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

Crystal structure of iridoid synthase in complex with NADP+ and 8-oxogeranial at 2.65-angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 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.13, V.14, T.15, G.16, I.17, A.42, R.43, R.44, C.60, D.61, V.62, V.84, S.85, W.86, I.87, M.98, Q.119, T.120, G.121, F.154, Y.155, P.178, A.179, V.181, S.188, M.189, M.190, F.319 Ligands: XOG.2, PG4.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:P.178, A:V.181 Hydrogen bonds: A:G.13, A:T.15, A:T.15, A:I.17, A:R.43, A:R.44, A:V.62, A:S.63, A:Q.119, A:V.181, A:C.187, A:S.188, A:M.189, A:M.190 Water bridges: A:V.18, A:V.18, A:S.85, A:Q.119, A:M.190, A:M.190 Salt bridges: A:R.44 NAP.4: 29 residues within 4Å: Chain B: G.13, T.15, G.16, I.17, A.42, R.43, R.44, C.60, D.61, V.62, V.84, S.85, W.86, I.87, M.98, Q.119, T.120, G.121, F.154, Y.155, P.178, A.179, V.181, S.188, M.189, M.190, F.319 Ligands: XOG.5, PG4.6 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:P.178, B:V.181 Hydrogen bonds: B:G.13, B:T.15, B:T.15, B:I.17, B:R.43, B:R.44, B:D.61, B:V.62, B:S.63, B:W.86, B:Q.119, B:Y.155, B:V.181, B:S.188, B:M.189, B:M.190, B:M.190 Water bridges: B:V.18, B:S.85, B:Q.119 Salt bridges: B:R.44

2 x XOG: (2E,6E)-2,6-dimethylocta-2,6-dienedial(Non-covalent)

XOG.2: 13 residues within 4Å: Chain A: G.121, I.122, K.123, F.126, Y.155, M.190, F.319, I.322, A.323, S.326, L.329 Ligands: NAP.1, PG4.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.123, A:F.126, A:F.319, A:L.329 Hydrogen bonds: A:K.123, A:Y.155, A:S.326 XOG.5: 12 residues within 4Å: Chain B: G.121, I.122, K.123, F.126, Y.155, M.190, F.319, I.322, A.323, S.326 Ligands: NAP.4, PG4.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.122, B:K.123, B:F.126, B:F.319 Hydrogen bonds: B:K.123, B:S.326

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

PG4.3: 11 residues within 4Å: Chain A: W.86, E.90, K.123, G.127, F.129, N.153, F.154, Y.155, M.190 Ligands: NAP.1, XOG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.123 PG4.6: 11 residues within 4Å: Chain B: W.86, E.90, K.123, G.127, F.129, N.153, F.154, Y.155, M.190 Ligands: NAP.4, XOG.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.123, B:I.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, L. et al., Structure of iridoid synthase in complex with NADP(+)/8-oxogeranial reveals the structural basis of its substrate specificity. J.Struct.Biol. (2016)

Release Date

2016-03-09

Peptides

Iridoid synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Iridoid synthase

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