6K7Q | pdb_00006k7q

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 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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

Macromolecule Content 

  • Total Structure Weight: 541.3 kDa 
  • Atom Count: 35,306 
  • Modeled Residue Count: 4,215 
  • Deposited Residue Count: 4,672 
  • Unique protein chains: 1

Macromolecules

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|  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
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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 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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