3N3M

Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 6-amino-UMP

• PDB DOI: https://doi.org/10.2210/pdb3N3M/pdb

• Classification: LYASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-20 Released: 2011-04-06 
• Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.191 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

Crystal structure of Plasmodium falciparum 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: 81.21 kDa 
• Atom Count: 6,503 
• Modelled Residue Count: 650 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	342	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: gi|9310996, PF10_0225 EC: 4.1.1.23
UniProt
Find proteins for Q8IJH3 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJH3  Go to UniProtKB:  Q8IJH3

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUP	G [auth A], L [auth B]	6-AMINOURIDINE 5'-MONOPHOSPHATE C9 H14 N3 O9 P DUFXRFNPGXQQOI-YXZULKJRSA-N
PGE	C [auth A], D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4	H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NUP	BindingDB:  3N3M	Ki: 2100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.191 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.802	α = 90
b = 83.131	β = 90
c = 89.983	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-07-25
  Changes: Other
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description