5OTN

Crystal structure of zebrafish MTH1 in complex with O6-methyl-dGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP.

Jemth, A.S.Gustafsson, R.Brautigam, L.Henriksson, L.Vallin, K.S.A.Sarno, A.Almlof, I.Homan, E.Rasti, A.Warpman Berglund, U.Stenmark, P.Helleday, T.

(2018) Nucleic Acids Res. 46: 10888-10904


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nudix (Nucleoside diphosphate linked moiety X)-type motif 1
A
159Danio rerioMutation(s): 0 
Gene Names: nudt1
Find proteins for Q7ZWC3 (Danio rerio)
Go to UniProtKB:  Q7ZWC3
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
6OG
Query on 6OG

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Download CCD File 
A
6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
C11 H16 N5 O7 P
GFRAHVJOXXMIDI-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.528α = 90.00
b = 55.379β = 90.00
c = 65.920γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden--
Wenner-Gren FoundationSweden--
Ake Wiberg FoundationSweden--
Swedish Foundation for Strategic ResearchSweden--
Swedish Pain Relief FoundationSweden--
Torsten and Ragnar Soderberg FoundationSweden--
Swedish Childrens Cancer FoundationSweden--
Swedish Cancer SocietySweden--

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Database references
  • Version 1.3: 2018-11-28
    Type: Data collection, Database references