SMTL ID : 1yi7.1

Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.6, H2O.8 CA.11: 3 residues within 4Å: Chain B: N.333, G.362, D.528 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.333, B:G.362, B:D.528, B:D.528, H2O.32, H2O.39 CA.19: 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.54, H2O.57 CA.27: 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.83, H2O.85

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

SO4.2: 3 residues within 4Å: Chain A: K.326, T.327, Y.328 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.327 Water bridges: A:T.327, A:T.327, A:T.327, A:T.327, A:Y.328 SO4.3: 3 residues within 4Å: Chain A: S.2, L.3, K.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.3 Salt bridges: A:K.5 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 SO4.13: 3 residues within 4Å: Chain B: S.311, V.312, N.313 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.312, B:N.313, B:N.313 Water bridges: B:N.242, B:N.242, B:G.310 SO4.20: 3 residues within 4Å: Chain C: K.326, T.327, Y.328 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.327 Water bridges: C:T.327, C:T.327, C:T.327, C:T.327, C:Y.328, C:Y.328 SO4.28: 3 residues within 4Å: Chain D: K.326, T.327, Y.328 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.327 SO4.29: 3 residues within 4Å: Chain D: S.311, V.312, N.313 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:V.312, D:N.313, D:N.313 Water bridges: D:N.242, D:N.242, D:Q.309, D:G.310

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

EPE.4: 7 residues within 4Å: Chain A: D.401, T.402, F.403, W.425 Chain B: Y.156, K.173, A.174 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.156, B:A.174, A:N.521 Water bridges: B:Q.161 Salt bridges: A:D.401 EPE.5: 8 residues within 4Å: Chain A: Y.145, Y.156, K.173, A.174, I.176 Chain B: D.401, T.402, W.425 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.156, A:A.174 Water bridges: A:Q.161, B:N.521, B:N.521, B:N.521 Salt bridges: B:D.401 EPE.21: 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: 4 interactions with chain D, 2 interactions with chain C Water bridges: D:N.521, D:N.521, D:N.521, C:Q.161 Salt bridges: D:D.401 Hydrogen bonds: C:A.174 EPE.30: 8 residues within 4Å: Chain C: D.401, T.402, W.425, N.521 Chain D: Y.156, K.173, A.174, I.176 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:A.174, C:N.521 Water bridges: D:Q.161, C:Q.405 Salt bridges: C:D.401

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: S.60, L.61, L.62, D.63, D.91, Y.105, P.119 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: D.15, F.32, W.74, A.75, D.128, T.207, R.288 Ligands: GOL.8 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: E.187, G.206, T.207, F.506 Ligands: GOL.7 Ligand excluded by PLIP 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 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: Y.209, Q.280, R.281, G.282, Y.283, D.498 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: S.60, L.61, L.62, D.63, D.91, Y.105, P.119 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain B: D.15, F.32, W.74, A.75, D.128, T.207, R.288 Ligands: GOL.16 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain B: Y.185, E.187, G.206, T.207, F.506 Ligands: GOL.15 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: P.240, R.241, L.278 Chain D: I.183, P.232, W.237 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: Y.209, Q.280, R.281, G.282, Y.283, D.498 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain C: S.60, L.61, L.62, D.63, D.91, Y.105, P.119 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain C: D.15, F.32, W.74, A.75, D.128, T.207, R.288 Ligands: GOL.24 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain C: Y.185, E.187, G.206, T.207, F.506 Ligands: GOL.23 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain A: I.183, P.232, T.235, W.237 Chain C: P.240, R.241, L.278 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain C: Y.209, Q.280, R.281, G.282, Y.283, D.498 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain D: S.60, L.61, L.62, D.63, D.91, Y.105, P.119 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain D: D.15, F.32, W.74, A.75, D.128, T.207, R.288 Ligands: GOL.33 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain D: Y.185, E.187, G.206, T.207, F.506 Ligands: GOL.32 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain B: I.183, P.232, T.235, W.237 Chain D: P.240, R.241, L.278 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain D: Q.280, R.281, G.282, Y.283, D.498 Ligand excluded by PLIP

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

2005-02-22

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

Related Entries With Identical Sequence