6GLV | pdb_00006glv

Crystal structure of hMTH1 D120N in complex with TH scaffold 1 in the absence of acetate

• PDB DOI: https://doi.org/10.2210/pdb6GLV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-05-23 Released: 2019-02-20 
• Deposition Author(s): Eberle, S.A., Wiedmer, L., Sledz, P., Caflisch, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

hMTH1 D120N in complex with TH scaffold 1

Eberle, S.A., Wiedmer, L., Sledz, P., Caflisch, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.66 kDa 
• Atom Count: 1,394 
• Modeled Residue Count: 155 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydro-8-oxoguanine triphosphatase	A	182	Homo sapiens	Mutation(s): 1  Gene Names: NUDT1, MTH1 EC: 3.6.1.55 (PDB Primary Data), 3.6.1.56 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens) Explore P36639  Go to UniProtKB:  P36639
PHAROS:  P36639 GTEx:  ENSG00000106268

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F3E	B [auth A]	4-phenylpyrimidin-2-amine C10 H9 N3 DMEGQEWPMXDRMO-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.41	α = 90
b = 59.837	β = 90
c = 65.573	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Eberle, S.A., Wiedmer, L., Sledz, P., Caflisch, A.

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Funding Organization	Location	Grant Number
	Switzerland	FK-16-032

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description