SMTL ID : 3ij7.1

Directed 'in situ' Elongation as a Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic a-Amylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x B9D- BGC- B8D: 4-O-methyl-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-2)-5-fluoro-alpha-L-idopyranose

B9D-BGC-B8D.1: 15 residues within 4Å: Chain A: W.58, W.59, Y.62, Q.63, H.101, G.104, L.162, T.163, L.165, R.195, D.197, E.233, H.299, D.300, H.305 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.104, A:A.198, A:E.233 Hydrogen bonds: A:R.195, A:R.195, A:D.300, A:Q.63, A:H.305 Halogen bonds: A:Y.62

1 x GLF- B8D: 4-O-methyl-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranosyl fluoride(Non-covalent)

GLF-B8D.2: 9 residues within 4Å: Chain A: A.318, K.322, D.375, T.376, T.377, R.387, W.388, R.389, Q.390 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.376, A:R.389, A:R.389, A:Q.390, A:Q.390, A:R.392, A:K.322, A:K.322, A:Q.390 Water bridges: A:R.389, A:R.389

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.9

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

CL.4: 5 residues within 4Å: Chain A: R.195, T.254, F.256, N.298, R.337 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., Directed "in situ" inhibitor elongation as a strategy to structurally characterize the covalent glycosyl-enzyme intermediate of human pancreatic alpha-amylase. Biochemistry (2009)

Release Date

2009-10-27

Peptides

Pancreatic alpha-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pancreatic alpha-amylase

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