0552540336103 Å °0.00968654788722 Å °
Refinement TLS groupSelection details: all

+
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