SMTL ID : 2vr5.1

Crystal structure of Trex from Sulfolobus Solfataricus in complex with acarbose intermediate and glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

12 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 2 residues within 4Å: Chain A: Y.408, K.423 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.423 GLC.2: 5 residues within 4Å: Chain A: W.401, D.402, V.403, Y.408, M.497 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.403 GLC.3: 4 residues within 4Å: Chain B: W.401, D.402, V.403 Ligands: GLC.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.402 GLC.7: 2 residues within 4Å: Chain B: Y.408 Ligands: GLC.3 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.426, B:D.426 GLC.9: 2 residues within 4Å: Chain C: Y.408, K.423 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.423 GLC.10: 5 residues within 4Å: Chain C: W.401, D.402, V.403, Y.408, M.497 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.403 GLC.11: 4 residues within 4Å: Chain D: W.401, D.402, V.403 Ligands: GLC.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.402 GLC.15: 2 residues within 4Å: Chain D: Y.408 Ligands: GLC.11 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.426, D:D.426 GLC.17: 2 residues within 4Å: Chain E: Y.408, K.423 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.423 GLC.18: 5 residues within 4Å: Chain E: W.401, D.402, V.403, Y.408, M.497 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.403 GLC.19: 4 residues within 4Å: Chain F: W.401, D.402, V.403 Ligands: GLC.23 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.402 GLC.23: 2 residues within 4Å: Chain F: Y.408 Ligands: GLC.19 2 PLIP interactions: 2 interactions with chain F Water bridges: F:D.426, F:D.426

6 x A16: 4-O-(4,6-dideoxy-4-{[(1S,2S,3S,4R,5S)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranosyl)-beta-D-glucopyranose

A16.4: 17 residues within 4Å: Chain A: Q.230, F.232, W.242, Y.244, D.245, H.291, G.328, T.329, R.361, D.363, L.364, E.399, H.470, D.471, F.491, D.495, N.555 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.244, A:H.291, A:G.328, A:R.361, A:R.361, A:H.470, A:D.471, A:D.495, A:N.555 Water bridges: A:G.496 A16.8: 15 residues within 4Å: Chain B: Q.230, F.232, W.242, Y.244, H.291, G.328, T.329, R.361, D.363, L.364, E.399, H.470, D.471, D.495, N.555 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.291, B:G.328, B:R.361, B:R.361, B:E.399, B:H.470, B:N.555 A16.12: 17 residues within 4Å: Chain C: Q.230, F.232, W.242, Y.244, D.245, H.291, G.328, T.329, R.361, D.363, L.364, E.399, H.470, D.471, F.491, D.495, N.555 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.244, C:H.291, C:G.328, C:R.361, C:R.361, C:H.470, C:D.471, C:D.495, C:N.555 Water bridges: C:G.496 A16.16: 15 residues within 4Å: Chain D: Q.230, F.232, W.242, Y.244, H.291, G.328, T.329, R.361, D.363, L.364, E.399, H.470, D.471, D.495, N.555 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.291, D:G.328, D:R.361, D:R.361, D:E.399, D:H.470, D:N.555 A16.20: 17 residues within 4Å: Chain E: Q.230, F.232, W.242, Y.244, D.245, H.291, G.328, T.329, R.361, D.363, L.364, E.399, H.470, D.471, F.491, D.495, N.555 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Y.244, E:H.291, E:G.328, E:R.361, E:R.361, E:H.470, E:D.471, E:D.495, E:N.555 Water bridges: E:G.496 A16.24: 15 residues within 4Å: Chain F: Q.230, F.232, W.242, Y.244, H.291, G.328, T.329, R.361, D.363, L.364, E.399, H.470, D.471, D.495, N.555 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:H.291, F:G.328, F:R.361, F:R.361, F:E.399, F:H.470, F:N.555

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

SO4.5: 4 residues within 4Å: Chain A: R.6, T.7, R.8, K.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.7 Water bridges: A:T.7, A:T.7 Salt bridges: A:R.6, A:K.63 SO4.13: 4 residues within 4Å: Chain C: R.6, T.7, R.8, K.63 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.7 Water bridges: C:T.7, C:T.7 Salt bridges: C:R.6, C:K.63 SO4.21: 4 residues within 4Å: Chain E: R.6, T.7, R.8, K.63 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.7 Water bridges: E:T.7, E:T.7 Salt bridges: E:R.6, E:K.63

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: P.154, F.156, W.158, K.270, E.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.156, A:K.270, A:E.354 Water bridges: A:E.354 GOL.14: 5 residues within 4Å: Chain C: P.154, F.156, W.158, K.270, E.354 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.156, C:K.270, C:E.354 Water bridges: C:E.354 GOL.22: 5 residues within 4Å: Chain E: P.154, F.156, W.158, K.270, E.354 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:F.156, E:K.270, E:E.354 Water bridges: E:E.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woo, E. et al., Structural Insight Into the Bifunctional Mechanism of the Glycogen-Debranching Enzyme Trex from the Archaeon Sulfolobus Solfataricus. J.Biol.Chem. (2008)

Release Date

2008-07-29

Peptides

GLYCOGEN OPERON PROTEIN GLGX: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

GLYCOGEN OPERON PROTEIN GLGX

Related Entries With Identical Sequence