SMTL ID : 1xsk.1

Structure of a Family 31 alpha glycosidase glycosyl-enzyme intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.147, Q.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.434 Salt bridges: A:R.147 SO4.2: 4 residues within 4Å: Chain A: T.246, K.248, A.249, R.583 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.246, A:K.248 Salt bridges: A:R.583 SO4.4: 4 residues within 4Å: Chain B: T.246, K.248, A.249, R.583 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.246, B:K.248 Salt bridges: B:R.583 SO4.5: 4 residues within 4Å: Chain B: R.568, A.687, H.689, Q.757 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.568, B:H.689 SO4.8: 3 residues within 4Å: Chain C: T.246, K.248, R.583 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.246 Water bridges: C:T.246, C:K.248 Salt bridges: C:R.583 SO4.9: 4 residues within 4Å: Chain C: E.24, V.25, N.96, K.114 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.25, C:N.96 Water bridges: C:K.114, C:K.114 Salt bridges: C:K.114 SO4.12: 4 residues within 4Å: Chain D: T.246, K.248, A.249, R.583 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.246 Salt bridges: D:R.583 SO4.14: 4 residues within 4Å: Chain E: T.246, K.248, A.249, R.583 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.246, E:T.246, E:A.249 Water bridges: E:K.248 Salt bridges: E:R.583 SO4.17: 3 residues within 4Å: Chain F: R.606, V.626, Q.627 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.627, F:Q.627 Salt bridges: F:R.606 SO4.18: 4 residues within 4Å: Chain F: R.568, A.687, H.689, Q.757 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.568, F:H.689 SO4.19: 3 residues within 4Å: Chain F: T.246, K.248, R.583 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.583 SO4.20: 2 residues within 4Å: Chain F: Y.680, V.681 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.681 Water bridges: F:V.681 SO4.21: 2 residues within 4Å: Chain F: R.333, R.334 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.333, F:R.334

4 x XYF: 5(R)-fluoro-beta-D-xylopyranose(Post Translational Modification)

XYF.3: 14 residues within 4Å: Chain A: F.277, D.306, C.307, W.345, W.380, K.414, D.416, F.417, R.466, W.479, D.482, F.515, R.538, H.540 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.414, A:R.466, A:D.482, A:R.538, A:H.540, A:H.540 Water bridges: A:D.482 XYF.6: 14 residues within 4Å: Chain B: F.277, D.306, C.307, W.345, W.380, K.414, D.416, F.417, R.466, W.479, D.482, F.515, R.538, H.540 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.414, B:R.466, B:D.482, B:R.538, B:H.540, B:H.540 Water bridges: B:D.482, B:D.482 XYF.10: 13 residues within 4Å: Chain C: F.277, D.306, C.307, W.345, W.380, K.414, D.416, F.417, R.466, W.479, D.482, F.515, H.540 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.414, C:R.466, C:D.482, C:R.538, C:H.540, C:H.540 XYF.15: 14 residues within 4Å: Chain E: F.277, D.306, C.307, W.345, W.380, K.414, D.416, F.417, R.466, W.479, D.482, F.515, R.538, H.540 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:K.414, E:R.466, E:D.482, E:R.538, E:H.540, E:H.540

4 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.7: 7 residues within 4Å: Chain B: H.640, D.642, Q.652, Q.653, H.654, G.655, S.658 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.655, B:S.658 Water bridges: B:Q.652 Salt bridges: B:H.640, B:D.642, B:H.654 MPO.11: 6 residues within 4Å: Chain C: H.640, D.642, Q.653, H.654, G.655, S.658 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.655, C:S.658 Salt bridges: C:H.640, C:D.642, C:H.654 MPO.13: 6 residues within 4Å: Chain D: H.640, D.642, Q.653, H.654, G.655, S.658 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.642, D:G.655 Water bridges: D:Q.652, D:S.658 Salt bridges: D:H.640, D:D.642, D:H.654 MPO.16: 7 residues within 4Å: Chain E: H.640, D.642, Q.652, Q.653, H.654, G.655, S.658 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.655 Water bridges: E:Q.652 Salt bridges: E:H.640, E:D.642

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

2004-11-10

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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