SMTL ID : 2f2h.1

Structure of the YicI thiosugar Michaelis complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: T.246, K.248, A.249, R.583 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.246 Water bridges: A:K.248 Salt bridges: A:K.248, A:R.583 SO4.6: 3 residues within 4Å: Chain B: T.246, K.248, R.583 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.249 Water bridges: B:T.246, B:K.248 Salt bridges: B:K.248, B:R.583 SO4.11: 4 residues within 4Å: Chain C: T.246, K.248, A.249, R.583 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.246, C:T.246, C:A.249 Water bridges: C:K.248 Salt bridges: C:R.583 SO4.17: 4 residues within 4Å: Chain D: T.246, K.248, A.249, R.583 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.246 Water bridges: D:T.246, D:K.248 Salt bridges: D:R.583 SO4.22: 4 residues within 4Å: Chain E: T.246, K.248, A.249, R.583 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.246, E:T.246 Water bridges: E:K.248 Salt bridges: E:R.583 SO4.23: 5 residues within 4Å: Chain E: F.23, E.24, V.25, N.96, K.114 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:V.25, E:N.96 Salt bridges: E:K.114 SO4.28: 3 residues within 4Å: Chain F: T.246, K.248, R.583 2 PLIP interactions: 2 interactions with chain F Water bridges: F:K.248 Salt bridges: F:R.583 SO4.29: 3 residues within 4Å: Chain F: R.677, Y.680, V.681 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:V.681 Water bridges: F:N.674, F:V.681 Salt bridges: F:R.677 SO4.30: 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

7 x XTG: 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE(Non-covalent)

XTG.2: 21 residues within 4Å: Chain A: D.185, F.277, T.278, D.306, C.307, W.380, K.414, D.416, F.417, R.420, R.466, W.479, D.482, F.515, R.538, H.540, S.542 Chain B: T.45, L.48, D.49 Chain D: W.8 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.185, A:D.306, A:K.414, A:R.420, A:R.420, A:R.466, A:R.466, A:R.538, A:H.540, B:D.49 Hydrophobic interactions: B:L.48 XTG.8: 20 residues within 4Å: Chain B: D.185, F.277, D.306, C.307, W.380, K.414, D.416, F.417, R.420, R.466, W.479, D.482, F.515, R.538, H.540, S.542 Chain C: W.8 Chain F: T.45, L.48, D.49 14 PLIP interactions: 10 interactions with chain B, 3 interactions with chain F, 1 interactions with chain C Hydrogen bonds: B:D.185, B:D.306, B:K.414, B:D.416, B:R.420, B:R.466, B:R.466, B:R.538, B:H.540, F:D.49 Water bridges: B:R.420, F:D.49 Hydrophobic interactions: F:L.48, C:W.8 XTG.13: 22 residues within 4Å: Chain B: W.8 Chain C: D.185, F.277, T.278, D.306, C.307, W.380, K.414, D.416, F.417, R.420, R.466, W.479, D.482, F.515, H.540, S.542, K.543 Chain D: T.45, L.48, D.49 Ligands: GOL.15 15 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:F.515, B:W.8, D:L.48 Hydrogen bonds: C:D.185, C:D.306, C:K.414, C:R.420, C:R.420, C:R.466, C:R.466, C:R.538, C:H.540, D:D.49 Water bridges: C:W.380, C:D.482 XTG.19: 21 residues within 4Å: Chain A: W.8 Chain D: D.185, F.277, H.304, D.306, C.307, K.414, D.416, F.417, R.420, R.466, W.479, D.482, F.515, R.538, H.540, S.542, K.543 Chain E: T.45, L.48, D.49 16 PLIP interactions: 13 interactions with chain D, 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: D:D.185, D:D.306, D:K.414, D:D.416, D:R.420, D:R.420, D:R.466, D:R.466, D:R.538, D:R.538, D:H.540, E:D.49 Water bridges: D:D.482, D:D.511 Hydrophobic interactions: A:W.8, E:L.48 XTG.25: 23 residues within 4Å: Chain C: T.45, L.48, D.49 Chain E: D.185, F.277, T.278, D.306, C.307, W.345, W.380, K.414, D.416, F.417, R.420, R.466, W.479, D.482, F.515, R.538, H.540, S.542, K.543 Chain F: W.8 15 PLIP interactions: 3 interactions with chain C, 11 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: C:L.48, F:W.8 Hydrogen bonds: C:D.49, C:D.49, E:D.185, E:D.306, E:D.416, E:R.420, E:R.420, E:R.466, E:R.466, E:R.538, E:H.540 Water bridges: E:D.482 pi-Stacking: E:F.277 XTG.32: 21 residues within 4Å: Chain A: T.45, L.48, D.49 Chain E: W.8 Chain F: D.185, F.277, D.306, C.307, W.380, K.414, D.416, F.417, R.420, R.466, W.479, D.482, F.515, R.538, H.540, S.542, K.543 15 PLIP interactions: 12 interactions with chain F, 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: F:D.185, F:D.306, F:K.414, F:D.416, F:R.420, F:R.466, F:R.466, F:R.538, F:H.540, A:D.49 Water bridges: F:D.185, F:R.420, F:D.482 Hydrophobic interactions: A:L.48, E:W.8 XTG.33: 10 residues within 4Å: Chain F: W.267, H.301, K.336, A.337, G.339, L.340, K.341, R.677, P.678, D.679 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:H.301, F:K.341 Hydrogen bonds: F:L.340, F:D.679 Water bridges: F:K.336, F:K.336, F:K.341

