3SY5

Crystal structure of the mutant S127A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor 6azaUMP

• PDB DOI: https://doi.org/10.2210/pdb3SY5/pdb

• Classification: LYASE/INHIBITOR
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-07-15 Released: 2011-09-21 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Iiams, V., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.218 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Crystal structure of the mutant S127A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor 6azaUMP

Fedorov, A.A., Fedorov, E.V., Desai, B., Iiams, V., Gerlt, J.A., Almo, S.C.

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: 50.39 kDa 
• Atom Count: 3,885 
• Modelled Residue Count: 439 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	228	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 1  Gene Names: pyrF, MTH_129 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UP6	C [auth A], D [auth B]	6-AZA URIDINE 5'-MONOPHOSPHATE C8 H12 N3 O9 P LRVZOSYMNMNQFR-SHUUEZRQSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UP6	BindingDB:  3SY5	Ki: 1.24e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.218 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.711	α = 90
b = 63.603	β = 115.19
c = 61.197	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Iiams, V., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Other
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description