SMTL ID : 6m4k.1

X-ray crystal structure of wild type alpha-amylase I from Eisenia fetida

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: N.105, R.161, D.170, H.204 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.161, A:D.170, A:H.204, H2O.5, H2O.13

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

CL.2: 5 residues within 4Å: Chain A: R.198, E.236, T.257, N.301, R.341 Ligand excluded by PLIP

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

ACT.3: 6 residues within 4Å: Chain A: Y.67, H.106, L.165, L.168, D.200, A.201 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.168 Hydrogen bonds: A:Y.67 Water bridges: A:A.201 Salt bridges: A:H.106

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

SO4.4: 3 residues within 4Å: Chain A: N.367, K.373, D.374 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.367, A:D.374 SO4.5: 4 residues within 4Å: Chain A: E.321, A.322, N.323, M.324 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.323, A:M.324 Water bridges: A:A.322, A:A.322, A:A.322, A:N.323, A:N.323 SO4.6: 3 residues within 4Å: Chain A: K.26, T.28, Q.83 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.83 Water bridges: A:K.26, A:T.28, A:R.32, A:T.372 Salt bridges: A:K.26 SO4.7: 1 residues within 4Å: Chain A: R.179 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.179, A:R.179, A:D.209 Salt bridges: A:R.179 SO4.8: 2 residues within 4Å: Chain A: S.407, N.408 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.408, A:N.408 Water bridges: A:W.409, A:W.409

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 7 residues within 4Å: Chain A: W.361, V.362, P.364, P.365, T.366, N.367, G.368 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.366, A:T.366

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.10: 3 residues within 4Å: Chain A: D.58, P.59, W.361 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.58 PG4.11: 3 residues within 4Å: Chain A: I.402, G.403, N.404 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirano, Y. et al., X-ray crystallographic structural studies of alpha-amylase I from Eisenia fetida. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-09-16

Peptides

Alpha-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-amylase