4N4D | pdb_00004n4d

Structure of ThiT with AV-38 bound

• PDB DOI: https://doi.org/10.2210/pdb4N4D/pdb

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


• Deposited: 2013-10-08 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: 2.40 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structural studies on the thiamine binding protein ThiT

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: 45.18 kDa 
• Atom Count: 3,165 
• Modeled Residue Count: 352 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	BA [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
BNG	D [auth A], E [auth A], F [auth A], V [auth B], W [auth B]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
1PE	EA [auth B], T [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
XX8	C [auth A], U [auth B]	{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}methanol C13 H15 N3 O WCYNVVXZGIHJNV-UHFFFAOYSA-N
PG4	AA [auth B], O [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	CA [auth B], DA [auth B], P [auth A], Q [auth A], R [auth A], S [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0	G [auth A], H [auth A], X [auth B]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	FA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
XX8	BindingDB:  4N4D	Kd: 266 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.16	α = 90
b = 84.26	β = 94.17
c = 127.25	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: 2014-09-17 
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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary