SMTL ID : 3olg.1

Structures of human pancreatic alpha-amylase in complex with acarviostatin III03

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x GLC- G6D: alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-G6D.1: 11 residues within 4Å: Chain A: W.58, W.59, Y.62, Q.63, T.163, L.165, D.300, H.305 Ligands: BGC-GLC-G6D.2, HSD.8, HSD.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.59, A:Q.63, A:D.300, A:H.305 Water bridges: A:G.306

1 x BGC- GLC- G6D: alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC-G6D.2: 13 residues within 4Å: Chain A: Y.151, A.198, K.200, H.201, E.233, I.235, L.237, E.240, D.300, G.306, A.307 Ligands: GLC-G6D.1, HSD.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.151, A:Y.151, A:A.198, A:H.201, A:K.200, A:E.240, A:E.240 Water bridges: A:I.235, A:L.237

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

BGC-GLC-GLC-GLC.3: 7 residues within 4Å: Chain A: P.130, Y.131, S.132, W.134, D.135, K.172, Y.174 No protein-ligand interaction detected (PLIP)

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

BGC-GLC-GLC.4: 6 residues within 4Å: Chain A: K.140, E.171, R.176, W.203, G.205, D.206 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.140, A:E.171, A:R.176, A:G.205 Water bridges: A:D.159, A:D.159, A:E.171

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.7, H2O.7

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

CL.6: 5 residues within 4Å: Chain A: R.195, E.233, T.254, N.298, R.337 Ligand excluded by PLIP

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

SO4.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x HSD: (1S,2S,3R,6R)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol(Non-covalent)

HSD.8: 4 residues within 4Å: Chain A: A.106, D.147, T.163 Ligands: GLC-G6D.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.163 HSD.9: 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-G6D.1, BGC-GLC-G6D.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.101, A:R.195, A:D.197, A:E.233, A:D.300 Water bridges: A:E.233, A:N.298

1 x PCA: PYROGLUTAMIC ACID(Covalent)

PCA.10: 7 residues within 4Å: Chain A: Y.2, S.3, K.227, P.228, F.229, I.230, N.250 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.2, A:I.230 Hydrogen bonds: A:Y.2, A:I.230 Water bridges: A:S.3, A:S.3, A:S.3, Q.10

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

GLC.11: 5 residues within 4Å: Chain A: A.318, K.322, T.377, W.388, Q.390 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.322, A:K.322, A:Q.390 Water bridges: A:C.378, A:V.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, X. et al., Structures of human pancreatic alpha-amylase in complex with acarviostatins: Implications for drug design against type II diabetes. J.Struct.Biol. (2011)

Release Date

2011-04-13

Peptides

Pancreatic alpha-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pancreatic alpha-amylase

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