6K7Q

Crystal structure of thymidylate synthase from shrimp

  • Classification: TRANSFERASE
  • Organism(s): Penaeus vannamei
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-06-08 Released: 2020-06-10 
  • Deposition Author(s): Ma, Q., Zang, K., Liu, C.
  • Funding Organization(s): Other government, Chinese Academy of Sciences, National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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

Structural analysis of a shrimp thymidylate synthase reveals species-specific interactions with dUMP and raltitrexed.

Liu, C.Zang, K.Li, S.Li, F.Ma, Q.

(2020) J Oceanol Limnol 38: 1891-1899


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
292Penaeus vannameiMutation(s): 0 
Gene Names: TS
EC: 2.1.1.45
UniProt
Find proteins for A0A423U5Z1 (Penaeus vannamei)
Explore A0A423U5Z1 
Go to UniProtKB:  A0A423U5Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A423U5Z1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth J]
CA [auth K]
DA [auth L]
EA [auth M]
AA [auth J],
BA [auth J],
CA [auth K],
DA [auth L],
EA [auth M],
FA [auth N],
GA [auth O],
HA [auth P],
Q [auth A],
R [auth A],
S [auth C],
T [auth C],
U [auth D],
V [auth E],
W [auth F],
X [auth G],
Y [auth G],
Z [auth I]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.27α = 77.4
b = 103.458β = 84.81
c = 125.768γ = 61.43
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina1000 talent program
Chinese Academy of SciencesChina100 talent program
National Natural Science Foundation of ChinaChina--
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description