3BPW

Crystal Structure of P. falciparum Orotidine 5'-monophosphate Decarboxylase Complexed with XMP

PDB DOI: https://doi.org/10.2210/pdb3BPW/pdb

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

Deposited: 2007-12-19 Released: 2008-11-18
Deposition Author(s): Liu, Y., Lau, W., Pai, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.205
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of P. falciparum Orotidine 5'-monophosphate Decarboxylase Complexed with XMP

Liu, Y., Lau, W., Pai, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 80.73 kDa
Atom Count: 5,963
Modelled Residue Count: 651
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	Mutation(s): 0 Gene Names: ompdc 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XMP Query on XMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	XANTHOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₄ O₉ P DCTLYFZHFGENCW-UUOKFMHZSA-O		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.205
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.902	α = 90
b = 83.582	β = 90
c = 89.793	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-11-18

Deposition Author(s):

Liu, Y.

Lau, W.

Pai, E.F.

Revision History (Full details and data files)

Version 1.0: 2008-11-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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3BPW

Crystal Structure of P. falciparum Orotidine 5'-monophosphate Decarboxylase Complexed with XMP

Crystal Structure of P. falciparum Orotidine 5'-monophosphate Decarboxylase Complexed with XMP

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)