8SZE | pdb_00008sze

Crystal structure of Yersinia pestis dihydrofolate reductase in complex with Trimethoprim

PDB DOI: https://doi.org/10.2210/pdb8SZE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Yersinia pestis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-05-29 Released: 2023-06-07
Deposition Author(s): Shaw, G.X., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.215 (Depositor), 0.216 (DCC)
R-Value Observed:
0.217 (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

Crystal structure of Yersinia pestis dihydrofolate reductase in complex with Trimethoprim

Shaw, G.X., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

To be published.

Macromolecule Content

Total Structure Weight: 38.13 kDa
Atom Count: 2,548
Modeled Residue Count: 300
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	164	Yersinia pestis	Mutation(s): 0 Gene Names: folA, tmrA, YPO0486 EC: 1.5.1.3
UniProt
Find proteins for A0A3N4BLI0 (Yersinia pestis) Explore A0A3N4BLI0 Go to UniProtKB: A0A3N4BLI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3N4BLI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TOP (Subject of Investigation/LOI) Query on TOP Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A], K [auth B]	TRIMETHOPRIM C₁₄ H₁₈ N₄ O₃ IEDVJHCEMCRBQM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] L [auth B] M [auth B] D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A], J [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B]