SMTL ID : 3oli.1

Structures of human pancreatic alpha-amylase in complex with acarviostatin IV03

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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: GLC-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:Q.63, A:G.306

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

GLC-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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.198, A:H.201, A:K.200, A:E.240

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

GLC-GLC-GLC.3: 8 residues within 4Å: Chain A: D.125, P.130, Y.131, S.132, W.134, D.135, K.172, Y.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.125 Water bridges: A:Y.131

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

GLC-GLC.4: 5 residues within 4Å: Chain A: K.140, E.171, W.203, G.205, D.206 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.140, A:K.140, A:E.171, A:E.171, A:R.176, A:G.205 Water bridges: A:K.140, 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.5, H2O.5

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

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

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

SO4.7: 1 residues within 4Å: Chain A: W.434 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: 3 residues within 4Å: Chain A: A.106, T.163 Ligands: GLC-G6D.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.163 Water bridges: A:N.105, A:N.105, A:D.147, A:D.147, A:D.147 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, GLC-GLC-G6D.2 8 PLIP interactions: 8 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:E.233, A:N.298

1 x PCA: PYROGLUTAMIC ACID(Covalent)

PCA.10: 8 residues within 4Å: Chain A: Y.2, S.3, K.227, P.228, F.229, I.230, N.250, G.251 12 PLIP interactions: 9 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.2, A:I.230 Hydrogen bonds: A:K.227, A:I.230 Water bridges: A:Y.2, A:Y.2, A:Y.2, A:S.3, A:K.227, Q.10, Q.10, Q.10

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

BGC.11: 6 residues within 4Å: Chain A: A.318, K.322, T.377, W.388, Q.390 Ligands: MPD.13 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.322, A:K.322, A:K.322, A:Q.390 Water bridges: A:C.378, A:C.378, A:V.383, A:V.383

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.12: 3 residues within 4Å: Chain A: N.88, N.220, W.221 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.221 Water bridges: A:N.88 MPD.13: 6 residues within 4Å: Chain A: D.375, T.376, T.377, R.387, R.389 Ligands: BGC.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.377, A:R.389 Hydrogen bonds: A:R.387, A:R.389, A:R.389 Water bridges: A:R.392

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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