6HY1

Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal

PDB DOI: https://doi.org/10.2210/pdb6HY1/pdb

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

Deposited: 2018-10-19 Released: 2019-10-30
Deposition Author(s): Sprenger, J., Coertzen, D., Persson, L., Carey, J., Birkholtz, L.M., Louw, B.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.200
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal

Sprenger, J., Coertzen, D., Persson, L., Carey, J., Birkholtz, L.M., Louw, B.I.

To be published.

Macromolecule Content

Total Structure Weight: 98.9 kDa
Atom Count: 7,713
Modelled Residue Count: 842
Deposited Residue Count: 843
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B, C	281	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF3D7_1129000 EC: 2.5.1.16
UniProt
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7)) Explore Q8II73 Go to UniProtKB: Q8II73
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8II73
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTA Query on MTA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C]	E [auth A], I [auth B], O [auth C]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C]
1PG Query on 1PG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A]	F [auth A], K [auth B]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
GXQ Query on GXQ Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine C₁₂ H₂₈ N₄ PYBOSIQOXDJMFB-HAQNSBGRSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
JFQ Query on JFQ Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C]	N [auth C]	trans-N-(3-aminopropyl)cyclohexane-1,4-diamine C₉ H₂₁ N₃ QIMPCSMJRMPRJC-KYZUINATSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain J [auth B]	G [auth A] J [auth B] L [auth B] M [auth B] P [auth C] G [auth A], J [auth B], L [auth B], M [auth B], P [auth C], Q [auth C], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]