SMTL ID : 3a22.1 (1 other biounit)

Crystal Structure of beta-L-Arabinopyranosidase complexed with L-arabinose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

5 x ARA: alpha-L-arabinopyranose(Non-covalent)

ARA.1: 13 residues within 4Å: Chain A: W.19, D.54, E.55, Y.96, C.104, K.140, D.142, C.180, W.182, R.199, D.203, M.239 Ligands: GOL.11 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.55, A:K.140, A:K.140, A:D.142, A:W.182, A:W.182, A:R.199, A:R.199 Water bridges: A:D.203, A:D.203, A:D.238 ARA.2: 9 residues within 4Å: Chain A: T.437, D.501, I.502, Y.503, N.504, W.516, N.519, N.523, Q.524 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.437, A:T.437, A:T.437, A:D.501, A:N.504, A:N.519, A:N.519, A:N.523, A:Q.524 Water bridges: A:N.504, A:N.505 ARA.3: 10 residues within 4Å: Chain A: D.543, A.544, Y.545, N.546, L.547, W.558, N.561, Q.563, N.565, Q.566 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.543, A:N.546, A:N.561, A:Q.563, A:N.565, A:Q.566 Water bridges: A:Q.563 ARA.4: 8 residues within 4Å: Chain A: D.586, A.587, Y.588, N.589, A.590, W.601, N.608, Q.609 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.586, A:N.589, A:A.590, A:N.608, A:Q.609 Water bridges: A:N.608 ARA.5: 3 residues within 4Å: Chain A: Y.503, E.514, G.595 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.514 Water bridges: A:E.514

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: K.302, E.305, T.308, R.531, E.533, G.538, C.560 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:G.309, A:Q.311, A:Q.311 GOL.7: 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.8: 8 residues within 4Å: Chain A: W.188, N.189, T.227, A.228, T.437, A.438, T.439, N.505 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.189, A:N.189, A:T.227 Water bridges: A:L.431, A:T.437 GOL.9: 7 residues within 4Å: Chain A: A.304, E.305, D.306, T.307, L.310, I.337, T.338 7 PLIP interactions: 7 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 GOL.10: 6 residues within 4Å: Chain A: T.338, T.367, G.368, Y.369, T.370 Ligands: SO4.18 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.367, A:T.370 Water bridges: A:S.365, A:T.370, A:T.370 GOL.11: 7 residues within 4Å: Chain A: C.104, Y.108, C.144, W.182, D.203, Y.206 Ligands: ARA.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.203, A:Y.206, A:Y.206 Water bridges: A:C.104, A:Y.108, A:R.199 GOL.12: 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.13: 3 residues within 4Å: Chain A: T.214, S.215, S.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.218 Water bridges: A:T.202, A:Q.222, A:Q.222 GOL.14: 7 residues within 4Å: Chain A: N.434, S.460, A.464, N.465, L.490, C.518, N.519 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.460, A:A.464, A:C.518 Water bridges: A:N.434, A:A.464 GOL.15: 2 residues within 4Å: Chain A: S.449, A.450 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.450 Water bridges: A:T.420, A:T.420

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

1PG.16: 4 residues within 4Å: Chain A: G.391, G.392, Y.394, T.406 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.394 Water bridges: A:G.392, A:T.406, A:A.408 1PG.17: 5 residues within 4Å: Chain A: P.109, T.110, Y.206, Y.207, N.209 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.109, A:G.111

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

SO4.18: 4 residues within 4Å: Chain A: S.365, A.366, T.367 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.365, A:A.366 SO4.19: 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:R.427 Salt bridges: A:R.427

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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