SMTL ID : 7csb.1 (1 other biounit)

AtPrR1 with NADP+ and (+)pinoresinol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

GEC.1: 18 residues within 4Å: Chain A: V.92, F.94, G.124, M.125, C.165, Y.169, F.170, N.173, Q.176, M.177, V.178, T.179, G.273, H.276, F.277, I.280 Chain B: L.46 Ligands: NDP.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.170 Hydrogen bonds: A:M.125, A:V.178 Water bridges: A:E.122, A:M.125, A:H.270 pi-Stacking: A:F.94, A:H.276, A:F.277 GEC.3: 18 residues within 4Å: Chain A: L.46 Chain B: V.92, F.94, G.124, M.125, C.165, Y.169, F.170, N.173, Q.176, M.177, V.178, T.179, G.273, H.276, F.277, I.280 Ligands: NDP.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:M.125, B:V.178 Water bridges: B:E.122, B:E.122, B:G.124, B:M.125 pi-Stacking: B:F.94, B:H.276, B:F.277

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

NDP.2: 30 residues within 4Å: Chain A: G.16, A.17, T.18, G.19, Y.20, I.21, R.41, K.50, F.69, A.88, M.89, S.90, G.91, V.92, R.95, S.96, N.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: GEC.1 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:V.92, A:F.166, A:F.166, A:Y.169 Hydrogen bonds: A:T.18, A:T.18, A:T.18, A:T.18, A:G.19, A:Y.20, A:I.21, A:K.50, A:M.89, A:S.90, A:S.90, A:G.91, A:S.96, A:N.98, A:K.144, A:K.144, A:F.166 Water bridges: A:G.16, A:G.16, A:G.22, A:R.41, A:R.41 Salt bridges: A:R.41, A:K.50, A:R.95, A:R.95 NDP.4: 30 residues within 4Å: Chain B: G.16, A.17, T.18, G.19, Y.20, I.21, R.41, K.50, F.69, A.88, M.89, S.90, G.91, V.92, R.95, S.96, N.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: GEC.3 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:V.92, B:F.166, B:F.166, B:Y.169, B:Y.169 Hydrogen bonds: B:G.16, B:T.18, B:Y.20, B:I.21, B:K.50, B:M.89, B:S.90, B:S.90, B:G.91, B:S.96, B:N.98, B:K.144, B:K.144, B:A.164, B:F.166 Water bridges: B:A.17, B:G.22, B:R.95, B:R.95, B:R.95 Salt bridges: B:R.41, B:K.50, B:R.95, B:R.95

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 reductase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Pinoresinol reductase 1

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