8BZ7

Crystal structure of the L. monocytogenes RmlT in complex with TDP-rhamnose

PDB DOI: https://doi.org/10.2210/pdb8BZ7/pdb

Classification: TRANSFERASE
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-14 Released: 2023-12-27
Deposition Author(s): Cereija, T.B., Morais-Cabral, J.H.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.215
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the L. monocytogenes RmlT in complex with TDP-rhamnose

Monteiro, R., Cereija, T.B., Morais-Cabral, J.H., Cabanes, D.

To be published.

Macromolecule Content

Total Structure Weight: 434.86 kDa
Atom Count: 30,744
Modelled Residue Count: 3,597
Deposited Residue Count: 3,744
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B, C, D, E A, B, C, D, E, F	624	Listeria monocytogenes	Mutation(s): 0 Gene Names: APD94_03445
UniProt
Find proteins for A0A401AAP7 (Listeria monocytogenes) Explore A0A401AAP7 Go to UniProtKB: A0A401AAP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A401AAP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRH (Subject of Investigation/LOI) Query on TRH Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth F] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D]	AA [auth E] FA [auth F] G [auth A] L [auth B] R [auth C] AA [auth E], FA [auth F], G [auth A], L [auth B], R [auth C], U [auth D]	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE C₁₆ H₂₆ N₂ O₁₅ P₂ ZOSQFDVXNQFKBY-CGAXJHMRSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain U [auth D]
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D]	DA [auth E] I [auth A] IA [auth F] O [auth B] T [auth C] DA [auth E], I [auth A], IA [auth F], O [auth B], T [auth C], Y [auth D]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain DA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Z [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth D]	EA [auth E] J [auth A] K [auth A] P [auth B] Q [auth B] EA [auth E], J [auth A], K [auth A], P [auth B], Q [auth B], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain X [auth D] MOL2 format, chain HA [auth F] MOL2 format, chain X [auth D]	HA [auth F], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth F] Focus chain X [auth D] Interactions & Density Focus chain HA [auth F] Focus chain X [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D]	BA [auth E] CA [auth E] GA [auth F] H [auth A] M [auth B] BA [auth E], CA [auth E], GA [auth F], H [auth A], M [auth B], N [auth B], S [auth C], V [auth D], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D]