SMTL ID : 7cs6.1 (2 other biounits)

IiPLR1 with NADP+ and (-)lariciresinol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x GFR: 4-[[(3S,4S,5R)-4-(hydroxymethyl)-5-(3-methoxy-4-oxidanyl-phenyl)oxolan-3-yl]methyl]-2-methoxy-phenol(Non-covalent)

GFR.1: 15 residues within 4Å: Chain A: G.124, M.125, K.144, A.164, Y.169, F.170, N.173, Q.176, M.177, G.178, T.179, H.276, F.277, I.280 Ligands: NDP.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.169 Hydrogen bonds: A:M.125, A:G.178 pi-Stacking: A:F.277 GFR.3: 16 residues within 4Å: Chain A: V.46 Chain B: G.124, M.125, K.144, A.164, Y.169, F.170, N.173, Q.176, M.177, G.178, T.179, H.276, F.277, I.280 Ligands: NDP.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.169 Hydrogen bonds: B:M.125, B:G.178 pi-Stacking: B:F.277

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: GFR.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.166, A:F.166, A:F.166, A:Y.169, A:Y.169 Hydrogen bonds: A:T.18, A:T.18, 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:S.98, A:K.144, A:K.144, A:F.166 Water bridges: A:G.16, A:T.20, A:G.22, A:L.39 Salt bridges: A:K.50 NDP.4: 28 residues within 4Å: Chain B: G.16, G.17, T.18, G.19, T.20, M.21, L.39, Q.41, K.50, F.69, A.88, M.89, S.90, G.91, H.97, 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: GFR.3 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:F.166, B:F.166, B:F.166, B:Y.169, B:Y.169 Hydrogen bonds: B:G.16, B:G.17, B:T.18, B:T.18, B:G.19, B:T.20, B:T.20, B:M.21, B:Q.41, B:K.50, B:M.89, B:S.90, B:E.122, B:K.144, B:F.166 Water bridges: B:T.20, B:G.22 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
C

Pinoresinol-lariciresinol reductase

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