SMTL ID : 3bmx.1 (1 other biounit)

Beta-N-hexosaminidase (YbbD) from Bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

ACT.1: 10 residues within 4Å: Chain A: V.187, R.191, H.222, H.226, S.233, H.234, D.318, M.322 Ligands: NA.4, NA.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.318 Water bridges: A:R.191 Salt bridges: A:R.191, A:H.222, A:H.226, A:H.234 ACT.2: 2 residues within 4Å: Chain A: K.477, R.478 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.477 Water bridges: A:R.478 ACT.3: 6 residues within 4Å: Chain A: P.274, A.275, F.276, D.277, D.278, K.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.278 Water bridges: A:D.277, A:K.299 Salt bridges: A:K.299

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 7 residues within 4Å: Chain A: H.226, S.233, A.269, H.270, D.318, M.322 Ligands: ACT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.233, A:H.270, A:D.318 NA.5: 2 residues within 4Å: Chain A: D.318 Ligands: ACT.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.318

2 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.6: 2 residues within 4Å: Chain A: D.530, T.531 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.548 P4G.7: 4 residues within 4Å: Chain A: Q.244, E.245, R.248, F.276 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Litzinger, S. et al., Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism. J.Biol.Chem. (2010)

Release Date

2008-12-16

Peptides

Uncharacterized lipoprotein ybbD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized lipoprotein ybbD

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