SMTL ID : 3a21.1 (1 other biounit)

Crystal Structure of Streptomyces avermitilis beta-L-Arabinopyranosidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: T.437, D.501, I.502, Y.503, N.504, W.516, N.519, N.523, Q.524 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.437, A:T.437, A:D.501, A:N.504, A:N.519, A:N.523, A:Q.524 Water bridges: A:N.505 GOL.2: 9 residues within 4Å: Chain A: D.543, A.544, Y.545, N.546, L.547, W.558, N.561, Q.563, N.565 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.543, A:N.546, A:N.561, A:Q.563, A:N.565, A:Q.566 GOL.3: 8 residues within 4Å: Chain A: D.586, A.587, Y.588, N.589, A.590, W.601, N.608, Q.609 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.589, A:N.589, A:A.590, A:N.608, A:N.608, A:Q.609 Water bridges: A:N.589 GOL.4: 8 residues within 4Å: Chain A: K.302, E.305, T.308, R.531, E.533, G.538, C.560 Ligands: GOL.10 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.302, A:T.308, A:R.531, A:E.533, A:G.538 Water bridges: A:T.308, A:G.309, A:Q.311 GOL.5: 5 residues within 4Å: Chain A: R.5, T.446, G.447, A.448, S.449 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.446, A:A.448, A:S.449 Water bridges: A:R.5, A:R.5 GOL.6: 8 residues within 4Å: Chain A: W.188, N.189, T.227, A.228, T.437, A.438, T.439, N.505 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.189, A:N.189, A:T.227, A:T.439 Water bridges: A:L.431, A:T.437 GOL.7: 7 residues within 4Å: Chain A: A.304, E.305, D.306, T.307, L.310, I.337, T.338 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.306, A:T.307, A:T.338, A:T.338, A:T.338 Water bridges: A:D.306, A:T.338, A:R.340 GOL.8: 6 residues within 4Å: Chain A: T.338, T.367, G.368, Y.369, T.370 Ligands: SO4.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.365, A:T.367, A:T.370 Water bridges: A:T.370, A:T.370 GOL.9: 5 residues within 4Å: Chain A: Y.108, W.182, T.202, D.203, Y.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.203, A:Y.206, A:Y.206 GOL.10: 7 residues within 4Å: Chain A: D.221, Q.311, R.330, N.539, D.559, C.560 Ligands: GOL.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.311, A:R.330, A:C.560 Water bridges: A:K.302, A:K.302, A:E.305, A:E.305, A:D.559 GOL.11: 4 residues within 4Å: Chain A: G.165, A.168, P.174, L.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.175 Water bridges: A:G.165 GOL.12: 3 residues within 4Å: Chain A: T.214, S.215, S.218 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.214, A:S.218 Water bridges: A:T.202, A:T.202, A:S.215, A:N.219, A:Q.222, A:Q.222

2 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.13: 4 residues within 4Å: Chain A: G.391, G.392, Y.394, T.406 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.394, A:A.408 Water bridges: A:T.406 1PG.14: 6 residues within 4Å: Chain A: P.109, T.110, Y.206, Y.207, G.208, N.209 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.109

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

SO4.15: 4 residues within 4Å: Chain A: S.365, A.366, T.367 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.365, A:A.366 SO4.16: 3 residues within 4Å: Chain A: R.427, G.471, G.472 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.472, A:G.472 Water bridges: A:R.427, A:T.428, A:T.428 Salt bridges: A:R.427 SO4.17: 3 residues within 4Å: Chain A: R.427, P.473, A.474 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.474 Water bridges: A:G.472 Salt bridges: A:R.427 SO4.18: 4 residues within 4Å: Chain A: G.122, H.123, Y.124, D.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.122, A:Y.124, A:D.125 SO4.19: 3 residues within 4Å: Chain A: R.253, I.282, W.357 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.357 Water bridges: A:N.285, A:N.285, A:N.285 Salt bridges: A:R.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ichinose, H. et al., A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27. J.Biol.Chem. (2009)

Release Date

2009-07-14

Peptides

Putative secreted alpha-galactosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative secreted alpha-galactosidase

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