SMTL ID : 8ay1.1

Crystal structure of the C. elegans POFUT2 (CePoFUT2) triple mutant (R298K-R299K-A418C) in complex with the Rattus norvegicus TSR4 single mutant (E10C) from F-spondin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 6 residues within 4Å: Chain A: F.111, K.113, Q.148, H.165, N.167, F.168 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.111 Hydrogen bonds: A:Q.148, A:H.165, A:N.167 NAG.14: 7 residues within 4Å: Chain B: K.113, Q.148, L.162, H.165, N.167, F.168 Ligands: EDO.18 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.162 Hydrogen bonds: B:K.113, B:Q.148, B:H.165, B:N.167

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

EDO.2: 3 residues within 4Å: Chain A: R.200, D.353, I.356 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.197 EDO.3: 5 residues within 4Å: Chain A: C.369, P.374, T.375, C.376, Q.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.375, A:Q.378 EDO.4: 7 residues within 4Å: Chain A: F.256, E.343, F.348, C.422, V.424, T.425, L.458 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.343, A:V.424 Water bridges: A:C.422 EDO.5: 8 residues within 4Å: Chain A: E.343, F.348, Q.351, F.365, P.379, C.380, W.382, D.421 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.343, A:Q.351 EDO.6: 3 residues within 4Å: Chain A: E.2, K.3, R.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.3, A:R.88 EDO.7: 7 residues within 4Å: Chain A: R.20, D.21, M.24, Y.192, R.196, R.349, E.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.20, A:Y.192 EDO.16: 4 residues within 4Å: Chain B: R.34, G.37, E.38, N.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.34, B:R.34, B:G.37 EDO.17: 5 residues within 4Å: Chain B: R.19, P.45, P.46, W.47, G.48 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.48 Water bridges: B:R.19 EDO.18: 5 residues within 4Å: Chain B: K.113, Q.148, N.167, F.168 Ligands: NAG.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.148, B:Q.148, B:N.167 EDO.19: 5 residues within 4Å: Chain B: D.67, S.70, R.200, N.203, D.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.70, B:R.200, B:R.200 EDO.20: 1 residues within 4Å: Chain B: K.110 No protein-ligand interaction detected (PLIP)

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 6 residues within 4Å: Chain A: G.15, F.16, N.17, L.50, T.345, F.346 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.16, A:N.17, A:N.17, A:T.345 Water bridges: A:G.15, A:S.344, A:F.346 SO4.9: 5 residues within 4Å: Chain A: C.380, K.381, W.382, S.417, C.418 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.382, A:C.418 SO4.10: 4 residues within 4Å: Chain A: R.253, T.266, I.267, P.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.267 Salt bridges: A:R.253 SO4.11: 6 residues within 4Å: Chain A: R.252, R.253, R.254, D.291, A.292 Chain B: K.125 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.253, A:R.254, A:D.291 Water bridges: A:A.292, A:A.292 Salt bridges: A:R.252, A:R.254, B:K.125 SO4.12: 2 residues within 4Å: Chain A: R.31, R.34 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.31, A:R.34 SO4.13: 6 residues within 4Å: Chain A: L.50, H.51, H.52, W.53, R.254 Chain B: S.122 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.52, B:S.122 Salt bridges: A:H.51, A:H.52, A:R.254 SO4.21: 8 residues within 4Å: Chain A: K.125 Chain B: W.251, R.252, R.253, R.254, T.290, D.291, A.292 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.251, B:R.253, B:R.254, B:T.290, B:D.291 Salt bridges: B:R.252, B:R.254, A:K.125 SO4.22: 7 residues within 4Å: Chain A: S.122 Chain B: L.50, H.51, H.52, W.53, R.254, F.256 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.50, B:H.52 Salt bridges: B:H.51, B:R.254 SO4.23: 7 residues within 4Å: Chain B: G.15, F.16, N.17, L.50, T.345, F.346 Ligands: GOL.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.16, B:N.17, B:N.17, B:T.345 Water bridges: B:G.15 SO4.24: 2 residues within 4Å: Chain B: R.31, R.34 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.31, B:R.34 SO4.25: 2 residues within 4Å: Chain B: R.239, K.383 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.239, B:K.383 SO4.26: 4 residues within 4Å: Chain B: R.253, T.266, I.267, P.268 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.267 Salt bridges: B:R.253

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 7 residues within 4Å: Chain B: R.252, E.343, S.344, T.345, F.346, T.425 Ligands: SO4.23 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.252, B:S.344, B:T.345, B:F.346 Water bridges: B:T.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanz-Martinez, I. et al., The Essential Role of Water Molecules in the Reaction Mechanism of Protein O-Fucosyltransferase 2. Angew.Chem.Int.Ed.Engl. (2022)

Release Date

2022-10-26

Peptides

GDP-fucose protein O-fucosyltransferase 2,Spondin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GDP-fucose protein O-fucosyltransferase 2,Spondin-1