SMTL ID : 5t67.1

x-ray structure of the KijD1 C3-methyltransferase from Actinomadura kijaniata in complex with SAH and dTDP-sugar product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.15, C.18, C.56, C.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.15, A:C.18, A:C.56, A:C.59 ZN.10: 4 residues within 4Å: Chain B: C.15, C.18, C.56, C.59 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.15, B:C.18, B:C.56, B:C.59

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 22 residues within 4Å: Chain A: F.74, Y.78, Y.80, S.82, F.92, E.113, I.114, G.115, N.117, F.135, E.136, P.137, S.138, F.156, F.157, A.178, N.179, T.180, H.183, I.184, Y.186 Ligands: JHZ.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:N.117 Hydrogen bonds: A:S.82, A:G.115, A:N.117, A:S.138, A:S.138, A:F.157, A:F.157, A:A.178, A:N.179 Water bridges: A:Y.80, A:A.178, A:Y.186, A:Y.186 pi-Stacking: A:F.74 SAH.11: 19 residues within 4Å: Chain B: F.74, S.82, F.92, I.114, G.115, N.117, F.135, E.136, P.137, S.138, F.156, F.157, A.178, N.179, T.180, H.183, I.184, Y.186 Ligands: JHZ.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:N.117 Hydrogen bonds: B:S.82, B:G.115, B:G.115, B:N.117, B:S.138, B:F.157, B:F.157, B:N.179, B:T.180, B:Y.186 Water bridges: B:A.178 pi-Stacking: B:F.74

2 x JHZ: (2R,4S,6R)-4-amino-4,6-dimethyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)(Non-covalent)

JHZ.3: 26 residues within 4Å: Chain A: D.35, Y.78, Y.80, N.179, H.183, Y.224, E.226, H.227, H.256, Y.325, G.326, A.327, T.328, A.329, K.330, D.350, T.351, T.352, K.355, A.385, N.387, H.388, E.391, I.392, K.395 Ligands: SAH.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:N.179, A:H.388 Hydrogen bonds: A:Y.78, A:H.183, A:Y.224, A:E.226, A:A.329, A:K.330, A:T.351, A:T.352, A:T.352, A:N.387, A:K.395 Water bridges: A:Y.80, A:Y.80, A:S.85, A:Y.325, A:Y.325, A:K.330, A:K.355 Salt bridges: A:H.256, A:H.256, A:K.330, A:K.330, A:H.388 JHZ.12: 26 residues within 4Å: Chain B: D.35, Y.78, Y.80, H.183, Y.224, E.226, H.227, H.256, Y.325, G.326, A.327, T.328, A.329, K.330, C.349, D.350, T.351, T.352, K.355, A.385, N.387, H.388, E.391, I.392, K.395 Ligands: SAH.11 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.329, B:I.392 Hydrogen bonds: B:Y.78, B:Y.224, B:Y.224, B:A.329, B:K.330, B:T.351, B:T.351, B:T.352, B:T.352, B:K.355, B:N.387, B:E.391, B:K.395, B:K.395 Water bridges: B:S.85, B:K.330, B:H.388 Salt bridges: B:H.256, B:K.330, B:K.330, B:H.388

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

EDO.4: 3 residues within 4Å: Chain A: P.411, E.412, R.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.412, A:R.414 EDO.5: 4 residues within 4Å: Chain A: H.126, G.129, V.130, H.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.130, A:H.132 EDO.6: 2 residues within 4Å: Chain A: R.70, Y.186 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.189 EDO.13: 6 residues within 4Å: Chain B: H.91, K.94, V.95, R.98, E.251, R.261 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.91, B:E.251, B:R.261, B:R.261

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain A: L.26, D.27, H.302 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dow, G.T. et al., Structural studies on KijD1, a sugar C-3'-methyltransferase. Protein Sci. (2016)

Release Date

2016-09-14

Peptides

Sugar 3-C-methyl transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sugar 3-C-methyl transferase

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