SMTL ID : 4bq5.1 (1 other biounit)

Structural analysis of an exo-beta-agarase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

GAL-AAL.1: 20 residues within 4Å: Chain A: I.288, R.290, N.293, D.319, S.320, W.418, W.436, N.490, Q.491, N.627, Y.629, E.652, H.654, L.667, F.699, R.709, Y.711, E.714, Y.716 Ligands: AAL.4 7 PLIP interactions: 7 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:Y.711, A:D.712, A:D.712, A:D.712, A:D.712 GAL-AAL.2: 7 residues within 4Å: Chain A: D.89, V.97, T.99, W.156, R.496 Ligands: GAL-AAL.3, GAL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.496, A:T.99 Water bridges: A:T.99, A:T.99, A:T.99 GAL-AAL.3: 4 residues within 4Å: Chain A: T.91, G.95, V.97 Ligands: GAL-AAL.2 No protein-ligand interaction detected (PLIP)

1 x AAL: 3,6-anhydro-alpha-L-galactopyranose(Non-covalent)

AAL.4: 6 residues within 4Å: Chain A: Q.491, W.607, Y.629, L.667 Ligands: GAL-AAL.1, GAL.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.491, A:Q.491, A:D.606, A:D.606 Water bridges: A:R.139, A:D.606, A:E.714

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.5: 7 residues within 4Å: Chain A: L.132, W.156, W.451, R.496, W.607 Ligands: GAL-AAL.2, AAL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.496, A:R.496, A:W.607 Water bridges: A:D.606

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: Q.209, N.210, Y.215, H.660, G.661, S.662, D.703, D.722, V.723, Y.728 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.210, A:D.703, A:V.723

3 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.2 CA.8: 5 residues within 4Å: Chain A: S.292, N.293, R.709, A.710, Y.711 No protein-ligand interaction detected (PLIP) CA.9: 4 residues within 4Å: Chain A: P.354, N.357, E.384, E.389 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.354, A:E.384, A:E.384, H2O.11

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

Related Entries With Identical Sequence