SMTL ID : 4bq4.1 (1 other biounit)

Structural analysis of an exo-beta-agarase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x GAL- AAL- GAL- AAL: 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose

GAL-AAL-GAL-AAL.1: 23 residues within 4Å: Chain A: L.132, W.156, I.288, R.290, N.293, D.319, S.320, W.418, W.436, W.451, N.490, Q.491, R.496, W.607, Y.629, E.652, H.654, L.667, F.699, R.709, Y.711, E.714, Y.716 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.290, A:N.293, A:D.319, A:R.709, A:R.709, A:N.490, A:Q.491, A:N.627, A:R.709, A:R.709 Water bridges: A:W.451, A:N.490, A:Y.711, A:D.712, A:D.712, A:D.712, A:D.712, A:E.714

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: Q.209, N.210, Y.215, H.660, G.661, S.662, D.703, L.706, D.722, V.723 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.210, A:S.662, A:V.723 Water bridges: A:L.706, A:Y.728 GOL.3: 5 residues within 4Å: Chain A: Q.309, D.314, K.321, R.363 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.314, A:D.314, A:K.321, A:R.363, A:R.363 GOL.4: 4 residues within 4Å: Chain A: T.316, K.321, G.322 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.316, A:T.316, A:G.322, A:G.322 Water bridges: A:K.321 GOL.5: 5 residues within 4Å: Chain A: Q.48, H.49, S.50, Q.636, K.637 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.48, A:H.49, A:S.50 Water bridges: A:Y.51

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.7, E.9, S.37, K.38, D.185, N.186 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:E.9, A:K.38, A:D.185, H2O.1 CA.7: 4 residues within 4Å: Chain A: N.293, R.709, A.710, Y.711 No protein-ligand interaction detected (PLIP)

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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