[English] 日本語
Yorodumi
- PDB-5go1: Structural, Functional characterization and discovery of novel in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5go1
TitleStructural, Functional characterization and discovery of novel inhibitors of Leishmania amazonensis Nucleoside Diphosphatase Kinase (NDK)
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Kinase / Leishmania amazonensis / inhibitor
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesLeishmania amazonensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMishra, A.K. / Agnihotri, P. / Singh, S.P. / Pratap, J.V.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2017
Title: Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization.
Authors: Mishra, A.K. / Singh, N. / Agnihotri, P. / Mishra, S. / Singh, S.P. / Kolli, B.K. / Chang, K.P. / Sahasrabuddhe, A.A. / Siddiqi, M.I. / Pratap, J.V.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)16,7141
Polymers16,7141
Non-polymers00
Water30617
1
A: Nucleoside diphosphate kinase
x 6


Theoretical massNumber of molelcules
Total (without water)100,2846
Polymers100,2846
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area9340 Å2
ΔGint-62 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.180, 115.180, 62.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein Nucleoside diphosphate kinase


Mass: 16714.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania amazonensis (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: A0A1Y0DDB3*PLUS, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.31 Å3/Da / Density % sol: 62.83 % / Description: hexagonal, compact, stable
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG MME 500, Bis-Tris Propane, Magnesium chloride, 30% ethylene glycol used as cryoprotectant
PH range: 5.8-7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2012 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→99.75 Å / Num. obs: 8621 / % possible obs: 98.4 % / Redundancy: 13.8 % / Biso Wilson estimate: 65.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Rsym value: 0.075 / Net I/σ(I): 19.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.768 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLM7.0.9data reduction
SCALA3.3.16data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGR

3ngr


Resolution: 2.5→99.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.803 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.218 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 407 4.7 %RANDOM
Rwork0.22525 ---
obs0.22707 8201 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.575 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å2-0 Å2
2--1.44 Å2-0 Å2
3----4.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→99.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 17 831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019838
X-RAY DIFFRACTIONr_bond_other_d0.0030.02802
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9451135
X-RAY DIFFRACTIONr_angle_other_deg1.17231834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4235112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97322.35334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16715126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.905158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021969
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02195
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_it8.4237.222448
X-RAY DIFFRACTIONr_mcbond_other8.4117.21447
X-RAY DIFFRACTIONr_mcangle_it12.1710.781557
X-RAY DIFFRACTIONr_mcangle_other12.15910.798558
X-RAY DIFFRACTIONr_scbond_it7.0627.355390
X-RAY DIFFRACTIONr_scbond_other7.0627.355390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.76210.947578
X-RAY DIFFRACTIONr_long_range_B_refined16.55467.3283647
X-RAY DIFFRACTIONr_long_range_B_other16.56167.343640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 29 -
Rwork0.384 558 -
obs--92.15 %

+
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