SMTL ID : 3u5y.1 (2 other biounits)

Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

8 x SCG: Secologanin(Non-covalent)

SCG.1: 14 residues within 4Å: Chain A: Q.36, H.140, Q.186, T.189, Y.200, T.275, Q.276, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.189, A:W.392 Hydrogen bonds: A:Q.36, A:Q.36, A:Q.186, A:Q.186, A:E.476, A:E.476 SCG.2: 13 residues within 4Å: Chain B: Q.36, H.140, Q.186, Y.200, T.275, Q.276, Y.347, T.348, E.420, W.469, E.476, W.477, F.485 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.36, B:Q.36, B:Q.186, B:Y.347, B:E.476 SCG.5: 14 residues within 4Å: Chain C: Q.36, H.140, Q.186, T.189, Y.200, T.275, Q.276, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:T.189, C:W.392 Hydrogen bonds: C:Q.36, C:Q.36, C:Q.186, C:Q.186, C:E.476, C:E.476 SCG.6: 13 residues within 4Å: Chain D: Q.36, H.140, Q.186, Y.200, T.275, Q.276, Y.347, T.348, E.420, W.469, E.476, W.477, F.485 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.36, D:Q.36, D:Q.186, D:Y.347, D:E.476 SCG.9: 14 residues within 4Å: Chain E: Q.36, H.140, Q.186, T.189, Y.200, T.275, Q.276, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:T.189, E:W.392 Hydrogen bonds: E:Q.36, E:Q.36, E:Q.186, E:Q.186, E:Y.347, E:E.476 SCG.10: 13 residues within 4Å: Chain F: Q.36, H.140, Q.186, Y.200, T.275, Q.276, Y.347, T.348, E.420, W.469, E.476, W.477, F.485 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.36, F:Q.36, F:Q.186, F:E.476 SCG.13: 14 residues within 4Å: Chain G: Q.36, H.140, Q.186, T.189, Y.200, T.275, Q.276, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:T.189, G:W.392 Hydrogen bonds: G:Q.36, G:Q.36, G:Q.186, G:Q.186, G:Y.347, G:E.476 SCG.14: 13 residues within 4Å: Chain H: Q.36, H.140, Q.186, Y.200, T.275, Q.276, Y.347, T.348, E.420, W.469, E.476, W.477, F.485 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.36, H:Q.36, H:Q.186, H:E.476

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

CL.3: 4 residues within 4Å: Chain B: T.432, S.434 Chain C: R.107, S.109 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: R.107, S.109 Chain E: T.432, S.434 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.107, S.109 Chain D: T.432, S.434 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain D: R.107, S.109 Chain G: T.432, S.434 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain F: T.432, S.434 Chain G: R.107, S.109 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: T.432, S.434 Chain F: R.107, S.109 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain E: R.107, S.109 Chain H: T.432, S.434 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: T.432, S.434 Chain H: R.107, S.109 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, L. et al., Structures of alkaloid biosynthetic glucosidases decode substrate specificity. Acs Chem.Biol. (2012)

Release Date

2011-11-30

Peptides

Raucaffricine-O-beta-D-glucosidase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Raucaffricine-O-beta-D-glucosidase

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