4MHW

Crystal structure of ThiT with small molecule BAT-25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of ThiT with small molecules modulators

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiamine transporter ThiTA, B192Lactococcus lactis subsp. cremoris NZ9000Mutation(s): 0 
Gene Names: LLNZ_01755
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download Ideal Coordinates CCD File 
N [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
BNG
Query on BNG

Download Ideal Coordinates CCD File 
D [auth A],
T [auth B],
U [auth B]
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
0YN
Query on 0YN

Download Ideal Coordinates CCD File 
C [auth A],
S [auth B]
2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethanol
C13 H17 N3 O S
HLBXMICRXICHJQ-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
G [auth A],
V [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
KA [auth B],
LA [auth B],
P [auth A],
Q [auth A],
R [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PG0
Query on PG0

Download Ideal Coordinates CCD File 
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
O [auth A]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0YN BindingDB:  4MHW Kd: 4.23 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.73α = 90
b = 84.09β = 94.58
c = 128.81γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary