SMTL ID : 8bz6.1 (2 other biounits)

Crystal structure of the L. monocytogenes RmlT in complex with UDP-glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.1: 18 residues within 4Å: Chain A: P.27, T.28, Y.29, D.60, N.87, G.89, W.90, G.91, R.95, D.111, H.112, D.113, P.173, H.174, E.198, W.224, N.230 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.29 Hydrogen bonds: A:P.27, A:D.60, A:D.60, A:N.87, A:G.89, A:R.95, A:R.95, A:D.111, A:H.112, A:H.174, A:E.198, A:W.224, A:N.230 Salt bridges: A:H.112 UPG.9: 20 residues within 4Å: Chain B: P.27, T.28, 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, W.224, N.230, N.231 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.29 Hydrogen bonds: B:P.27, B:Y.29, B:D.60, B:G.89, B:R.95, B:R.95, B:D.111, B:H.112, B:H.174, B:W.224, B:N.230, B:N.231 Salt bridges: B:H.112

11 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 9 residues within 4Å: Chain A: K.139, S.147, W.148, G.149, W.150, F.153, T.424, W.425, K.426 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.150 Hydrogen bonds: A:W.148, A:T.424, A:T.424 Water bridges: A:K.139, A:K.426 Salt bridges: A:K.139 ACT.4: 5 residues within 4Å: Chain A: D.218, W.425, D.458, Y.459 Ligands: ACT.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.425, A:Y.459 Hydrogen bonds: A:D.458 ACT.5: 4 residues within 4Å: Chain A: I.460, L.461, D.462, A.463 No protein-ligand interaction detected (PLIP) ACT.6: 4 residues within 4Å: Chain A: I.492, L.493, I.494 Chain B: Q.338 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.335 Hydrogen bonds: A:I.494 ACT.7: 2 residues within 4Å: Chain A: A.574, D.575 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.575 ACT.8: 6 residues within 4Å: Chain A: S.154, E.155, A.217, D.218, W.425 Ligands: ACT.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.425 Hydrogen bonds: A:A.217 Water bridges: A:N.156, A:N.156 ACT.11: 5 residues within 4Å: Chain B: I.460, L.461, D.462, A.463, K.466 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.460, B:K.466 ACT.12: 3 residues within 4Å: Chain B: I.492, L.493, I.494 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.492, B:I.494 Salt bridges: B:K.495 ACT.13: 9 residues within 4Å: Chain B: K.139, S.147, W.148, G.149, W.150, F.153, T.424, W.425, K.426 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.150 Hydrogen bonds: B:W.148, B:T.424, B:T.424 Water bridges: B:K.139, B:K.426 Salt bridges: B:K.139 ACT.14: 5 residues within 4Å: Chain B: D.218, W.425, D.458, Y.459 Ligands: ACT.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.425, B:Y.459 Hydrogen bonds: B:D.458 ACT.15: 6 residues within 4Å: Chain B: F.153, S.154, E.155, N.156, A.217 Ligands: ACT.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.154, B:N.156

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.113, D.114 Ligands: UPG.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.113, A:D.113, H2O.1, H2O.4 MG.10: 4 residues within 4Å: Chain B: D.113, D.114, N.230 Ligands: UPG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.113, B:D.113, H2O.7, H2O.8

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 3 residues within 4Å: Chain B: R.419, Y.507, N.509 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2023-12-27

Peptides

Glycosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycosyltransferase

Related Entries With Identical Sequence