4POV

ThiT with LMG135 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiamine transporter ThiT
A, B
192Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
Gene Names: llmg_0334LLNZ_01755thiT
Membrane Entity: Yes 
UniProt
Find proteins for A2RI47 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RI47 
Go to UniProtKB:  A2RI47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RI47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BNG
Query on BNG

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CA [auth B]
DA [auth B]
EA [auth B]
J [auth A]
K [auth A]
CA [auth B],
DA [auth B],
EA [auth B],
J [auth A],
K [auth A],
L [auth A]
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
P6G
Query on P6G

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V [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
2VY
Query on 2VY

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C [auth A],
W [auth B]
4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophene-2-carbaldehyde
C12 H13 N3 O S
NWGVSSQLYKZANM-UHFFFAOYSA-N
1PE
Query on 1PE

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KA [auth B],
LA [auth B],
R [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

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AA [auth B]
BA [auth B]
E [auth A]
F [auth A]
G [auth A]
AA [auth B],
BA [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
Y [auth B],
Z [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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S [auth A],
T [auth A],
U [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0
Query on PG0

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

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FA [auth B]
GA [auth B]
HA [auth B]
IA [auth B]
JA [auth B]
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL
Query on CL

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MA [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
2VY BindingDB:  4POV Kd: 7.44 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.72α = 90
b = 84.35β = 96.08
c = 127.25γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
CCP4model building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary