4N4D | pdb_00004n4d

Structure of ThiT with AV-38 bound

PDB DOI: https://doi.org/10.2210/pdb4N4D/pdb

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

Deposited: 2013-10-08 Released: 2014-09-17
Deposition Author(s): Swier, L.J.Y.M., Guskov, A., Slotboom, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.204 (Depositor), 0.211 (DCC)
R-Value Observed:
0.207 (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

Structural studies on the thiamine binding protein ThiT

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

To be published.

Macromolecule Content

Total Structure Weight: 45.18 kDa
Atom Count: 3,165
Modeled Residue Count: 352
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 binding protein ThiT	A, B	182	Lactococcus cremoris subsp. cremoris NZ9000	Mutation(s): 0 Gene Names: LLNZ_01755

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
BNG Query on BNG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	D [auth A], E [auth A], F [auth A], V [auth B], W [auth B]	nonyl beta-D-glucopyranoside C₁₅ H₃₀ O₆ QFAPUKLCALRPLH-UXXRCYHCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain V [auth B] Focus chain W [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain T [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain T [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain T [auth A]	EA [auth B], T [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain T [auth A] Interactions & Density Focus chain EA [auth B] Focus chain T [auth A]
XX8 Query on XX8 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain U [auth B] MOL2 format, chain C [auth A] MOL2 format, chain U [auth B] mmCIF format, chain C [auth A] mmCIF format, chain U [auth B]	C [auth A], U [auth B]	{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}methanol C₁₃ H₁₅ N₃ O WCYNVVXZGIHJNV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain U [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain O [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain O [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain O [auth A]	AA [auth B], O [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain O [auth A] Interactions & Density Focus chain AA [auth B] Focus chain O [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain DA [auth B]	CA [auth B] DA [auth B] P [auth A] Q [auth A] R [auth A] CA [auth B], DA [auth B], P [auth A], Q [auth A], R [auth A], S [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain X [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain X [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain X [auth B]	G [auth A], H [auth A], X [auth B]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain X [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain X [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File 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 N [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] 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 N [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] 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 N [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions 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 N [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density 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 N [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] MOL2 format, chain FA [auth B] mmCIF format, chain FA [auth B]	FA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth B] Interactions & Density Focus chain FA [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
XX8	BindingDB: 4N4D	Kd: 266 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.257 (Depositor), 0.260 (DCC)
R-Value Work: 0.204 (Depositor), 0.211 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.16	α = 90
b = 84.26	β = 94.17
c = 127.25	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: 2014-09-17

Deposition Author(s):

Swier, L.J.Y.M.

Guskov, A.

Slotboom, D.J.

Revision History (Full details and data files)

Version 1.0: 2014-09-17
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