SMTL ID : 1y7b.1

BETA-D-XYLOSIDASE, A FAMILY 43 GLYCOSIDE HYDROLASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: N.333, G.362, D.528 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.333, A:G.362, A:D.528, A:D.528, H2O.8, H2O.8 CA.10: 3 residues within 4Å: Chain B: N.333, G.362, D.528 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.333, B:G.362, B:D.528, H2O.37, H2O.38 CA.18: 3 residues within 4Å: Chain C: N.333, G.362, D.528 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.333, C:G.362, C:D.528, C:D.528, H2O.67, H2O.67 CA.23: 3 residues within 4Å: Chain D: N.333, G.362, D.528 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:N.333, D:G.362, D:D.528, D:D.528, H2O.94, H2O.96

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

SO4.2: 3 residues within 4Å: Chain A: K.326, T.327, Y.328 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.327 Water bridges: A:Y.328, A:N.342, A:N.342 SO4.3: 3 residues within 4Å: Chain A: R.58, T.59, S.60 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.59, A:S.60, A:S.60, A:S.60 Water bridges: A:T.59 SO4.11: 3 residues within 4Å: Chain B: S.311, V.312, N.313 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:V.312, B:N.313, B:N.313 Water bridges: B:N.242, B:N.242, B:S.243, B:Q.309, B:Q.309, B:S.311, B:S.311 SO4.12: 3 residues within 4Å: Chain B: K.326, T.327, Y.328 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.327 Water bridges: B:Y.328, B:Y.328, B:Y.328, B:N.342, B:N.342 SO4.24: 3 residues within 4Å: Chain D: S.311, V.312, N.313 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:V.312, D:N.313, D:N.313 Water bridges: D:N.242, D:N.242, D:S.243, D:Q.309, D:N.313 SO4.25: 3 residues within 4Å: Chain D: K.326, T.327, Y.328 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.327 Water bridges: D:N.342, D:N.342

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 8 residues within 4Å: Chain A: Y.156, K.173, A.174, I.176 Chain B: D.401, T.402, W.425, N.521 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.156, A:A.174, B:N.521 Water bridges: A:Q.161, B:Q.405 Salt bridges: B:D.401 EPE.13: 7 residues within 4Å: Chain A: D.401, T.402, F.403, W.425 Chain B: Y.156, K.173, A.174 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.156, B:A.174 Water bridges: A:N.521, A:N.521, A:N.521 Salt bridges: A:D.401 EPE.19: 7 residues within 4Å: Chain C: Y.156, K.173, A.174 Chain D: D.401, T.402, F.403, W.425 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:A.174 Water bridges: D:D.401, D:N.521, D:N.521, D:N.521 Salt bridges: D:D.401 EPE.26: 7 residues within 4Å: Chain C: D.401, T.402, W.425, N.521 Chain D: Y.156, K.173, A.174 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.521, D:A.174 Water bridges: C:D.401, C:K.523 Salt bridges: C:D.401

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 7 residues within 4Å: Chain A: I.194, G.195, D.196, Y.197, Y.199, W.297, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.196, A:D.196, A:Y.199

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: D.15, F.32, W.74, A.75, D.128, T.207, R.288 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.75, A:D.128, A:R.288, A:R.288 Water bridges: A:T.207, A:T.207 GOL.7: 7 residues within 4Å: Chain A: S.60, L.61, L.62, D.63, D.91, Y.105, P.119 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.63, A:D.91 Water bridges: A:S.60, A:S.60, A:K.93, A:Y.105, A:Y.105, A:Y.105 GOL.8: 6 residues within 4Å: Chain A: F.155, Y.185, E.187, G.206, T.207 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.187, A:T.207 GOL.9: 8 residues within 4Å: Chain A: H.238, P.240, R.241, L.278 Chain C: I.183, P.232, T.235, W.237 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.238, A:R.241, A:R.241 Water bridges: C:T.235 GOL.14: 7 residues within 4Å: Chain B: S.60, L.61, L.62, D.63, D.91, Y.105, P.119 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.63, B:D.91 Water bridges: B:S.60, B:S.60, B:K.93, B:Y.105 GOL.15: 8 residues within 4Å: Chain B: D.15, F.32, W.74, A.75, D.128, H.249, R.288 Ligands: GOL.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.75, B:D.128, B:R.288, B:R.288 Water bridges: B:T.207, B:H.249 GOL.16: 5 residues within 4Å: Chain B: E.187, G.206, T.207, F.506 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.187, B:T.207 Water bridges: B:K.100 GOL.17: 8 residues within 4Å: Chain B: H.238, P.240, R.241, L.278 Chain D: I.183, P.232, T.235, W.237 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:H.238, B:R.241, B:R.241 Water bridges: D:T.235, D:T.235 GOL.20: 7 residues within 4Å: Chain C: S.60, L.61, L.62, D.63, D.91, Y.105, P.119 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.63, C:D.91, C:D.91 Water bridges: C:S.60, C:D.91, C:K.93, C:Y.105 GOL.21: 7 residues within 4Å: Chain C: D.15, F.32, W.74, A.75, D.128, T.207, R.288 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.75, C:D.128, C:R.288, C:R.288 Water bridges: C:E.187, C:E.187 GOL.22: 4 residues within 4Å: Chain C: I.194, Y.199, W.297, N.300 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.194, C:D.196, C:W.297 Water bridges: C:N.300, C:N.300 GOL.27: 8 residues within 4Å: Chain D: D.15, F.32, W.74, A.75, D.128, T.207, R.288 Ligands: GOL.29 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.75, D:D.128, D:R.288, D:R.288 GOL.28: 7 residues within 4Å: Chain D: S.60, L.61, L.62, D.63, D.91, Y.105, P.119 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.63, D:D.91, D:D.91 Water bridges: D:S.60, D:S.60, D:K.93, D:Y.105 GOL.29: 6 residues within 4Å: Chain D: Y.185, E.187, G.206, T.207, F.506 Ligands: GOL.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.187, D:T.207 Water bridges: D:K.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teplyakov, A. et al., Crystal structure of beta-xylosidase from Clostridium acetobutylicum. To be Published

Release Date

2005-01-25

Peptides

Beta-xylosidase, family 43 glycosyl hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-xylosidase, family 43 glycosyl hydrolase

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