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: 50.3 kDa 
• Atom Count: 3,367 
• Modelled Residue Count: 353 
• Deposited Residue Count: 384 
• Unique protein chains: 1

 4POP

ThiT with LMG139 bound

• PDB DOI:  https://doi.org/10.2210/pdb4POP/pdb

• Classification: PROTEIN BINDING
• Organism(s): Lactococcus cremoris subsp. cremoris MG1363
• Expression System: Lactococcus lactis
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2014-02-26 Released: 2014-09-17 
• 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: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.199 

Literature

Structure-Based Design of Potent Small-Molecule Binders to the S-Component of the ECF Transporter for Thiamine.

Swier, L.J., Monjas, L., Guskov, A., de Voogd, A.R., Erkens, G.B., Slotboom, D.J., Hirsch, A.K.

(2015) Chembiochem 16: 819-826

• PubMed: 25676607 
• DOI: https://doi.org/10.1002/cbic.201402673
• Primary Citation of Related Structures:  
  4POP, 4POV


• PubMed Abstract: 
  

Energy-coupling factor (ECF) transporters are membrane-protein complexes that mediate vitamin uptake in prokaryotes. They bind the substrate through the action of a specific integral membrane subunit (S-component) and power transport by hydrolysis of ATP in the three-subunit ECF module. Here, we have studied the binding of thiamine derivatives to ThiT, a thiamine-specific S-component. We designed and synthesized derivatives of thiamine that bind to ThiT with high affinity; this allowed us to evaluate the contribution of the functional groups to the binding affinity. We determined six crystal structures of ThiT in complex with our derivatives. The structure of the substrate-binding site in ThiT remains almost unchanged despite substantial differences in affinity. This work indicates that the structural organization of the binding site is robust and suggests that substrate release, which is required for transport, requires additional changes in conformation in ThiT that might be imposed by the ECF module.

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Organizational Affiliation: 

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands) http://www.rug.nl/research/membrane-enzymology/

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine transporter ThiT	A, B	192	Lactococcus cremoris subsp. cremoris MG1363	Mutation(s): 0  Gene Names: llmg_0334, LLNZ_01755, thiT Membrane Entity: Yes
UniProt
Find proteins for A2RI47 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RI47  Go to UniProtKB:  A2RI47

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	VA [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
BNG	CA [auth B], DA [auth B], F [auth A], G [auth A], H [auth A]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
P6G	Z [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
2VY	AA [auth B], C [auth A]	4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophene-2-carbaldehyde C12 H13 N3 O S NWGVSSQLYKZANM-UHFFFAOYSA-N
1PE	UA [auth B], W [auth A], X [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	PA [auth B], QA [auth B], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], V [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	Y [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0	BA [auth B], D [auth A], E [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG	EA [auth B], FA [auth B], GA [auth B], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], Q [auth A], R [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2VY	BindingDB:  4POP	Kd: 7.44 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.199 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.61	α = 90
b = 84.12	β = 95.13
c = 127.15	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
CCP4	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Swier, L.J.Y.M., Guskov, A., Slotboom, D.J.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary