SMTL ID : 4bq2.1 (3 other biounits)

Structural analysis of an exo-beta-agarase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: K.257, A.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.257, A:A.258 Water bridges: A:L.256 GOL.2: 9 residues within 4Å: Chain A: Q.209, N.210, Y.215, H.660, S.662, D.703, L.706, D.722, V.723 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.210, A:Y.215, A:D.703, A:V.723 Water bridges: A:L.706, A:Y.728 GOL.3: 9 residues within 4Å: Chain A: R.290, N.293, D.319, S.320, W.418, W.436, F.699, R.709 Ligands: GOL.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.290, A:N.293, A:D.319, A:D.319, A:R.709, A:R.709 Water bridges: A:N.490, A:N.490, A:N.490 GOL.4: 6 residues within 4Å: Chain A: H.587, K.619, Y.620, A.621, D.622, K.646 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.620, A:K.646 Water bridges: A:D.622, A:D.622, A:K.646 GOL.5: 11 residues within 4Å: Chain A: W.451, E.491, Y.629, E.652, H.654, L.667, F.699, R.709, E.714, Y.716 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.629, A:E.652, A:H.654, A:R.709 GOL.6: 4 residues within 4Å: Chain A: T.316, S.320, K.321, G.322 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.316, A:S.320, A:K.321, A:G.322 Water bridges: A:T.316

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.7, E.9, S.37, K.38, D.185 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:E.9, A:S.37, A:K.38, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pluvinage, B. et al., Substrate Recognition and Hydrolysis by a Family 50 Exo-Beta-Agarase Aga50D from the Marine Bacterium Saccharophagus Degradans. J.Biol.Chem. (2013)

Release Date

2013-08-14

Peptides

B-AGARASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B-AGARASE

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