7XYK | pdb_00007xyk

Structure of WSSV thymidylate synthase in complex with dUMP and raltitrexed

PDB DOI: https://doi.org/10.2210/pdb7XYK/pdb

Classification: TRANSFERASE
Organism(s): Shrimp white spot syndrome virus (isolate Tongan)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-01 Released: 2023-06-07
Deposition Author(s): Ma, Q., Liu, C., Zang, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.170 (Depositor), 0.182 (DCC)
R-Value Work:
0.148 (Depositor), 0.161 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of WSSV thymidylate synthase in complex with dUMP and raltitrexed

Ma, Q., Liu, C., Zang, K.

To be published.

Macromolecule Content

Total Structure Weight: 136.84 kDa
Atom Count: 10,444
Modeled Residue Count: 1,156
Deposited Residue Count: 1,168
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C, D	292	Shrimp white spot syndrome virus (isolate Tongan)	Mutation(s): 0 EC: 2.1.1.45
UniProt
Find proteins for Q77J90 (White spot syndrome virus (isolate Shrimp/China/Tongan/1996)) Explore Q77J90 Go to UniProtKB: Q77J90
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q77J90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D16 (Subject of Investigation/LOI) Query on D16 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain F [auth A]	F [auth A], I [auth B], K [auth C], M [auth D]	TOMUDEX C₂₁ H₂₂ N₄ O₆ S IVTVGDXNLFLDRM-HNNXBMFYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
UMP (Subject of Investigation/LOI) Query on UMP Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], J [auth C], L [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain G [auth A] MOL2 format, chain N [auth D] MOL2 format, chain G [auth A] mmCIF format, chain N [auth D] mmCIF format, chain G [auth A]	G [auth A], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth D]