4MWZ | pdb_00004mwz

Crystal structure of N-methyl transferase from Plasmodium vivax complexed with S-adenosyl methionine, phosphate and amodiaquine

PDB DOI: https://doi.org/10.2210/pdb4MWZ/pdb

Classification: transferase/transferase inhibitor
Organism(s): Plasmodium vivax Sal-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-09-25 Released: 2014-10-01
Deposition Author(s): Lukk, T., Nair, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.178 (Depositor), 0.183 (DCC)
R-Value Work:
0.152 (Depositor)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Phosphoethanolamine N-methyl transferase is a Malarial drug target

Lukk, T., Nair, S.K., Mamoun, C.B.

To be published.

Macromolecule Content

Total Structure Weight: 63.91 kDa
Atom Count: 5,145
Modeled Residue Count: 520
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoethanolamine N-methyltransferase, putative	A, B	267	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PMT, PVX_083045 EC: 2.1.1.103
UniProt
Find proteins for A5K867 (Plasmodium vivax (strain Salvador I)) Explore A5K867 Go to UniProtKB: A5K867
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K867
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM 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] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CQA Query on CQA 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]	4-[(7-CHLOROQUINOLIN-4-YL)AMINO]-2-[(DIETHYLAMINO)METHYL]PHENOL C₂₀ H₂₂ Cl N₃ O OVCDSSHSILBFBN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.178 (Depositor), 0.183 (DCC)
R-Value Work: 0.152 (Depositor)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.44	α = 90
b = 86.62	β = 103.23
c = 78.27	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-10-01

Deposition Author(s):

Lukk, T.

Nair, S.K.

Revision History (Full details and data files)

Version 1.0: 2014-10-01
Type: Initial release
Version 1.1: 2014-11-12
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

4MWZ | pdb_00004mwz

Crystal structure of N-methyl transferase from Plasmodium vivax complexed with S-adenosyl methionine, phosphate and amodiaquine

Literature

Phosphoethanolamine N-methyl transferase is a Malarial drug target

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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