SMTL ID : 5df1.1 (1 other biounit)

Iridoid synthase from Catharanthus roseus - ternary complex with NADP+ and geranic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 30 residues within 4Å: Chain A: G.16, V.17, T.18, G.19, I.20, A.45, R.46, R.47, C.63, D.64, V.65, V.87, S.88, W.89, I.90, M.101, Q.122, T.123, G.124, F.157, Y.158, P.181, A.182, L.183, V.184, S.191, M.192, M.193, F.322 Ligands: 58X.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:P.181, A:V.184 Hydrogen bonds: A:G.16, A:T.18, A:T.18, A:T.18, A:G.19, A:I.20, A:R.46, A:R.47, A:D.64, A:D.64, A:V.65, A:S.66, A:Q.122, A:Q.122, A:Y.158, A:V.184, A:M.192, A:M.193 Water bridges: A:V.21, A:V.21, A:K.126 Salt bridges: A:R.47 NAP.5: 30 residues within 4Å: Chain B: G.16, V.17, T.18, G.19, I.20, A.45, R.46, R.47, C.63, D.64, V.65, V.87, S.88, W.89, I.90, M.101, Q.122, T.123, G.124, F.157, Y.158, P.181, A.182, L.183, V.184, S.191, M.192, M.193, F.322 Ligands: 58X.6 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:P.181, B:V.184 Hydrogen bonds: B:G.16, B:T.18, B:T.18, B:T.18, B:G.19, B:I.20, B:R.46, B:R.47, B:D.64, B:V.65, B:S.66, B:Q.122, B:Q.122, B:V.184, B:M.192, B:M.193 Water bridges: B:V.21, B:V.21, B:K.126 Salt bridges: B:R.47

2 x 58X: (2E)-3,7-dimethylocta-2,6-dienoic acid(Non-covalent)

58X.2: 11 residues within 4Å: Chain A: G.124, I.125, K.126, Y.158, L.183, M.193, F.322, A.326, S.329, L.332 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.125, A:K.126, A:A.326, A:L.332 Hydrogen bonds: A:G.124, A:K.126 Water bridges: A:K.126 Salt bridges: A:K.126 58X.6: 11 residues within 4Å: Chain B: G.124, I.125, K.126, Y.158, L.183, M.193, F.322, A.326, S.329, L.332 Ligands: NAP.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.125, B:K.126, B:A.326, B:L.332 Hydrogen bonds: B:G.124, B:K.126, B:Y.158 Water bridges: B:K.126 Salt bridges: B:K.126

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

EDO.3: 4 residues within 4Å: Chain A: H.127, R.151, E.162, R.180 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.147, A:R.151, A:R.151, A:R.180, A:R.180 EDO.7: 4 residues within 4Å: Chain B: H.127, R.151, E.162, R.180 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.147, B:R.151, B:R.151, B:R.180, B:R.180

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 7 residues within 4Å: Chain A: Y.202, I.205, C.206, E.209, K.211, M.293, K.296 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.202, A:Y.202, A:K.211 pi-Cation interactions: A:K.211 IMD.8: 7 residues within 4Å: Chain B: Y.202, I.205, C.206, E.209, K.211, M.293, K.296 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.202, B:K.211 pi-Cation interactions: B:K.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kries, H. et al., Structural determinants of reductive terpene cyclization in iridoid biosynthesis. Nat.Chem.Biol. (2016)

Release Date

2015-10-28

Peptides

Iridoid synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Iridoid synthase

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