SMTL ID : 3p9c.1

Crystal structure of perennial ryegrass LpOMT1 bound to SAH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 12 residues within 4Å: Chain A: G.209, G.211, D.232, L.233, V.236, G.251, D.252, M.253, F.254, K.266, W.267, W.272 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.211, A:L.233, A:D.252, A:D.252, A:M.253, A:K.266, A:K.266 Water bridges: A:S.185, A:T.215, A:T.215, A:K.266, A:K.266 Salt bridges: A:K.266 SAH.7: 12 residues within 4Å: Chain B: G.209, G.211, D.232, L.233, V.236, G.251, D.252, M.253, F.254, K.266, W.267, W.272 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.211, B:L.233, B:D.252, B:M.253, B:K.266, B:K.266 Water bridges: B:S.185, B:S.185, B:T.215, B:K.266, B:K.266 Salt bridges: B:K.266

2 x DTV: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTV.2: 7 residues within 4Å: Chain A: F.23, Q.26, Y.88 Chain B: F.23, Q.26, Y.88 Ligands: DTV.8 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.26, B:Q.312, A:Q.26, A:Q.312 DTV.8: 7 residues within 4Å: Chain A: F.23, Q.26, Y.88 Chain B: F.23, Q.26, Y.88 Ligands: DTV.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.26, B:Q.312, A:Q.26, A:Q.312

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: K.182, S.185, I.186, T.189, A.214 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.189 Hydrogen bonds: A:S.185 Water bridges: A:T.215 Salt bridges: A:K.182 ACT.9: 5 residues within 4Å: Chain B: K.182, S.185, I.186, T.189, A.214 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.189 Hydrogen bonds: B:S.185 Water bridges: B:T.215 Salt bridges: B:K.182

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

EDO.4: 7 residues within 4Å: Chain A: T.117, P.118, G.122, S.124, A.126, A.127, N.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.124, A:A.127 EDO.5: 5 residues within 4Å: Chain A: R.80, R.83, R.105 Chain B: R.329, Y.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.83, A:R.83 Water bridges: A:R.80 EDO.6: 5 residues within 4Å: Chain A: R.102, L.103, R.105 Chain B: Y.332, E.335 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.102, A:L.103, A:R.105, A:R.105 Water bridges: A:R.102, A:R.102 EDO.10: 7 residues within 4Å: Chain B: T.117, P.118, G.122, S.124, A.126, A.127, N.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.124, B:A.127 EDO.11: 5 residues within 4Å: Chain A: R.329, Y.332 Chain B: R.80, R.83, R.105 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.83, B:R.83 Water bridges: B:R.80 EDO.12: 5 residues within 4Å: Chain A: Y.332, E.335 Chain B: R.102, L.103, R.105 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.102, B:L.103, B:R.105, B:R.105 Water bridges: B:R.102, B:R.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Louie, G.V. et al., Structure-Function Analyses of a Caffeic Acid O-Methyltransferase from Perennial Ryegrass Reveal the Molecular Basis for Substrate Preference. Plant Cell (2010)

Release Date

2011-01-12

Peptides

Caffeic acid O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Caffeic acid O-methyltransferase

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