SMTL ID : 8bz7.2 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x TRH: 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE(Non-covalent)

TRH.1: 20 residues within 4Å: Chain A: P.27, Y.29, D.60, N.87, G.89, W.90, G.91, P.94, R.95, D.111, H.112, D.113, P.173, H.174, E.198, D.199, W.224, N.230 Ligands: MG.2, GOL.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.29, A:Y.29, A:W.90, A:W.90 Hydrogen bonds: A:D.60, A:D.60, A:N.87, A:G.89, A:G.91, A:R.95, A:D.111, A:D.111, A:D.111, A:H.112, A:N.230 Salt bridges: A:H.112 TRH.7: 14 residues within 4Å: Chain B: P.27, Y.29, D.60, N.87, G.89, W.90, G.91, P.94, D.111, H.112, D.113, W.224, N.230 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.29, B:W.90, B:W.90 Hydrogen bonds: B:D.60, B:N.87, B:G.89, B:D.111, B:D.111, B:H.112, B:D.113, B:W.224, B:N.230 Salt bridges: B:H.112

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.113, N.230 Ligands: TRH.1 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.113, A:D.113, H2O.1, H2O.2, TRH.1 MG.3: 4 residues within 4Å: Chain A: Y.348, D.371 Chain B: Y.348, D.371 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:Y.348, B:D.371, A:Y.348, H2O.6, H2O.13 MG.8: 3 residues within 4Å: Chain B: D.113, D.114 Ligands: TRH.7 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.113, B:D.113, TRH.7, H2O.10, H2O.11

2 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.4: 6 residues within 4Å: Chain A: S.147, W.148, G.149, W.150, P.170 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.149, A:W.150 Water bridges: A:K.151, A:Q.152 TAR.9: 4 residues within 4Å: Chain B: S.147, W.148, G.149, W.150 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.149, B:W.150 Water bridges: B:K.151, B:Q.152

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: W.148, T.172, W.197, D.199, V.200 Ligands: TRH.1, TAR.4 No protein-ligand interaction detected (PLIP) GOL.6: 4 residues within 4Å: Chain A: D.351, A.352, Y.353, K.495 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.352, A:K.495

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Monteiro, R. et al., Crystal structure of the L. monocytogenes RmlT in complex with TDP-rhamnose. To Be Published

Release Date

2023-12-27

Peptides

Glycosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Glycosyltransferase

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