5YFY | pdb_00005yfy

Plasmodium vivax SHMT bound with PLP-glycine and GS625

PDB DOI: https://doi.org/10.2210/pdb5YFY/pdb

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

Deposited: 2017-09-22 Released: 2018-09-26
Deposition Author(s): Chitnumsub, P., Jaruwat, A., Leartsakulpanich, U., Schwertz, G., Diederich, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.276 (Depositor), 0.272 (DCC)
R-Value Work:
0.218 (Depositor), 0.217 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

to be published

Chitnumsub, P., Jaruwat, A.

To be published.

Macromolecule Content

Total Structure Weight: 150.06 kDa
Atom Count: 10,791
Modeled Residue Count: 1,326
Deposited Residue Count: 1,326
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B, C	442	Plasmodium vivax	Mutation(s): 0 Gene Names: PVC01_140059500, PVP01_1453700, PVT01_140059000 EC: 2.1.2.1
UniProt
Find proteins for A5K8L9 (Plasmodium vivax (strain Salvador I)) Explore A5K8L9 Go to UniProtKB: A5K8L9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K8L9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8UL Query on 8UL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C]	E [auth A], H [auth B], J [auth C]	1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidine-4-carboxylic acid C₂₃ H₂₆ F N₅ O₃ JPUKBKCOTBHVDC-QHCPKHFHSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C]
PLG Query on PLG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C]	D [auth A], G [auth B], I [auth C]	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] C₁₀ H₁₅ N₂ O₇ P FEVQWBMNLWUBTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C]	F [auth A], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]