SMTL ID : 5axh.1

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus, D312G mutant in complex with isomaltohexaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

1 x GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC.1: 22 residues within 4Å: Chain A: Y.184, D.185, H.190, I.208, Y.235, L.237, H.268, L.270, P.271, W.274, L.279, G.312, T.313, L.314, N.352, E.374, Y.408, D.415, K.450, E.451, Y.452, F.453 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.450, A:K.450 Water bridges: A:Y.452

1 x BGC- GLC- GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose

BGC-GLC-GLC-GLC-GLC-GLC.2: 25 residues within 4Å: Chain B: Y.184, D.185, H.190, I.208, Y.235, L.237, H.268, L.270, P.271, W.274, L.279, T.313, L.314, G.315, P.316, N.352, V.354, E.374, W.376, Y.408, D.415, K.450, E.451, Y.452, F.453 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.450, B:K.450, B:L.314, B:P.316, B:P.316

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain A: K.422, S.461, S.463 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.461, A:S.461, A:S.463 Water bridges: A:S.463 Salt bridges: A:K.422 PO4.4: 5 residues within 4Å: Chain A: Y.188, K.189, K.192, K.247, D.248 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.188 Salt bridges: A:K.189, A:K.192, A:K.247 PO4.7: 4 residues within 4Å: Chain B: K.422, S.461, E.462, S.463 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.461, B:S.461, B:E.462, B:S.463 Salt bridges: B:K.422 PO4.8: 3 residues within 4Å: Chain B: K.287, D.336, N.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.336, B:N.340 Salt bridges: B:K.287

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: I.169, D.172, D.444, G.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.172 GOL.6: 7 residues within 4Å: Chain A: K.136, N.137, K.466, R.469, N.470, D.473, D.574 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.136, A:N.137, A:N.137, A:K.466 Water bridges: A:N.137, A:D.473

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, N. et al., Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus. J.Biochem. (2016)

Release Date

2015-11-11

Peptides

Dextranase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dextranase