4MES

Crystal structure of ThiT complexed with LMG116


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
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiamine transporter ThiT
A, B
182Lactococcus cremoris subsp. cremoris NZ9000Mutation(s): 0 
Gene Names: LLNZ_01755thiT
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BNG
Query on BNG

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AA [auth B]
BA [auth B]
C [auth A]
D [auth A]
X [auth B]
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
Query on P6G

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T [auth A]
U [auth A]
UA [auth B]
V [auth A]
VA [auth B]
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
Query on 26G

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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
Query on 1PE

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SA [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

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DA [auth B]
EA [auth B]
F [auth A]
FA [auth B]
G [auth A]
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
Query on PG0

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S [auth A],
TA [auth B]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG
Query on PEG

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GA [auth B]
HA [auth B]
IA [auth B]
JA [auth B]
KA [auth B]
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 
IDSourceBinding 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 = 61.53α = 90
b = 84.2β = 93.52
c = 127.21γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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