7DP5 | pdb_00007dp5

Crystal structure of mutant V45A Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate and methotrexate

PDB DOI: https://doi.org/10.2210/pdb7DP5/pdb

Classification: TRANSFERASE
Organism(s): Brugia malayi
Expression System: Escherichia coli
Mutation(s): Yes

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: 1.60 Å
R-Value Free:
0.189 (Depositor), 0.199 (DCC)
R-Value Work:
0.171 (Depositor), 0.181 (DCC)

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

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: 35.6 kDa
Atom Count: 2,666
Modeled Residue Count: 287
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	306	Brugia malayi	Mutation(s): 1 Gene Names: Bma-tyms-1.1, BM_BM7277 EC: 2.1.1.45
UniProt
Find proteins for A0A1P6CBU1 (Brugia malayi) Explore A0A1P6CBU1 Go to UniProtKB: A0A1P6CBU1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1P6CBU1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]