3N3M | pdb_00003n3m

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 81.21 kDa
Atom Count: 6,503
Modeled Residue Count: 650
Deposited Residue Count: 684
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	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IJH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NUP Query on NUP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	6-AMINOURIDINE 5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₉ P DUFXRFNPGXQQOI-YXZULKJRSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	E [auth A], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

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 (Depositor), 0.190 (DCC)
R-Value Work: 0.163 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Liu, Y.

Kotra, L.P.

Pai, E.F.

Revision History (Full details and data files)

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

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Validate Data

Deposit Data

Help and Resources

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3N3M | pdb_00003n3m