SMTL ID : 6cig.1

CRYSTAL STRUCTURE ANALYSIS OF SELENOMETHIONINE SUBSTITUTED ISOFLAVONE O-METHYLTRANSFERASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: D.171, L.174, Y.254, T.342, G.343, F.344, L.345 Chain B: Q.17, Y.21 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.171, A:F.344, B:Q.17, B:Y.21 Water bridges: A:Y.254, A:T.342, A:T.342 GOL.2: 4 residues within 4Å: Chain A: N.40, N.43, N.47, R.105 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.40, A:N.40, A:N.43, A:N.47, A:R.105 Water bridges: A:N.43, A:N.43 GOL.9: 9 residues within 4Å: Chain A: Q.17, Y.21 Chain B: D.171, L.174, Y.254, T.342, G.343, F.344, L.345 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.17, B:D.171, B:D.171, B:Y.254, B:F.344 Water bridges: B:T.342 GOL.10: 4 residues within 4Å: Chain B: N.40, N.43, N.47, R.105 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.40, B:N.40, B:N.43, B:N.47, B:R.105 Water bridges: B:N.43, B:N.43

2 x T3A: N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC ACID(Non-covalent)

T3A.3: 8 residues within 4Å: Chain A: G.149, F.150, W.151, D.152, D.239, F.241, R.266 Ligands: SAH.8 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.151, A:D.152, A:D.239, A:R.266, A:R.266 Water bridges: A:G.149, A:W.151, A:T.242, A:D.263, A:D.263 T3A.11: 8 residues within 4Å: Chain B: G.149, F.150, W.151, D.152, D.239, F.241, R.266 Ligands: SAH.16 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:W.151, B:D.152, B:D.239, B:R.266, B:R.266 Water bridges: B:G.149, B:W.151, B:T.242, B:D.263, B:D.263

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

SO4.4: 3 residues within 4Å: Chain A: G.69, R.72, R.73 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Water bridges: B:K.317, B:K.317, B:E.323, B:E.323, A:G.69, A:G.69, A:R.73, A:R.73 Salt bridges: B:K.317, A:R.72, A:R.73 SO4.5: 2 residues within 4Å: Chain A: K.293 Chain B: R.76 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Water bridges: B:R.76, B:R.76, B:R.76, A:N.320, A:N.320, A:N.320, A:N.320, A:N.320, A:N.320 Salt bridges: B:R.76, A:K.293 SO4.6: 1 residues within 4Å: Chain A: N.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.56, A:N.56 SO4.12: 3 residues within 4Å: Chain B: G.69, R.72, R.73 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Water bridges: B:G.69, B:G.69, B:R.73, B:R.73, A:K.317, A:K.317, A:K.317, A:K.317 Salt bridges: B:R.72, B:R.73, A:K.317 SO4.13: 2 residues within 4Å: Chain A: R.76 Chain B: K.293 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Water bridges: A:R.76, A:R.76, A:R.76, B:N.320, B:N.320, B:N.320, B:N.320, B:N.320, B:N.320, B:N.320 Salt bridges: A:R.76, B:K.293 SO4.14: 1 residues within 4Å: Chain B: N.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.56, B:N.56

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 11 residues within 4Å: Chain A: F.27, M.31, S.124, G.125, H.128 Chain B: F.27, M.31, S.124, G.125, H.128 Ligands: PG4.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.124, B:S.124 PG4.15: 11 residues within 4Å: Chain A: F.27, M.31, S.124, G.125, H.128 Chain B: F.27, M.31, S.124, G.125, H.128 Ligands: PG4.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.124, B:S.124

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

SAH.8: 18 residues within 4Å: Chain A: W.151, F.164, M.168, G.196, G.198, D.219, R.220, V.223, G.238, D.239, M.240, F.241, K.253, Y.254, I.255, N.258, W.259 Ligands: T3A.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.198, A:R.220, A:R.220, A:D.239, A:D.239, A:K.253, A:K.253 Water bridges: A:T.202, A:T.202, A:T.202, A:R.220, A:K.253 Salt bridges: A:K.253 pi-Stacking: A:W.151 pi-Cation interactions: A:R.220 SAH.16: 18 residues within 4Å: Chain B: W.151, F.164, M.168, G.196, G.198, D.219, R.220, V.223, G.238, D.239, M.240, F.241, K.253, Y.254, I.255, N.258, W.259 Ligands: T3A.11 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.198, B:R.220, B:R.220, B:D.239, B:K.253, B:K.253 Water bridges: B:T.201, B:T.202, B:T.202, B:R.220, B:K.253 Salt bridges: B:K.253 pi-Stacking: B:W.151 pi-Cation interactions: B:R.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zubieta, C. et al., Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases. Nat. Struct. Biol. (2001)

Release Date

2018-03-07

Peptides

Isoflavone-7-O-methyltransferase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Isoflavone-7-O-methyltransferase 8

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