SMTL ID : 1wdr.1

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC.1: 31 residues within 4Å: Chain A: M.17, L.20, D.53, W.55, I.89, H.93, N.98, V.99, D.101, A.184, E.186, R.188, Y.192, Q.194, W.198, F.200, K.295, S.297, G.298, H.300, W.301, S.342, C.343, M.346, E.380, N.381, A.382, L.383, L.419, R.420 Ligands: GLC.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.93, A:D.101, A:R.420, A:R.420 Water bridges: A:D.53, A:D.53, A:D.53, A:D.53, A:Q.94, A:N.98

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.2: 12 residues within 4Å: Chain A: V.99, Y.192, Q.194, W.198, F.200, H.300, W.301, M.346, L.383 Ligands: GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.300

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: R.326, R.330, R.372, E.373, K.478 9 PLIP interactions: 9 interactions with chain A Water bridges: A:R.330, A:R.330, A:R.372, A:R.372, A:R.372, A:R.372 Salt bridges: A:R.326, A:R.330, A:R.372 SO4.4: 2 residues within 4Å: Chain A: H.119, R.130 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.130, A:R.130 Salt bridges: A:H.119, A:R.130 SO4.5: 1 residues within 4Å: Chain A: G.225 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.224, A:G.225 SO4.6: 2 residues within 4Å: Chain A: R.347, S.349 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.349 Water bridges: A:R.347, A:S.349, A:S.349 Salt bridges: A:R.347 SO4.7: 4 residues within 4Å: Chain A: R.372, P.479, T.480, L.481 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.481, A:L.481 Water bridges: A:R.372, A:R.372 Salt bridges: A:R.372 SO4.8: 2 residues within 4Å: Chain A: T.256, E.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.257 Water bridges: A:E.257, A:E.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, Y.N. et al., Structural analysis of threonine 342 mutants of soybean beta-amylase: role of a conformational change of the inner loop in the catalytic mechanism. Biochemistry (2005)

Release Date

2005-04-05

Peptides

Beta-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-amylase