SMTL ID : 3a21.2 (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

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: Q.436, T.437, D.501, I.502, Y.503, N.504, W.516, N.519, N.523, Q.524 9 PLIP interactions: 9 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.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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.543, A:N.546, A:N.561, A:Q.563, A:N.565 GOL.3: 8 residues within 4Å: Chain A: D.586, A.587, Y.588, N.589, A.590, W.601, N.608, Q.609 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.589, A:A.590, A:N.608, A:N.608, A:Q.609 GOL.4: 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.307, A:T.338, A:T.338, A:T.338 Water bridges: A:R.340 GOL.5: 3 residues within 4Å: Chain A: T.276, S.277, E.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.276, A:S.277, A:E.278 GOL.6: 10 residues within 4Å: Chain A: K.302, E.305, T.308, T.529, R.531, E.533, V.535, G.538, C.560 Ligands: GOL.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.302, A:T.308, A:R.531, A:G.538 Water bridges: A:K.302, A:G.309, A:Q.311 GOL.7: 7 residues within 4Å: Chain A: D.27, Y.28, S.29, A.73, E.74, P.76 Ligands: 1PG.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.27, A:Y.28, A:S.29, A:S.29 Water bridges: A:D.27, A:D.27, A:D.27 GOL.8: 7 residues within 4Å: Chain A: D.221, Q.311, R.330, N.539, D.559, C.560 Ligands: GOL.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.311, A:R.330, A:C.560 Water bridges: A:K.302, A:E.305, A:E.305, A:G.538 GOL.9: 6 residues within 4Å: Chain A: Y.108, C.144, W.182, T.202, D.203, Y.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.199, A:D.203, A:Y.206 Water bridges: A:R.199 GOL.10: 4 residues within 4Å: Chain A: G.165, A.168, P.174, L.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.175, A:L.175 Water bridges: A:S.161, A:G.165 GOL.11: 2 residues within 4Å: Chain A: D.147, A.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.148 Water bridges: A:D.147, A:G.150 GOL.12: 5 residues within 4Å: Chain A: G.548, T.550, N.551, G.552, T.553 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.552, A:T.553 GOL.13: 3 residues within 4Å: Chain A: S.212, M.213, T.214 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:M.213, A:T.214, A:T.214, A:Q.251 Water bridges: A:P.211, A:S.212, A:T.214

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

EPE.14: 9 residues within 4Å: Chain A: A.37, A.40, A.41, L.272, T.273, M.275, S.277, A.280, K.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.277 Water bridges: A:G.281, A:K.284 Salt bridges: A:K.284

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

1PG.15: 3 residues within 4Å: Chain A: Y.28, P.76 Ligands: GOL.7 No protein-ligand interaction detected (PLIP) 1PG.16: 6 residues within 4Å: Chain A: P.109, T.110, Y.206, Y.207, G.208, N.209 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.109, A:G.111

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

SO4.17: 3 residues within 4Å: Chain A: R.427, G.471, G.472 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.472 Water bridges: A:R.427, A:T.428 Salt bridges: A:R.427 SO4.18: 6 residues within 4Å: Chain A: G.122, H.123, Y.124, D.125, Q.126 Ligands: SO4.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.125, A:Q.126, A:Q.126 Water bridges: A:D.125 SO4.19: 5 residues within 4Å: Chain A: G.122, H.123, Y.124, D.125 Ligands: SO4.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.122, A:G.122, A:Y.124, A:D.125

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
B

Putative secreted alpha-galactosidase

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