SMTL ID : 3w5n.1

Crystal Structure of Streptomyces avermitilis alpha-L-rhamnosidase complexed with L-rhamnose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.179, N.180, N.228, P.233 Ligands: RAM.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.179, A:P.233, H2O.10

5 x RAM: alpha-L-rhamnopyranose(Non-covalent)

RAM.2: 12 residues within 4Å: Chain A: D.630, R.634, E.636, W.640, D.643, W.695, Y.744, W.747, F.851, E.895, M.911, H.916 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.640, A:W.695, A:Y.744 Hydrogen bonds: A:D.630, A:R.634, A:E.636, A:E.636, A:D.643, A:H.916 Water bridges: A:E.895, A:E.895 RAM.3: 7 residues within 4Å: Chain A: D.179, N.180, E.201, W.203, P.233, W.292 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.203 Hydrogen bonds: A:N.180, A:P.233 Water bridges: A:N.180, A:E.201, A:E.201, A:S.230 RAM.4: 4 residues within 4Å: Chain A: K.484, F.598, W.618, R.621 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.484, A:R.621 Water bridges: A:K.484, A:K.484, A:R.621, A:R.621 Salt bridges: A:R.621 RAM.5: 7 residues within 4Å: Chain A: R.160, T.162, T.221, P.271, D.272, F.273 Ligands: NA.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.162 Hydrogen bonds: A:R.160, A:T.162, A:P.271, A:D.272, A:D.272 Water bridges: A:T.162, A:T.221 RAM.6: 6 residues within 4Å: Chain A: R.351, Q.392, Y.393, V.685, G.686, N.687 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.393, A:V.685 Hydrogen bonds: A:R.351, A:G.686, A:N.687, A:N.687 Water bridges: A:R.351, A:R.351, A:Q.392, A:Q.392 Salt bridges: A:R.351

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 6 residues within 4Å: Chain A: V.530, L.531, R.571, Y.572, K.888, G.889 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.531, A:Y.572 Water bridges: A:E.529, A:R.571, A:G.889 MPD.8: 7 residues within 4Å: Chain A: E.603, T.604, S.955, A.956, R.957, R.970, W.971 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.603, A:R.970 Hydrogen bonds: A:S.955, A:R.970 MPD.9: 6 residues within 4Å: Chain A: D.769, A.772, R.773, T.776, T.786, F.789 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.772, A:R.773, A:T.786, A:F.789 Hydrogen bonds: A:D.769, A:T.776 Water bridges: A:R.773

3 x NA: SODIUM ION(Non-functional Binders)

NA.10: 2 residues within 4Å: Chain A: F.273 Ligands: RAM.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.273 Water bridges: A:R.160 NA.11: 1 residues within 4Å: Chain A: V.71 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.711 NA.12: 1 residues within 4Å: Chain A: L.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujimoto, Z. et al., The structure of a Streptomyces avermitilis alpha-L-rhamnosidase reveals a novel carbohydrate-binding module CBM67 within the six-domain arrangement. J.Biol.Chem. (2013)

Release Date

2013-03-20

Peptides

Putative rhamnosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative rhamnosidase

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