SMTL ID : 3voc.1

Crystal structure of the catalytic domain of beta-amylase from paenibacillus polymyxa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.48, D.52, N.53, Q.132, E.135 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.48, A:D.52, A:E.135, H2O.2

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

CL.2: 3 residues within 4Å: Chain A: C.91, N.92, I.93 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: K.16, Y.46 No protein-ligand interaction detected (PLIP) EDO.4: 6 residues within 4Å: Chain A: H.294, E.297, Q.298, Y.302, Y.303, Y.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.298 Water bridges: A:Y.303 EDO.5: 3 residues within 4Å: Chain A: H.265, D.314, A.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.314 Water bridges: A:A.262

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: L.205, D.206, T.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.206, A:T.217 GOL.7: 2 residues within 4Å: Chain A: T.233, G.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.235 GOL.8: 3 residues within 4Å: Chain A: Y.177, H.284, L.362 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.284

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

TRS.9: 5 residues within 4Å: Chain A: D.328, S.339, D.343, E.374, K.375 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.328, A:S.339, A:K.375 Water bridges: A:K.371, A:K.371, A:K.371, A:K.371, A:K.378, A:K.378 TRS.10: 7 residues within 4Å: Chain A: P.13, I.17, N.18, D.19, S.22, Q.26, N.395 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.18, A:D.19, A:D.19, A:Q.26, A:Q.26, A:N.395

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 4 residues within 4Å: Chain A: M.287, N.288, P.293, H.294 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishimura, S. et al., Structural analysis by X-ray crystallography and small-angle scattering of the multi-domain beta-amylase from Paenibacillus polymyxa. To be Published

Release Date

2013-02-20

Peptides

Beta/alpha-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta/alpha-amylase