SMTL ID : 6bgd.1

The crystal structure of the W145A variant of TpMglB-2 (Tp0684) with bound ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: F.46, A.48, G.51, G.52, D.91, V.94, R.95, Y.194, N.272 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.91, A:D.91, A:R.95, A:R.95, A:Y.194 EDO.2: 10 residues within 4Å: Chain A: G.85, D.86, D.91, S.92, R.95, T.144, A.145, N.171, N.172, M.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.86, A:N.171 EDO.3: 3 residues within 4Å: Chain A: N.352, D.354, M.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.354 EDO.4: 6 residues within 4Å: Chain A: F.62, G.188, L.189, P.190, T.210 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.188 Water bridges: A:T.210 EDO.5: 9 residues within 4Å: Chain A: L.180, Y.185, P.186, R.187, G.188, G.207, E.208 Ligands: EDO.4, EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.188, A:G.207 EDO.6: 5 residues within 4Å: Chain A: R.187, G.188, G.207, E.208 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) EDO.7: 8 residues within 4Å: Chain A: V.241, A.242, I.245, S.246, V.259, Q.260, Y.261, I.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.241, A:S.246 Water bridges: A:V.259 EDO.8: 7 residues within 4Å: Chain A: N.19, Q.21, Y.43, G.45, F.46, A.48, M.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.43, A:F.46 Water bridges: A:Q.21, A:Y.43 EDO.9: 7 residues within 4Å: Chain A: Y.42, G.237, E.238, V.240, V.241, Y.261, E.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.42, A:Y.42, A:G.237 EDO.10: 8 residues within 4Å: Chain A: N.19, R.20, Q.215, H.307, N.311, F.313, L.314, N.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.19, A:H.307 Water bridges: A:N.19

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 7 residues within 4Å: Chain A: D.71, N.73, D.75, I.77, I.78, G.79, D.166 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.71, A:D.75, A:I.77, A:D.166, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brautigam, C.A. et al., Crystal structures of MglB-2 (TP0684), a topologically variant d-glucose-binding protein from Treponema pallidum, reveal a ligand-induced conformational change. Protein Sci. (2018)

Release Date

2018-01-31

Peptides

Glucose/galactose-binding lipoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucose/galactose-binding lipoprotein