SMTL ID : 3ole.1

Structures of human pancreatic alpha-amylase in complex with acarviostatin II03

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

GLC-G6D.1: 13 residues within 4Å: Chain A: W.58, W.59, Y.62, Q.63, G.104, T.163, L.165, D.300, H.305 Ligands: GLC-GLC-G6D.2, ACI.9, ACI.10, MPD.12 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.63 Hydrogen bonds: A:Q.63, A:T.163, A:D.300, A:H.305

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

GLC-GLC-G6D.2: 14 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, ACI.10, MPD.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.151, A:A.198, A:H.201, A:Y.151, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.125 Water bridges: A:D.125, A:Y.131

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

BGC-GLC-GLC.4: 11 residues within 4Å: Chain A: A.318, K.322, D.375, T.376, T.377, R.387, W.388, R.389, Q.390, R.392, E.484 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.376, A:R.389, A:R.389, A:R.389, A:Q.390, A:Q.390, A:R.392 Water bridges: A:R.319, A:R.319, A:K.322, A:K.322

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.16, H2O.16

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)

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.8: 2 residues within 4Å: Chain A: N.459, N.461 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.461

2 x ACI: 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL(Non-covalent)

ACI.9: 5 residues within 4Å: Chain A: N.105, A.106, D.147, T.163 Ligands: GLC-G6D.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.105, A:D.147, A:T.163 Water bridges: A:N.105, A:A.106, A:A.106 ACI.10: 12 residues within 4Å: Chain A: W.58, Y.62, H.101, L.162, 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:E.233, A:E.233, A:H.299 Water bridges: A:D.300, A:D.300

1 x PCA: PYROGLUTAMIC ACID(Covalent)

PCA.11: 7 residues within 4Å: Chain A: Y.2, S.3, K.227, P.228, F.229, I.230, N.250 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:Y.2, A:I.230 Hydrogen bonds: A:I.230 Water bridges: A:S.3, A:S.3, A:K.227

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

MPD.12: 5 residues within 4Å: Chain A: T.163, H.305, G.306 Ligands: GLC-G6D.1, GLC-GLC-G6D.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.163 Hydrogen bonds: A:H.305, A:G.306

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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