4MHW | pdb_00004mhw

Crystal structure of ThiT with small molecule BAT-25

PDB DOI: https://doi.org/10.2210/pdb4MHW/pdb

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

Deposited: 2013-08-30 Released: 2014-09-03
Deposition Author(s): Swier, L.J.Y.M., Guskov, A., Slotboom, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.250 (Depositor), 0.231 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.192 (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 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.

Macromolecule Content

Total Structure Weight: 48.57 kDa
Atom Count: 3,207
Modeled Residue Count: 353
Deposited Residue Count: 384
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	192	Lactococcus cremoris subsp. cremoris NZ9000	Mutation(s): 0 Gene Names: LLNZ_01755

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE4 Query on PE4 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
BNG Query on BNG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain D [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain D [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	D [auth A], T [auth B], U [auth B]	nonyl beta-D-glucopyranoside C₁₅ H₃₀ O₆ QFAPUKLCALRPLH-UXXRCYHCSA-N		Interactions Focus chain D [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain T [auth B] Focus chain U [auth B]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
0YN Query on 0YN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain S [auth B] mmCIF format, chain C [auth A] mmCIF format, chain S [auth B]	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		Interactions Focus chain C [auth A] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain S [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain V [auth B] MOL2 format, chain G [auth A] MOL2 format, chain V [auth B] mmCIF format, chain G [auth A] mmCIF format, chain V [auth B]	G [auth A], V [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain V [auth B] Interactions & Density Focus chain G [auth A] Focus chain V [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain P [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain P [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain P [auth A]	KA [auth B], LA [auth B], P [auth A], Q [auth A], R [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Focus chain LA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain KA [auth B] Focus chain LA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain O [auth A] SDF format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain HA [auth B]	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		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain O [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain O [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] 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] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] 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] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] 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] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] 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] Focus chain W [auth B] 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 CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] 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] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding 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 (Depositor), 0.231 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.73	α = 90
b = 84.09	β = 94.58
c = 128.81	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

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Entry History

Deposition Data

Released Date: 2014-09-03

Deposition Author(s):

Swier, L.J.Y.M.

Guskov, A.

Slotboom, D.J.

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
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary