5V0X

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001114

PDB DOI: https://doi.org/10.2210/pdb5V0X/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Plasmodium vivax
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-28 Released: 2018-03-07
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.221
R-Value Work: 0.163
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001114

Mayclin, S.J., Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 147.95 kDa
Atom Count: 10,731
Modelled Residue Count: 1,143
Deposited Residue Count: 1,215
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A, B, C	405	Plasmodium vivax	Mutation(s): 0 Gene Names: PVC01_130042700, PVP01_1336100 EC: 2.3.1.97
UniProt
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I)) Explore A5K1A2 Go to UniProtKB: A5K1A2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5K1A2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYA Query on MYA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain V [auth C] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain V [auth C] MOL2 format, chain N [auth B]	D [auth A], N [auth B], V [auth C]	TETRADECANOYL-COA C₃₅ H₆₂ N₇ O₁₇ P₃ S DUAFKXOFBZQTQE-QSGBVPJFSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain D [auth A] Focus chain N [auth B] Focus chain V [auth C]
8RD Query on 8RD Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain W [auth C] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] MOL2 format, chain E [auth A]	E [auth A], O [auth B], W [auth C]	{4-[2-(5-fluoro-2-{3-[(methylamino)methyl][1,2,4]triazolo[4,3-a]pyridin-6-yl}phenoxy)ethyl]-1,5-dimethyl-1H-pyrazol-3-yl}(morpholin-4-yl)methanone C₂₆ H₃₀ F N₇ O₃ NIWAAHIPMDGEGU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain O [auth B] Focus chain W [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain AA [auth C] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B]	AA [auth C] BA [auth C] CA [auth C] G [auth A] H [auth A] AA [auth C], BA [auth C], CA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain F [auth A] SDF format, chain P [auth B] MOL2 format, chain X [auth C] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B]	F [auth A], P [auth B], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain F [auth A] Focus chain P [auth B] Focus chain X [auth C]