SMTL ID : 6jtd.2 (1 other biounit)

Crystal structure of TcCGT1 in complex with UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 21 residues within 4Å: Chain A: M.22, G.23, I.26, R.253, Y.278, G.282, S.283, G.284, V.309, W.354, G.355, Q.357, H.372, G.374, W.375, N.376, S.377, E.380, Y.394, Q.397 Ligands: EDO.27 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.23, A:R.253, A:S.283, A:G.284, A:G.355, A:G.355, A:Q.357, A:Q.357, A:N.376, A:N.376, A:S.377, A:E.380, A:Y.394, A:Y.394, A:Q.397 Water bridges: A:G.23, A:R.253, A:W.375 Salt bridges: A:H.372, A:H.372 pi-Stacking: A:W.354

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

EDO.2: 6 residues within 4Å: Chain A: H.13, Q.42, M.112, T.114, P.115, P.116 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: P.20, G.21, L.25, V.48, S.49, N.50, R.56 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: D.189, A.320, Y.394, A.395 Ligands: EDO.34 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: F.91, P.190, G.198, P.201, Y.202, M.205 Ligands: EDO.34 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: I.26, L.29, E.30, K.33, L.59, S.63, R.253 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: L.361, A.362, H.363, N.384, G.385, V.386 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: E.30, K.33, R.34, T.37, F.66 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: R.34, V.248, I.459, S.465, Y.466, L.469 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: N.64, H.67, P.68, L.70, E.71 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: D.127, P.130, R.208 Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: K.103, E.106, V.131 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: E.106, S.107, S.110, R.134 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: V.123, F.124, S.125, M.126, D.127, R.208 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: Y.140, D.213, G.214, P.244, Y.246, E.475 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: R.157, T.158, I.240 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: K.180, P.181, R.183, T.402, E.406 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: R.253, T.254, T.255, V.256, D.358, A.362, N.384 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: W.148, K.180, E.224, S.227, L.403 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: L.341, G.348, M.349, V.350 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: W.267, K.345, G.348, M.349 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: L.281, G.285, I.287, W.308, V.309, V.310, R.311 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: P.418, T.419, K.420, A.421, V.422 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: V.422 Ligands: EDO.23 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: T.293, W.297, R.425 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: E.300, R.303, R.343 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: G.21, S.283, G.284, C.321, F.323, Y.394 Ligands: UDP.1 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain A: L.333, L.336, P.337, G.339, F.340, L.341, D.342 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: G.409, M.443, K.444, R.447 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: A.411, V.412, R.413, R.434, K.444 Ligands: EDO.31 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain A: R.413, P.414, E.415, E.427, K.430, M.431, R.434 Ligands: EDO.30 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain A: E.274, K.442, R.445, N.446, R.449 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain A: G.23, H.24, F.124, T.144, L.145, N.376 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain A: F.124, F.188, D.189, P.190, A.395 Ligands: EDO.4, EDO.5 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain A: L.192, K.398, T.419, K.420 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: I.109, S.110, M.112, T.114, P.115, F.135 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain A: R.232, L.245, P.247 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, J.B. et al., Molecular and Structural Characterization of a Promiscuous C-Glycosyltransferase from Trollius chinensis. Angew.Chem.Int.Ed.Engl. (2019)

Release Date

2019-06-19

Peptides

C-glycosyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C-glycosyltransferase

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