[English] 日本語
Yorodumi
- PDB-5lbz: Structure of the human quinone reductase 2 (NQO2) in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lbz
TitleStructure of the human quinone reductase 2 (NQO2) in complex with pacritinib
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE / quinone reductase 2 / kinase inhibitor / pancritinib / Ribosyldihydronicotinamide dehydrogenase (NQO2)
Function / homology
Function and homology information


ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding / electron transfer activity / oxidoreductase activity / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6T3 / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsSchneider, S. / Medard, G. / Kuster, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Science / Year: 2017
Title: The target landscape of clinical kinase drugs.
Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / ...Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / Koch, H. / Schoof, M. / Canevari, G. / Casale, E. / Depaolini, S.R. / Feuchtinger, A. / Wu, Z. / Schmidt, T. / Rueckert, L. / Becker, W. / Huenges, J. / Garz, A.K. / Gohlke, B.O. / Zolg, D.P. / Kayser, G. / Vooder, T. / Preissner, R. / Hahne, H. / Tonisson, N. / Kramer, K. / Gotze, K. / Bassermann, F. / Schlegl, J. / Ehrlich, H.C. / Aiche, S. / Walch, A. / Greif, P.A. / Schneider, S. / Felder, E.R. / Ruland, J. / Medard, G. / Jeremias, I. / Spiekermann, K. / Kuster, B.
History
DepositionJun 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribosyldihydronicotinamide dehydrogenase [quinone]
B: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,58212
Polymers53,5512
Non-polymers3,03110
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-77 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.454, 79.220, 106.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 3 - 229 / Label seq-ID: 4 - 230

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ribosyldihydronicotinamide dehydrogenase [quinone] / NRH dehydrogenase [quinone] 2 / NRH:quinone oxidoreductase 2 / Quinone reductase 2 / QR2


Mass: 26775.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P16083, ribosyldihydronicotinamide dehydrogenase (quinone)

-
Non-polymers , 5 types, 437 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-6T3 / 11-(2-pyrrolidin-1-yl-ethoxy)-14,19-dioxa-5,7,26-triaza-tetracyclo[19.3.1.1(2,6).1(8,12)]heptacosa-1(25),2(26),3,5,8,10,12(27),16,21,23-decaene


Mass: 472.579 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H32N4O3 / Comment: medication, anticancer, inhibitor*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 200 mM sodium sulphate, 2.2 M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.4→48.6 Å / Num. obs: 97699 / % possible obs: 95 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.11
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.3 / % possible all: 91

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LBU

5lbu


Resolution: 1.4→48.6 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.146 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.131 4913 5 %RANDOM
Rwork0.10896 ---
obs0.11005 93339 94.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 14.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0 Å2
2--0.25 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 198 427 4229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194020
X-RAY DIFFRACTIONr_bond_other_d0.0040.023670
X-RAY DIFFRACTIONr_angle_refined_deg1.60925499
X-RAY DIFFRACTIONr_angle_other_deg1.20438483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75724.235170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38215631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4681516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214490
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02948
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_it1.6331.0351877
X-RAY DIFFRACTIONr_mcbond_other1.591.0321876
X-RAY DIFFRACTIONr_mcangle_it1.9161.5642364
X-RAY DIFFRACTIONr_mcangle_other1.9171.5652365
X-RAY DIFFRACTIONr_scbond_it4.4881.4112143
X-RAY DIFFRACTIONr_scbond_other4.4431.3962128
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8332.6763108
X-RAY DIFFRACTIONr_long_range_B_refined4.34414.785345
X-RAY DIFFRACTIONr_long_range_B_other4.09813.7235108
X-RAY DIFFRACTIONr_rigid_bond_restr7.69837686
X-RAY DIFFRACTIONr_sphericity_free29.752591
X-RAY DIFFRACTIONr_sphericity_bonded13.60857898
Refine LS restraints NCS

Ens-ID: 1 / Number: 15610 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.395→1.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 320 -
Rwork0.15 6098 -
obs--84.73 %

+
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