7XYJ | pdb_00007xyj

Structure of WSSV thymidylate synthase in complex with dUMP

PDB DOI: https://doi.org/10.2210/pdb7XYJ/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: 2.27 Å
R-Value Free:
0.208 (Depositor), 0.210 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (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

Structure of WSSV thymidylate synthase in complex with dUMP

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

To be published.

Macromolecule Content

Total Structure Weight: 136.66 kDa
Atom Count: 9,433
Modeled Residue Count: 1,120
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UMP (Subject of Investigation/LOI) Query on UMP Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [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], Q [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 Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain Q [auth D]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], K [auth C], R [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain R [auth D]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain L [auth C] MOL2 format, chain S [auth D] MOL2 format, chain L [auth C] mmCIF format, chain S [auth D] mmCIF format, chain L [auth C]	L [auth C], S [auth D]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain S [auth D] Interactions & Density Focus chain L [auth C] Focus chain S [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C]	G [auth A], M [auth C], N [auth C], O [auth C], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]