SMTL ID : 7yp5.1

Crystal structure of elaiophylin glycosyltransferase in complex with TDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 16 residues within 4Å: Chain A: S.32, H.247, N.248, S.270, G.271, V.272, S.273, A.302, F.323, V.324, P.325, L.326, H.339, G.343, S.344 Ligands: PGR.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.32, A:N.248, A:V.272, A:S.273, A:S.273, A:V.324, A:V.324, A:L.326, A:S.344 Water bridges: A:F.342 Salt bridges: A:H.339 pi-Stacking: A:F.323 TYD.8: 17 residues within 4Å: Chain B: S.32, H.247, N.248, S.270, G.271, S.273, A.274, A.302, F.323, V.324, P.325, L.326, H.339, G.341, G.343, S.344 Ligands: PGR.9 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.248, B:S.273, B:S.273, B:S.273, B:A.274, B:V.324, B:V.324, B:L.326, B:S.344 Water bridges: B:F.35, B:H.247, B:H.339, B:F.342, B:F.342, B:G.343, B:G.343, B:S.344 Salt bridges: B:H.339, B:H.339 pi-Stacking: B:F.323

9 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.2: 7 residues within 4Å: Chain A: S.32, H.33, W.170, G.341, F.342, W.365 Ligands: TYD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.170 Hydrogen bonds: A:F.342 Water bridges: A:G.343 PGR.3: 8 residues within 4Å: Chain A: S.95, W.97, S.117, Y.122, I.174, Y.175, A.363 Ligands: PGR.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.122, A:Y.175, A:A.363 Water bridges: A:W.97 PGR.4: 5 residues within 4Å: Chain A: A.121, Y.122, Y.175, Y.362 Ligands: PGR.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.121, A:Y.122 Hydrogen bonds: A:Y.175 PGR.5: 8 residues within 4Å: Chain A: L.268, T.269, A.274, L.278, M.288, H.338, H.339, P.358 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.278 Hydrogen bonds: A:H.339 PGR.7: 4 residues within 4Å: Chain A: A.47, E.429 Chain B: H.422, D.423 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.47 Hydrogen bonds: B:D.423 PGR.9: 8 residues within 4Å: Chain B: S.32, H.33, T.36, W.170, G.341, F.342, W.365 Ligands: TYD.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.36, B:W.170 Hydrogen bonds: B:F.342 PGR.10: 7 residues within 4Å: Chain B: S.95, W.97, Y.122, I.174, Y.175, A.363 Ligands: PGR.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.174, B:Y.175 Hydrogen bonds: B:Y.122, B:Y.122, B:A.363 PGR.11: 6 residues within 4Å: Chain B: T.269, S.270, A.274, L.278, H.339, P.358 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.274, B:H.339 Hydrogen bonds: B:P.358 PGR.12: 5 residues within 4Å: Chain B: Y.122, Y.175, Y.362, A.363 Ligands: PGR.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.362 Hydrogen bonds: B:Y.175, B:Y.175

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

CL.6: 1 residues within 4Å: Chain A: R.263 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, T. et al., Substrate-induced dimerization of elaiophylin glycosyltransferase reveals a novel self-activating form of glycosyltransferase for symmetric glycosylation. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-11-02

Peptides

Glycosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycosyltransferase

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