4MES | pdb_00004mes

Crystal structure of ThiT complexed with LMG116

PDB DOI: https://doi.org/10.2210/pdb4MES/pdb

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

Deposited: 2013-08-27 Released: 2014-08-27
Deposition Author(s): Swier, L.J.Y.M., Guskov, A., Slotboom, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.208 (Depositor), 0.211 (DCC)
R-Value Work:
0.174 (Depositor), 0.182 (DCC)
R-Value Observed:
0.176 (Depositor)

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.

Macromolecule Content

Total Structure Weight: 48.87 kDa
Atom Count: 3,551
Modeled Residue Count: 353
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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| 3D Structure

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BNG Query on BNG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain D [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain C [auth A] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain C [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain C [auth A] mmCIF format, chain BA [auth B]	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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain VA [auth B] SDF format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain T [auth A]	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		Interactions Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Interactions & Density Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B]
26G Query on 26G Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain CA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth B]	CA [auth B], E [auth A]	2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}ethanol C₁₄ H₁₇ N₃ O CLAXVJRRXGSGJP-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain E [auth A] Interactions & Density Focus chain CA [auth B] Focus chain E [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain SA [auth B] MOL2 format, chain SA [auth B] mmCIF format, chain SA [auth B]	SA [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain SA [auth B] Interactions & Density Focus chain SA [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	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		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain TA [auth B] SDF format, chain S [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain S [auth A]	S [auth A], TA [auth B]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Focus chain TA [auth B] Interactions & Density Focus chain S [auth A] Focus chain TA [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain GA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B]	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		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B]

Binding Affinity Annotations
ID	Source	Binding 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 (Depositor), 0.211 (DCC)
R-Value Work: 0.174 (Depositor), 0.182 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.53	α = 90
b = 84.2	β = 93.52
c = 127.21	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Swier, L.J.Y.M.

Guskov, A.

Slotboom, D.J.

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