SMTL ID : 1xsj.1

Structure of a Family 31 alpha glycosidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

12 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 12 residues within 4Å: Chain A: F.277, D.306, C.307, K.414, D.416, F.417, R.466, W.479, D.482, F.515, H.540 Ligands: TRS.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.306, A:K.414, A:D.416, A:R.466 Water bridges: A:W.479, A:R.538 TRS.2: 9 residues within 4Å: Chain A: D.185, W.380, F.417, R.466, D.482 Chain B: L.48, D.49 Chain D: W.8 Ligands: TRS.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.185, A:R.466, A:R.466, B:D.49 TRS.3: 9 residues within 4Å: Chain A: W.8 Chain D: D.185, F.277, W.380, F.417, R.466, D.482 Chain E: D.49 Ligands: TRS.8 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: E:D.49, A:W.8, D:R.466, D:R.466 TRS.4: 13 residues within 4Å: Chain B: F.277, D.306, C.307, W.345, K.414, D.416, F.417, R.466, W.479, D.482, F.515, H.540 Ligands: TRS.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.306, B:K.414, B:D.416, B:R.466 Water bridges: B:W.479, B:R.538 TRS.5: 8 residues within 4Å: Chain B: D.185, W.380, F.417, R.466, D.482 Chain C: W.8 Chain F: D.49 Ligands: TRS.4 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:D.49, B:D.185, B:R.466, B:R.466 Water bridges: B:D.482 TRS.6: 11 residues within 4Å: Chain C: F.277, D.306, K.414, D.416, F.417, R.466, W.479, D.482, F.515, H.540 Ligands: TRS.7 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.306, C:K.414, C:D.416, C:R.466 Water bridges: C:W.479, C:H.540 TRS.7: 8 residues within 4Å: Chain B: W.8 Chain C: D.185, W.380, F.417, R.466, D.482 Chain D: D.49 Ligands: TRS.6 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: B:W.8, D:D.49, C:R.466, C:R.466 TRS.8: 13 residues within 4Å: Chain D: F.277, D.306, C.307, W.345, K.414, D.416, F.417, R.466, W.479, D.482, F.515, H.540 Ligands: TRS.3 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.306, D:K.414, D:D.416, D:R.466 Water bridges: D:W.479, D:G.481 TRS.9: 13 residues within 4Å: Chain E: F.277, D.306, C.307, W.345, K.414, D.416, F.417, R.466, W.479, D.482, F.515, H.540 Ligands: TRS.10 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:D.306, E:K.414, E:D.416, E:R.466 Water bridges: E:W.479, E:G.481 TRS.10: 8 residues within 4Å: Chain C: D.49 Chain E: D.185, W.380, F.417, R.466, D.482 Chain F: W.8 Ligands: TRS.9 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:D.185, E:R.466, E:R.466, C:D.49 Water bridges: E:R.420, E:D.482 TRS.11: 8 residues within 4Å: Chain A: D.49 Chain E: W.8 Chain F: D.185, W.380, F.417, R.466, D.482 Ligands: TRS.12 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: F:R.466, A:D.49, E:W.8 Water bridges: F:D.482 TRS.12: 12 residues within 4Å: Chain F: F.277, D.306, C.307, K.414, D.416, F.417, R.466, W.479, D.482, F.515, H.540 Ligands: TRS.11 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.306, F:K.414, F:D.416, F:R.466 Water bridges: F:W.479, F:G.481

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lovering, A.L. et al., Mechanistic and Structural Analysis of a Family 31 alpha-Glycosidase and Its Glycosyl-enzyme Intermediate. J.Biol.Chem. (2005)

Release Date

2004-10-26

Peptides

Putative family 31 glucosidase yicI: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Putative family 31 glucosidase yicI

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