SMTL ID : 1mxg.1

Crystal Structure of a (Ca,Zn)-dependent alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei in complex with acarbose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

3 x GLC- GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC-AC1.1: 14 residues within 4Å: Chain A: E.7, E.8, G.9, K.241, P.278, F.279, E.307, G.308, Q.309, G.338, G.339, S.340, D.358, R.361 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.241, A:P.278, A:F.279, A:G.308, A:R.361, A:E.307, A:E.307, A:G.339, A:D.358, A:D.358, A:R.361 Water bridges: A:F.279, A:Q.309, A:R.355, A:R.355, A:R.361, A:E.307, A:E.307, A:S.340 GLC-GLC-AC1.2: 9 residues within 4Å: Chain A: S.132, T.140, A.141, N.142, L.144, D.145, E.150, K.169, W.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.140, A:A.141, A:N.142, A:N.142, A:D.145, A:E.150, A:K.169, A:K.169 Water bridges: A:D.130, A:A.141 GLC-GLC-AC1.3: 10 residues within 4Å: Chain A: Y.3, N.328, W.331, H.390, E.391, Y.392, T.393, G.394, W.399, G.435 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.2, A:W.331, A:D.324 Hydrogen bonds: A:G.435

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.147, H.152, C.166, H.168 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.147, A:H.152, A:C.166, H2O.2

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: N.110, D.155, G.157, D.164, G.202 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:G.157, A:D.164, A:D.164, H2O.1

3 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: D.252, D.256, I.292 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.252, A:D.256, A:I.292, H2O.3, H2O.3, H2O.3 MG.7: 3 residues within 4Å: Chain A: D.347, D.349, E.350 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.347, A:E.350, H2O.5, H2O.6, H2O.12 MG.8: 3 residues within 4Å: Chain A: G.24, E.80, E.88 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.24, A:E.80, A:E.88, A:E.88, H2O.6

2 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.9: 5 residues within 4Å: Chain A: R.31, S.32, P.35, R.91, T.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.31, A:R.31 ETE.10: 6 residues within 4Å: Chain A: F.68, Y.73, K.138, N.180, A.185, Y.186 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.186

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.11: 8 residues within 4Å: Chain A: Y.62, F.159, R.196, D.198, Y.199, E.222, H.288, D.289 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.196, A:R.196 Water bridges: A:D.198, A:D.198, A:E.222, A:E.222, A:N.287, A:H.288, A:D.289, A:D.289

4 x EOH: ETHANOL(Non-functional Binders)

EOH.12: 4 residues within 4Å: Chain A: Y.38, A.98, Y.99 Ligands: EOH.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.38, A:Y.99 EOH.13: 3 residues within 4Å: Chain A: A.98, Y.99 Ligands: EOH.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.98, A:Y.99 EOH.14: 7 residues within 4Å: Chain A: H.390, Y.392, W.399, C.432, G.433, V.434, G.435 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.433 EOH.15: 2 residues within 4Å: Chain A: Y.431, C.432 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Linden, A. et al., Differential Regulation of a Hyperthermophilic alpha-Amylase with a Novel (Ca,Zn) Two-metal Center by Zinc. J.Biol.Chem. (2003)

Release Date

2003-06-10

Peptides

alpha amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

alpha amylase

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