6P8C

2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus

PDB DOI: https://doi.org/10.2210/pdb6P8C/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-06 Released: 2020-06-10
Deposition Author(s): Carbone, V., Schofield, L.R., Hannus, I., Sutherland-Smith, A.J., Ronimus, R.S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.222
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus

Carbone, V., Schofield, L.R., Hannus, I., Sutherland-Smith, A.J., Ronimus, R.S.

To be published.

Macromolecule Content

Total Structure Weight: 56.75 kDa
Atom Count: 3,740
Modelled Residue Count: 432
Deposited Residue Count: 498
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase	A, B	249	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0 Gene Names: MTH_235 EC: 1.1.1.302
UniProt
Find proteins for O26337 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26337 Go to UniProtKB: O26337
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O26337
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B]	I [auth A], K [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain I [auth A] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A]	C [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.222
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.921	α = 90
b = 89.597	β = 90
c = 107.013	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-10

Deposition Author(s):

Carbone, V.

Schofield, L.R.

Hannus, I.

Sutherland-Smith, A.J.

Ronimus, R.S.

Funding Organization	Location	Grant Number
Other government	New Zealand	--

Revision History (Full details and data files)

Version 1.0: 2020-06-10
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

6P8C

2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus

The Crystal Structure of 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)