[English] 日本語
Yorodumi
- PDB-4pvv: Micobacterial Adenosine Kinase in complex with inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pvv
TitleMicobacterial Adenosine Kinase in complex with inhibitor
ComponentsAdenosine kinase
KeywordsTransferase/Transferase inhibitor / Adenosine Kinase / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / ketohexokinase activity / dGTP binding / regulation of glycogen metabolic process / response to sucrose / response to fructose / AMP salvage / fructose metabolic process / purine ribonucleoside salvage ...adenosine kinase / adenosine kinase activity / ketohexokinase activity / dGTP binding / regulation of glycogen metabolic process / response to sucrose / response to fructose / AMP salvage / fructose metabolic process / purine ribonucleoside salvage / response to zinc ion / response to glucose / response to insulin / GTP binding / magnesium ion binding / ATP binding / plasma membrane
Similarity search - Function
pfkB family of carbohydrate kinases signature 1. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HO4 / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsPichova, I. / Hocek, M. / Dostal, J. / Rezacova, P.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structural Basis for Inhibition of Mycobacterial and Human Adenosine Kinase by 7-Substituted 7-(Het)aryl-7-deazaadenine Ribonucleosides
Authors: Snasel, J. / Naus, P. / Dostal, J. / Hnizda, A. / Fanfrlik, J. / Brynda, J. / Bourderioux, A. / Dusek, M. / Dvorakova, H. / Stolarikova, J. / Zabranska, H. / Pohl, R. / Konecny, P. / Dzubak, ...Authors: Snasel, J. / Naus, P. / Dostal, J. / Hnizda, A. / Fanfrlik, J. / Brynda, J. / Bourderioux, A. / Dusek, M. / Dvorakova, H. / Stolarikova, J. / Zabranska, H. / Pohl, R. / Konecny, P. / Dzubak, P. / Votruba, I. / Hajduch, M. / Rezacova, P. / Veverka, V. / Hocek, M. / Pichova, I.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7942
Polymers34,5041
Non-polymers2901
Water1448
1
A: Adenosine kinase
hetero molecules

A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5884
Polymers69,0082
Non-polymers5812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area2740 Å2
ΔGint-19 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.985, 46.985, 244.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

-
Components

#1: Protein Adenosine kinase / AK


Mass: 34503.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: adoK / Production host: Escherichia coli (E. coli)
References: UniProt: P83734, UniProt: P9WID5*PLUS, adenosine kinase
#2: Chemical ChemComp-HO4 / 5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 290.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.26 Å3/Da / Density % sol: 45.47 % / Mosaicity: 1.05 °

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97826 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97826 Å / Relative weight: 1
ReflectionResolution: 2.5→81.417 Å / Num. all: 10333 / Num. obs: 10333 / % possible obs: 92.3 % / Redundancy: 8.2 % / Rsym value: 0.11 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.648.30.2263.21341016160.0870.2266.8100
2.64-2.88.10.1793.8944911700.0690.1798.477.7
2.8-2.998.30.1614.11180014190.0610.16110.1100
2.99-3.238.40.1335.11129413420.050.13312.3100
3.23-3.548.20.1165.9886210870.0440.11614.387.5
3.54-3.9580.1056.161107660.040.10515.568.5
3.95-4.568.30.1095.881919850.0410.10917.2100
4.56-5.598.10.1364.870218620.0510.13616.7100
5.59-7.917.90.0797.254456910.030.07915.6100
7.91-40.697.10.03118.628223950.0140.03115.898.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation40.69 Å3.5 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREP11.0.02phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.69 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.809 / WRfactor Rfree: 0.3629 / WRfactor Rwork: 0.2839 / FOM work R set: 0.7118 / SU B: 17.168 / SU ML: 0.386 / SU R Cruickshank DPI: 2.6224 / SU Rfree: 0.4419 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.622 / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3411 533 5.2 %RANDOM
Rwork0.2641 ---
obs0.2679 10287 92.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 70.04 Å2 / Biso mean: 28.092 Å2 / Biso min: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20.73 Å20 Å2
2--1.47 Å20 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 21 8 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022434
X-RAY DIFFRACTIONr_bond_other_d0.0070.021549
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.9673316
X-RAY DIFFRACTIONr_angle_other_deg1.1353.0033779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1065319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28524.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.32315363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5931514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022773
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02496
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 42 -
Rwork0.265 694 -
all-736 -
obs--100 %

+
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://pdbjlvh1.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