4NX5

Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

PDB DOI: https://doi.org/10.2210/pdb4NX5/pdb

Classification: LYASE
Organism(s): Methanothermobacter thermautotrophicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-12-08 Released: 2013-12-25
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.168
R-Value Work: 0.148
R-Value Observed: 0.148

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 50.86 kDa
Atom Count: 3,951
Modelled Residue Count: 439
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	228	Methanothermobacter thermautotrophicus	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O26232
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UP6 Query on UP6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	6-AZA URIDINE 5'-MONOPHOSPHATE C₈ H₁₂ N₃ O₉ P LRVZOSYMNMNQFR-SHUUEZRQSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
UP6	BindingDB: 4NX5	Ki: 1.24e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.168
R-Value Work: 0.148
R-Value Observed: 0.148
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.737	α = 90
b = 64.148	β = 115.36
c = 61.527	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

4NX5

Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

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)