SMTL ID : 3a22.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

4 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.10 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.96, 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 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.437, A:T.437, A:T.437, A:T.437, A:D.501, A:N.504, A:N.504, A:N.519, A:N.523, A:Q.524 Water bridges: A:N.505, A:N.519, A:N.523 ARA.3: 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 ARA.4: 7 residues within 4Å: Chain A: D.586, A.587, Y.588, N.589, W.601, N.608 Ligands: 1PG.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.586, A:N.589, A:N.589, A:A.590, A:N.608, A:N.608, A:Q.609

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.307, A:T.307, A:T.338, A:T.338, A:T.338 Water bridges: A:R.340 GOL.6: 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.7: 10 residues within 4Å: Chain A: K.302, E.305, T.308, T.529, R.531, E.533, V.535, G.538, N.539, C.560 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.302, A:K.302, A:T.308, A:R.531, A:G.538 Water bridges: A:Q.311 GOL.8: 7 residues within 4Å: Chain A: D.27, Y.28, S.29, A.73, E.74, P.76 Ligands: 1PG.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.27, A:Y.28, A:S.29 GOL.9: 6 residues within 4Å: Chain A: P.10, P.196, T.231, G.232, Y.233, S.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.232, A:S.442, A:S.442 GOL.10: 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:W.182, A:Y.206, A:Y.206 Water bridges: A:C.104, A:Y.108, A:D.203 GOL.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.12: 3 residues within 4Å: Chain A: S.212, M.213, T.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.213, A:T.214, A:T.214 Water bridges: A:S.212

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

EPE.13: 8 residues within 4Å: Chain A: A.37, A.40, A.41, L.272, 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.14: 4 residues within 4Å: Chain A: Y.28, P.76, G.77 Ligands: GOL.8 No protein-ligand interaction detected (PLIP) 1PG.15: 6 residues within 4Å: Chain A: N.551, G.552, Y.588, N.589, W.601 Ligands: ARA.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.588, A:N.589

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

SO4.16: 4 residues within 4Å: Chain A: R.427, T.428, 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

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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