7DP4

Crystal structure of wild type Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate and methotrexate

PDB DOI: https://doi.org/10.2210/pdb7DP4/pdb

Classification: TRANSFERASE
Organism(s): Brugia malayi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-12-18 Released: 2021-12-22
Deposition Author(s): Keyunratsami, K., Nualnoi, T., Wongkamchai, S., Songsiriritthigul, C., Chen, C.-J., Canyuk, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.191
R-Value Work: 0.177

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystallographic investigation and inhibition of Brugia malayi thymidylate synthase by a folate analog

Keyunratsami, K., Nualnoi, T., Wongkamchai, S., Songsiriritthigul, C., Chen, C.-J., Canyuk, B.

To be published.

Macromolecule Content

Total Structure Weight: 35.68 kDa
Atom Count: 2,728
Modelled Residue Count: 287
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	306	Brugia malayi	Mutation(s): 0 Gene Names: Bma-tyms-1.1, BM_BM7277 EC: 2.1.1.45
UniProt
Find proteins for A0A4E9EZW9 (Brugia malayi) Explore A0A4E9EZW9 Go to UniProtKB: A0A4E9EZW9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4E9EZW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTX Query on MTX Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	METHOTREXATE C₂₀ H₂₂ N₈ O₅ FBOZXECLQNJBKD-ZDUSSCGKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
UMP Query on UMP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]