SMTL ID : 1mxd.1

Structure of a (Ca,Zn)-dependent alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

4 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: 13 residues within 4Å: Chain A: E.7, E.8, G.9, K.241, P.278, F.279, E.307, G.308, G.338, G.339, S.340, D.358, R.361 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.241, A:K.241, A:E.8, A:P.278, A:G.308, A:R.361 Water bridges: A:K.241, A:Y.306, A:G.308, A:R.355, A:R.355, A:R.361 GLC-GLC-AC1.2: 7 residues within 4Å: Chain A: S.132, T.140, A.141, N.142, L.144, D.145, W.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.140, A:A.141, A:N.142, A:W.171, A:N.142, A:D.145 GLC-GLC-AC1.3: 9 residues within 4Å: Chain A: 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:Y.3, A:Y.3 Hydrogen bonds: A:N.328, A:G.435 GLC-GLC-AC1.4: 13 residues within 4Å: Chain A: W.18, Y.62, H.111, F.159, R.196, D.198, Y.199, K.201, E.222, W.224, H.288, D.289 Ligands: ZN.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.62 Hydrogen bonds: A:H.111, A:R.196, A:R.196, A:Y.199, A:E.222, A:E.222, A:E.222, A:K.201, A:W.224 Water bridges: A:K.201, A:W.224

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 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 ZN.6: 5 residues within 4Å: Chain A: D.252, D.256, I.292, I.293, W.294 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.252, A:D.256, A:I.292 ZN.7: 4 residues within 4Å: Chain A: E.36, E.318, K.323 Ligands: ACT.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.36, A:E.36, A:E.318, A:E.318, ACT.13 ZN.8: 4 residues within 4Å: Chain A: D.347, D.349, E.350, R.377 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.347, A:D.347, A:D.349, A:E.350, H2O.2 ZN.9: 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:E.80, A:E.80, A:E.88, A:E.88, H2O.3 ZN.10: 4 residues within 4Å: Chain A: D.198, E.222, D.289 Ligands: GLC-GLC-AC1.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.222, A:E.222, H2O.12

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 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:D.155, A:D.164, A:G.202, H2O.1

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

GLC.12: 5 residues within 4Å: Chain A: D.291, W.294, K.296, D.316, W.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.291, A:D.291 Water bridges: A:D.291 Salt bridges: A:K.296

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 5 residues within 4Å: Chain A: K.33, E.36, E.318, K.323 Ligands: ZN.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.36 Salt bridges: A:K.33, A:K.323

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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