SMTL ID : 3u57.1

Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-octamer

Ligands

8 x DH8: (2beta,7beta,16S,17R,19E,21beta)-21-(beta-D-glucopyranosyloxy)-2,7-dihydro-7,17-cyclosarpagan-17-yl acetate(Non-covalent)

DH8.1: 15 residues within 4Å: Chain A: Q.36, H.140, Q.186, W.188, T.189, H.193, L.199, Y.200, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.189, A:L.199, A:Y.200, A:Y.347, A:W.392 Hydrogen bonds: A:Q.36, A:Q.36, A:H.140, A:Q.186, A:Q.186, A:E.476 Salt bridges: A:H.193 pi-Stacking: A:H.193 DH8.3: 15 residues within 4Å: Chain B: Q.36, H.140, Q.186, T.189, H.193, L.199, Y.200, T.275, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.189, B:L.199, B:Y.347, B:W.392 Hydrogen bonds: B:Q.36, B:Q.36, B:H.140, B:Q.186, B:H.193, B:Y.347 Salt bridges: B:H.193 DH8.5: 15 residues within 4Å: Chain C: Q.36, H.140, Q.186, W.188, T.189, H.193, L.199, Y.200, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:T.189, C:L.199, C:Y.200, C:Y.347, C:W.392 Hydrogen bonds: C:Q.36, C:Q.36, C:H.140, C:Q.186, C:Q.186, C:E.476 Salt bridges: C:H.193 pi-Stacking: C:H.193 DH8.7: 15 residues within 4Å: Chain D: Q.36, H.140, Q.186, T.189, H.193, L.199, Y.200, T.275, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:T.189, D:L.199, D:Y.347, D:W.392 Hydrogen bonds: D:Q.36, D:Q.36, D:H.140, D:Q.186, D:H.193, D:Y.347 Salt bridges: D:H.193 DH8.9: 15 residues within 4Å: Chain E: Q.36, H.140, Q.186, W.188, T.189, H.193, L.199, Y.200, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:T.189, E:L.199, E:Y.200, E:Y.347, E:W.392 Hydrogen bonds: E:Q.36, E:Q.36, E:H.140, E:Q.186, E:Q.186 Salt bridges: E:H.193 pi-Stacking: E:H.193 DH8.11: 15 residues within 4Å: Chain F: Q.36, H.140, Q.186, T.189, H.193, L.199, Y.200, T.275, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:T.189, F:L.199, F:Y.347, F:W.392 Hydrogen bonds: F:Q.36, F:Q.36, F:H.140, F:Q.186, F:H.193 Salt bridges: F:H.193 DH8.13: 15 residues within 4Å: Chain G: Q.36, H.140, Q.186, W.188, T.189, H.193, L.199, Y.200, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:T.189, G:L.199, G:Y.200, G:Y.347, G:W.392 Hydrogen bonds: G:Q.36, G:Q.36, G:H.140, G:Q.186, G:Q.186 Salt bridges: G:H.193 pi-Stacking: G:H.193 DH8.15: 15 residues within 4Å: Chain H: Q.36, H.140, Q.186, T.189, H.193, L.199, Y.200, T.275, Y.347, W.392, E.420, W.469, E.476, W.477, F.485 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:T.189, H:L.199, H:Y.347, H:W.392 Hydrogen bonds: H:Q.36, H:Q.36, H:H.140, H:Q.186, H:H.193 Salt bridges: H:H.193

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

CL.2: 4 residues within 4Å: Chain A: R.107, S.109 Chain D: T.432, S.434 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.6: 4 residues within 4Å: Chain B: T.432, S.434 Chain C: R.107, S.109 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.10: 4 residues within 4Å: Chain E: R.107, S.109 Chain H: T.432, S.434 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.14: 4 residues within 4Å: Chain F: T.432, S.434 Chain G: R.107, S.109 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

Related Entries With Identical Sequence