SMTL ID : 7cs5.2 (2 other biounits)

IiPLR1 with NADP+ and (-)pinoresinol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x GEF: 4-[(3R,3aS,6R,6aS)-6-(3-methoxy-4-oxidanyl-phenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-3-yl]-2-methoxy-phenol(Non-covalent)

GEF.1: 13 residues within 4Å: Chain A: G.124, M.125, Y.169, F.170, N.173, Q.176, M.177, G.178, T.179, H.276, F.277 Chain B: V.46 Ligands: NDP.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.170 Hydrogen bonds: A:M.125, A:G.178 pi-Stacking: A:H.276, A:F.277 GEF.3: 18 residues within 4Å: Chain A: V.46 Chain B: G.91, G.124, M.125, A.164, Y.169, F.170, N.173, Q.176, M.177, G.178, T.179, A.272, G.273, H.276, F.277, I.280 Ligands: NDP.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.125, B:G.178 Water bridges: B:A.272 pi-Stacking: B:F.277 pi-Cation interactions: B:H.276

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 26 residues within 4Å: Chain A: G.16, G.17, T.18, G.19, T.20, M.21, Q.41, K.50, F.69, A.88, M.89, S.90, G.91, S.98, I.99, S.121, E.122, F.123, G.124, K.144, A.164, C.165, F.166, Y.169, F.170 Ligands: GEF.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.166, A:F.166, A:F.166, A:Y.169, A:Y.169 Hydrogen bonds: A:G.16, A:T.18, A:G.19, A:T.20, A:T.20, A:M.21, A:Q.41, A:K.50, A:M.89, A:S.90, A:K.144, A:K.144, A:A.164, A:F.166 Water bridges: A:T.20, A:G.22 Salt bridges: A:K.50 NDP.4: 27 residues within 4Å: Chain B: G.16, G.17, T.18, G.19, T.20, M.21, Q.41, K.50, F.69, A.88, M.89, S.90, G.91, S.98, I.99, V.101, S.121, E.122, F.123, G.124, K.144, A.164, C.165, F.166, Y.169, F.170 Ligands: GEF.3 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:F.166, B:F.166, B:F.166, B:Y.169, B:Y.169 Hydrogen bonds: B:T.18, B:T.18, B:T.18, B:G.19, B:T.20, B:M.21, B:Q.41, B:K.50, B:M.89, B:S.90, B:K.144, B:K.144, B:A.164, B:F.166 Water bridges: B:G.16, B:G.17, B:T.20, B:T.20, B:T.20, B:G.22, B:G.91, B:G.91 Salt bridges: B:K.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, Y. et al., Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases. Nat Commun (2021)

Release Date

2021-06-09

Peptides

Pinoresinol-lariciresinol reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pinoresinol-lariciresinol reductase

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