SMTL ID : 2zxq.1

Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.283, N.285, D.287, A.289, D.294 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.283, A:D.287, A:A.289, A:D.294, H2O.3 MN.2: 3 residues within 4Å: Chain A: E.409, D.434, H.981 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.409, A:D.434, A:H.981, H2O.9, H2O.11, H2O.13 MN.3: 4 residues within 4Å: Chain A: G.790, N.817, A.818, D.930 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.790, A:A.818, A:D.930, H2O.7, H2O.14 MN.4: 5 residues within 4Å: Chain A: G.956, E.958, D.1004, W.1007, D.1124 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.956, A:E.958, A:D.1004, A:W.1007, H2O.22

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

MPD.5: 7 residues within 4Å: Chain A: Y.939, T.954, N.955, G.956, F.957, E.958, N.959 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.939, A:Y.939, A:E.958, A:N.959 Hydrogen bonds: A:N.955, A:G.956, A:E.958, A:N.959 MPD.6: 2 residues within 4Å: Chain A: V.223, W.505 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.223, A:W.505 MPD.7: 5 residues within 4Å: Chain A: P.553, G.556, G.557, N.560, T.653 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.653 Hydrogen bonds: A:G.557, A:T.653, A:T.653

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, R. et al., Crystallographic and mutational analyses of substrate recognition of endo-{alpha}-N-acetylgalactosaminidase from Bifidobacterium longum. J.Biochem. (2009)

Release Date

2009-06-16

Peptides

Endo-alpha-N-acetylgalactosaminidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-alpha-N-acetylgalactosaminidase