SMTL ID : 1wds.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

1 x BGC- GLC: alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GLC.1: 18 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, K.295, A.342, E.380, A.382, L.419, R.420 Ligands: GLC.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.99, A:K.295, A:A.382, A:H.93, A:D.101, A:R.420, A:R.420 Water bridges: A:E.186, A:E.380, A:E.380, A:R.420, A:D.53, A:D.53, A:N.98, A:D.101

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

GLC.2: 10 residues within 4Å: Chain A: V.99, Y.192, Q.194, W.198, F.200, H.300, W.301, M.346, L.383 Ligands: BGC-GLC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.300, A:Q.351 Water bridges: A:V.99

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

SO4.3: 4 residues within 4Å: Chain A: R.326, R.330, R.372, E.373 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.330, A:R.330, A:R.330, A:K.478 Salt bridges: A:R.326, A:R.330, A:R.372 SO4.4: 3 residues within 4Å: Chain A: H.119, G.128, R.130 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.130, A:R.130, A:R.130 Salt bridges: A:H.119, A:R.130 SO4.5: 2 residues within 4Å: Chain A: A.222, G.225 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.225, 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:R.347, A:S.349 Salt bridges: A:R.347 SO4.7: 4 residues within 4Å: Chain A: R.372, P.479, T.480, L.481 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.481, A:L.481 Water bridges: A:R.372 Salt bridges: A:R.372 SO4.8: 2 residues within 4Å: Chain A: T.256, E.257 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.257 Water bridges: A:T.256, A:T.256, A:E.257, A:E.257 SO4.9: 6 residues within 4Å: Chain A: N.125, S.127, T.129, E.205, K.237, Y.238 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.125, A:S.127, A:T.129 Water bridges: A:S.127, A:T.129, A:Q.196 Salt bridges: A:K.237 SO4.10: 2 residues within 4Å: Chain A: P.352, S.353 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.353 Water bridges: A:S.353, A:D.354

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