6K7Q

Crystal structure of thymidylate synthase from shrimp

PDB DOI: https://doi.org/10.2210/pdb6K7Q/pdb

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
View more details

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

DOI: https://doi.org/10.1007/s00343-019-9184-8

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	292	Penaeus vannamei	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A423U5Z1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth J] SDF format, chain CA [auth K] SDF format, chain DA [auth L] SDF format, chain EA [auth M] SDF format, chain FA [auth N] SDF format, chain GA [auth O] SDF format, chain HA [auth P] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth I] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth J] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain EA [auth M] MOL2 format, chain FA [auth N] MOL2 format, chain GA [auth O] MOL2 format, chain HA [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth I] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth J] mmCIF format, chain CA [auth K] mmCIF format, chain DA [auth L] mmCIF format, chain EA [auth M] mmCIF format, chain FA [auth N] mmCIF format, chain GA [auth O] mmCIF format, chain HA [auth P] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth I]	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		Interactions Focus chain AA [auth J] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth P] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth P] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth I]

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 = 103.27	α = 77.4
b = 103.458	β = 84.81
c = 125.768	γ = 61.43

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-10

Deposition Author(s):

Ma, Q.

Zang, K.

Liu, C.

Funding Organization	Location	Grant Number
Other government	China	1000 talent program
Chinese Academy of Sciences	China	100 talent program
National Natural Science Foundation of China	China	--
National Natural Science Foundation of China	China	--

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