SMTL ID : 3dhp.1

Probing the role of aromatic residues at the secondary saccharide binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x GLC- AGL: 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-AGL.1: 12 residues within 4Å: Chain A: Y.151, A.198, K.200, H.201, E.233, I.235, E.240, D.300, G.306, A.307 Ligands: GLC.2, HMC.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.151, A:Y.151, A:A.198, A:H.201, A:E.233, A:Y.151, A:K.200, A:E.240 Water bridges: A:E.233, A:I.235, A:E.240

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

GLC.2: 9 residues within 4Å: Chain A: W.58, W.59, Y.62, Q.63, L.165, D.300, H.305 Ligands: GLC-AGL.1, HMC.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.63, A:D.300, A:H.305 Water bridges: A:G.306

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: N.100, R.158, D.167, H.201 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.158, A:D.167, A:H.201, H2O.1, H2O.2

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: R.195, T.254, N.298, R.337 Ligand excluded by PLIP

1 x HMC: 5-HYDROXYMETHYL-CHONDURITOL(Non-covalent)

HMC.5: 11 residues within 4Å: Chain A: W.58, Y.62, H.101, L.165, R.195, D.197, E.233, H.299, D.300 Ligands: GLC-AGL.1, GLC.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.101, A:R.195, A:R.195, A:D.197, A:E.233, A:D.300 Water bridges: A:N.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ragunath, C. et al., Probing the role of aromatic residues. To be Published

Release Date

2008-07-01

Peptides

Alpha-amylase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-amylase 1