SMTL ID : 3ij9.1

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 1.85 Å

Oligo State

monomer

Ligands

1 x B9D- BGC: beta-D-glucopyranose-(1-2)-5-fluoro-alpha-L-idopyranose(Post Translational Modification)

B9D-BGC.1: 14 residues within 4Å: Chain A: W.58, W.59, Y.62, Q.63, H.101, L.162, T.163, L.165, R.195, D.197, E.233, H.299, D.300, H.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.195, A:R.195, A:D.300, A:Q.63, A:T.163, A:H.305 Water bridges: A:A.198, A:E.233 Halogen bonds: A:Y.62

2 x B0D: (2R,3S,4R,5R,6R)-2,6-difluoro-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol(Non-covalent)

B0D.2: 6 residues within 4Å: Chain A: K.140, E.171, R.176, W.203, G.205, D.206 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.140, A:K.140, A:R.176 Water bridges: A:K.140, A:W.203 B0D.3: 5 residues within 4Å: Chain A: P.204, G.205, K.208, G.249, N.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.250, A:N.250 Water bridges: A:G.249

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.2, H2O.9

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

CL.5: 5 residues within 4Å: Chain A: R.195, E.233, T.254, 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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