6GLT

Crystal structure of hMTH1 D120N in the presence of acetate

PDB DOI: https://doi.org/10.2210/pdb6GLT/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.213
R-Value Work: 0.182
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

in progress

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

To be published.

Macromolecule Content

Total Structure Weight: 21.18 kDa
Atom Count: 1,397
Modelled Residue Count: 154
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36639
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.213
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.32	α = 90
b = 60.441	β = 90
c = 65.859	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-02-20

Deposition Author(s):

Funding Organization	Location	Grant Number
	Switzerland	FK-16-032

Revision History (Full details and data files)

Version 1.0: 2019-02-20
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.