7XYJ

Structure of WSSV thymidylate synthase in complex with dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B, C, D
292Shrimp 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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ77J90
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UMP (Subject of Investigation/LOI)
Query on UMP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
Q [auth D]
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
R [auth D]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
M [auth C],
N [auth C],
O [auth C],
P [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.91α = 90
b = 132.35β = 90
c = 234.11γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description