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Q.27, D.29, N.30, V.92, T.93, I.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.27, A:I.94 GOL.4: 6 residues within 4Å: Chain A: E.31, R.56, F.58, R.68, E.238 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.31, A:R.68, A:E.238 GOL.5: 6 residues within 4Å: Chain A: R.68, H.81, L.84, N.211, E.238 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.68, A:H.81, A:N.211, A:Y.236, A:Y.236 GOL.9: 6 residues within 4Å: Chain B: E.31, R.56, F.58, R.68, E.238 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.31, B:R.68, B:E.238 GOL.10: 6 residues within 4Å: Chain B: R.68, H.81, L.84, N.211, E.238 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.68, B:H.81, B:N.211, B:E.238 Water bridges: B:Y.82 GOL.14: 5 residues within 4Å: Chain C: R.68, L.84, N.211, E.238 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.68, C:R.68, C:N.211 Water bridges: C:Y.82 GOL.15: 8 residues within 4Å: Chain B: N.7, W.8 Chain C: D.482, C.483, Y.484, F.515, E.516 Ligands: XTG.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:C.483 Water bridges: C:T.188, C:D.482, C:Y.484 GOL.16: 6 residues within 4Å: Chain C: E.31, R.56, F.58, R.68, E.238 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.31, C:R.68, C:E.238 GOL.20: 6 residues within 4Å: Chain D: E.31, R.56, F.58, R.68, E.238 Ligands: GOL.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.31, D:R.68, D:E.238 GOL.21: 7 residues within 4Å: Chain D: R.68, H.81, L.84, N.211, Y.236, E.238 Ligands: GOL.20 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.68, D:H.81, D:N.211, D:Y.236, D:Y.236 Water bridges: D:Y.82 GOL.26: 5 residues within 4Å: Chain E: E.31, R.56, F.58, R.68, E.238 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.31, E:R.68, E:E.238 Water bridges: E:N.211, E:N.211 GOL.27: 7 residues within 4Å: Chain E: D.482, C.483, Y.484, F.515, E.516 Chain F: N.7, W.8 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:C.483, E:E.516 Water bridges: E:T.188, E:D.482, E:N.517 GOL.34: 6 residues within 4Å: Chain F: P.265, A.266, W.267, E.460, Y.574, D.679 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:A.266, F:W.267, F:Y.574, F:D.679, F:D.679 GOL.35: 4 residues within 4Å: Chain F: E.31, F.58, R.68, E.238 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.31, F:R.68, F:E.238 Water bridges: F:N.211, F:N.211

5 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.12: 7 residues within 4Å: Chain C: H.640, D.642, Q.652, Q.653, H.654, G.655, S.658 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.655, C:S.658 Water bridges: C:D.642, C:Q.652 Salt bridges: C:H.640, C:D.642, C:H.654 MPO.18: 7 residues within 4Å: Chain D: H.640, D.642, Q.652, Q.653, H.654, G.655, S.658 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.655, D:S.658 Salt bridges: D:H.640, D:D.642, D:H.654 MPO.24: 6 residues within 4Å: Chain E: H.640, Q.652, Q.653, H.654, G.655, S.658 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.655 Water bridges: E:D.642, E:Q.652 Salt bridges: E:H.640, E:D.642, E:H.654 MPO.31: 7 residues within 4Å: Chain F: H.640, D.642, Q.652, Q.653, H.654, G.655, S.658 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.655, F:S.658 Water bridges: F:Q.653, F:Y.662 Salt bridges: F:H.640, F:D.642, F:H.654

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y.-W. et al., Expanding the Thioglycoligase Strategy to the Synthesis of alpha-linked Thioglycosides Allows Structural Investigation of the Parent Enzyme/Substrate Complex. J.Am.Chem.Soc. (2006)

Release Date

2006-02-28

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