3THQ

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase complexed with 6-amino-UMP

• PDB DOI: https://doi.org/10.2210/pdb3THQ/pdb

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


• Deposited: 2011-08-19 Released: 2012-05-02 
• Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.192 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase complexed with 6-amino-UMP

Liu, Y., Kotra, L.P., Pai, E.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 54.51 kDa 
• Atom Count: 3,813 
• Modelled Residue Count: 430 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	247	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0  Gene Names: 1470090, MTH_129, pyrF EC: 4.1.1.23
UniProt
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26232  Go to UniProtKB:  O26232

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUP	C [auth A], D [auth B]	6-AMINOURIDINE 5'-MONOPHOSPHATE C9 H14 N3 O9 P DUFXRFNPGXQQOI-YXZULKJRSA-N
EPE	E [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NUP	BindingDB:  3THQ	Ki: 840 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.192 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.621	α = 90
b = 64.343	β = 115.32
c = 61.255	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description