5ILN | pdb_00005iln

Crystal structure of Aspartate Transcarbamoylase from Plasmodium falciparum (PfATC) with bound citrate

PDB DOI: https://doi.org/10.2210/pdb5ILN/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2016-03-04 Released: 2017-03-29
Deposition Author(s): Lunev, S., Bosch, S.S., Batista, F.D.A., Wrenger, C., Groves, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of truncated Aspartate Transcarbamoylase from Plasmodium falciparum

Lunev, S., Bosch, S.S., Batista, F.D.A., Wrenger, C., Groves, M.R.

To be published.

Macromolecule Content

Total Structure Weight: 134.46 kDa
Atom Count: 8,418
Modeled Residue Count: 1,009
Deposited Residue Count: 1,155
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase	A, B, C	385	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: atcasE, MAL13P1.221 EC: 2.1.3.2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], K [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], I [auth C], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B, C	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.180 (Depositor), 0.190 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.45	α = 90
b = 107.29	β = 117.46
c = 87.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2018-01-31
Changes: Database references
Version 1.2: 2024-05-01
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary