4MES

Crystal structure of ThiT complexed with LMG116

• PDB DOI: https://doi.org/10.2210/pdb4MES/pdb

• Classification: THIAMINE BINDING PROTEIN
• Organism(s): Lactococcus cremoris subsp. cremoris NZ9000
• Expression System: Lactococcus cremoris subsp. cremoris NZ9000
• Mutation(s): No 


• Deposited: 2013-08-27 Released: 2014-08-27 
• Deposition Author(s): Swier, L.J.Y.M., Guskov, A., Slotboom, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Crystal structures of ThiT with small molecule modulators

Swier, L.J.Y.M., Gomez, L., Guskov, A., Hirsch, A.K.H., Slotboom, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.87 kDa 
• Atom Count: 3,551 
• Modelled Residue Count: 353 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine transporter ThiT	A, B	182	Lactococcus cremoris subsp. cremoris NZ9000	Mutation(s): 0  Gene Names: LLNZ_01755, thiT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNG	AA [auth B], BA [auth B], C [auth A], D [auth A], X [auth B], Y [auth B], Z [auth B]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
P6G	T [auth A], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
26G	CA [auth B], E [auth A]	2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}ethanol C14 H17 N3 O CLAXVJRRXGSGJP-UHFFFAOYSA-N
1PE	SA [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	DA [auth B], EA [auth B], F [auth A], FA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PG0	S [auth A], TA [auth B]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG	GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
26G	BindingDB:  4MES	Kd: 528 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.53	α = 90
b = 84.2	β = 93.52
c = 127.21	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Swier, L.J.Y.M., Guskov, A., Slotboom, D.J.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary