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

Structure of YBBD in complex with pugnac

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x OAN: O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE(Non-covalent)

OAN.1: 22 residues within 4Å: Chain A: I.90, F.92, D.123, R.131, F.173, V.187, I.188, R.191, K.221, H.222, H.226, S.233, H.234, M.267, D.318, A.319, N.321, M.322, K.323, L.347, M.348 Ligands: NA.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.187, A:H.234, A:M.322 Hydrogen bonds: A:R.191, A:R.191, A:K.221, A:H.222, A:H.234, A:D.318, A:A.319, A:N.321, A:N.321 Water bridges: A:R.57, A:R.131, A:R.131 pi-Stacking: A:H.234

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

PG4.2: 6 residues within 4Å: Chain A: V.495, F.496, D.530, T.531, I.532, S.533 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.495

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

NA.3: 8 residues within 4Å: Chain A: H.226, S.233, A.269, H.270, V.271, D.318, M.322 Ligands: OAN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.226, A:S.233, A:H.270, A:D.318

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

ACT.4: 6 residues within 4Å: Chain A: P.274, F.276, D.277, D.278, T.279, K.299 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.299 Hydrogen bonds: A:D.278 Salt bridges: A:K.299 ACT.5: 2 residues within 4Å: Chain A: K.477, R.478 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.477 Salt bridges: A:K.477

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

2010-08-04

Peptides

Uncharacterized lipoprotein ybbD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized lipoprotein ybbD

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