SMTL ID : 5icc.1

Crystal structure of (S)-norcoclaurine 6-O-methyltransferase with S-adenosyl-L-homocysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 18 residues within 4Å: Chain A: W.151, M.168, T.172, G.197, G.199, D.220, L.221, V.224, G.239, D.240, M.241, F.242, K.254, C.255, I.256, D.259, W.260 Ligands: EDO.14 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.197, A:L.221, A:D.240, A:M.241 Water bridges: A:M.168, A:T.172, A:G.198, A:G.198, A:H.223, A:K.254, A:D.259 Salt bridges: A:K.254 pi-Stacking: A:W.151 SAH.16: 18 residues within 4Å: Chain B: W.151, M.168, T.172, G.197, G.199, D.220, L.221, V.224, G.239, D.240, M.241, F.242, K.254, C.255, I.256, D.259, W.260 Ligands: EDO.29 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.197, B:L.221, B:D.240, B:M.241 Water bridges: B:M.168, B:T.172, B:G.198, B:G.198, B:H.223, B:K.254, B:D.259 Salt bridges: B:K.254 pi-Stacking: B:W.151

4 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: H.126 Chain B: H.126 Ligands: K.17 No protein-ligand interaction detected (PLIP) K.3: 3 residues within 4Å: Chain A: H.157, P.158, E.159 No protein-ligand interaction detected (PLIP) K.17: 3 residues within 4Å: Chain A: H.126 Chain B: H.126 Ligands: K.2 No protein-ligand interaction detected (PLIP) K.18: 3 residues within 4Å: Chain B: H.157, P.158, E.159 No protein-ligand interaction detected (PLIP)

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: L.51, Y.69, L.90, Y.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.92 NA.5: 4 residues within 4Å: Chain A: D.291, H.296, T.299, R.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.291, A:D.291, A:H.296, A:R.302 NA.19: 4 residues within 4Å: Chain B: L.51, Y.69, L.90, Y.92 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.92 NA.20: 4 residues within 4Å: Chain B: D.291, H.296, T.299, R.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.291, B:D.291, B:H.296, B:R.302

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

EDO.6: 3 residues within 4Å: Chain A: K.16, N.19, F.20 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: P.222, H.223 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: R.271, D.274, A.275 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: V.292, T.319, E.320, E.321 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: R.302, H.339, S.341, A.342, S.345 Chain B: L.11 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: K.31, L.114, T.117, D.118 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: I.42, H.43, G.46, S.47, P.48, G.93, L.94 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: H.43, K.103, G.104, W.105 Chain B: M.3 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: D.240, F.242, K.243 Ligands: SAH.1 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Y.69, K.83, L.90 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: K.16, N.19, F.20 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: P.222, H.223 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: R.271, D.274, A.275 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: V.292, T.319, E.320, E.321 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: L.11 Chain B: R.302, H.339, S.341, A.342, S.345 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: K.31, L.114, T.117, D.118 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: I.42, H.43, G.46, S.47, P.48, G.93, L.94 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: M.3 Chain B: H.43, K.103, G.104, W.105 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: D.240, F.242, K.243 Ligands: SAH.16 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: Y.69, K.83, L.90 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robin, A.Y. et al., Crystal structure of norcoclaurine-6-O-methyltransferase, a key rate-limiting step in the synthesis of benzylisoquinoline alkaloids. Plant J. (2016)

Release Date

2016-06-08

Peptides

(S)-norcoclaurine 6-O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

(S)-norcoclaurine 6-O-methyltransferase

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