SMTL ID : 2vq5.1

X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: W.50, G.52, K.55, H.56 Chain D: H.56 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Salt bridges: A:H.56, D:H.56 ACT.2: 4 residues within 4Å: Chain A: V.100, D.101, N.102, E.103 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.103 Hydrogen bonds: A:V.100, A:N.102, A:N.102 ACT.11: 5 residues within 4Å: Chain B: H.56 Chain C: W.50, G.52, K.55, H.56 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:H.56, B:H.56 ACT.12: 4 residues within 4Å: Chain C: V.100, D.101, N.102, E.103 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.103 Hydrogen bonds: C:V.100, C:N.102, C:N.102

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: F.89, P.90, H.91, E.92, G.115 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: R.105, P.132 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: H.129, K.141 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: F.89, P.90, H.91, E.92, G.115 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: W.50, K.55, H.56 Chain C: H.56 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain C: F.89, P.90, H.91, E.92, G.115 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: R.105, P.132 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: H.129, K.141 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain D: F.89, P.90, H.91, E.92, G.115 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: H.56 Chain D: W.50, K.55, H.56 Ligand excluded by PLIP

4 x HBA: P-HYDROXYBENZALDEHYDE(Non-covalent)

HBA.6: 8 residues within 4Å: Chain A: Y.48, L.80, M.82, E.95, F.97, K.107, V.109, M.168 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.80, A:F.97 Hydrogen bonds: A:K.107 HBA.10: 9 residues within 4Å: Chain B: E.95, K.107, V.109, D.126, I.128, P.164, L.165, M.168 Ligands: LDP.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.109, B:V.109, B:D.126, B:I.128, B:L.165 Hydrogen bonds: B:K.107 HBA.16: 8 residues within 4Å: Chain C: Y.48, L.80, M.82, E.95, F.97, K.107, V.109, M.168 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.80, C:F.97 Hydrogen bonds: C:K.107 HBA.20: 9 residues within 4Å: Chain D: E.95, K.107, V.109, D.126, I.128, P.164, L.165, M.168 Ligands: LDP.19 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.109, D:V.109, D:D.126, D:I.128, D:L.165 Hydrogen bonds: D:K.107, D:D.126 Water bridges: D:Y.124

2 x LDP: L-DOPAMINE(Non-covalent)

LDP.9: 10 residues within 4Å: Chain B: L.57, L.61, F.65, L.80, M.82, Y.93, E.95, P.164, M.168 Ligands: HBA.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.57, B:L.61 Hydrogen bonds: B:Y.93 Water bridges: B:Y.93 LDP.19: 10 residues within 4Å: Chain D: L.57, L.61, F.65, L.80, M.82, Y.93, E.95, P.164, M.168 Ligands: HBA.20 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.57, D:L.61 Hydrogen bonds: D:Y.93, D:Y.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ilari, A. et al., Structural Basis of Enzymatic S-Norcoclaurine Biosynthesis. J.Biol.Chem. (2009)

Release Date

2008-08-05

Peptides

S-NORCOCLAURINE SYNTHASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

S-NORCOCLAURINE SYNTHASE

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