SMTL ID : 4h04.3 (2 other biounits)

Lacto-N-biosidase from Bifidobacterium bifidum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- GAL: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL.1: 15 residues within 4Å: Chain A: C.168, Q.171, E.197, N.240, H.244, D.301, E.302, W.354, W.375, Y.400, Y.408, W.446, P.447, D.448, L.555 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.171, A:N.240, A:D.301, A:D.448, A:D.301, A:D.301, A:E.302, A:Y.400 Water bridges: A:E.197, A:E.197, A:H.244, A:N.246, A:Y.408, A:D.448 Hydrophobic interactions: A:D.301, A:W.354, A:W.375 NAG-GAL.2: 16 residues within 4Å: Chain B: C.168, C.170, Q.171, E.197, N.240, H.244, D.301, E.302, W.354, W.375, Y.400, Y.408, W.446, P.447, D.448, L.555 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.171, B:N.240, B:H.244, B:D.301, B:D.448, B:D.448, B:D.301, B:E.302 Water bridges: B:E.197, B:E.197, B:N.246, B:D.448 Hydrophobic interactions: B:D.301, B:W.354, B:W.375

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

SO4.3: 3 residues within 4Å: Chain A: Q.406, F.452, R.580 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.580 SO4.4: 3 residues within 4Å: Chain A: L.99, T.127, D.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.128 Water bridges: A:T.127, A:I.129 SO4.5: 1 residues within 4Å: Chain A: R.568 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.568 SO4.6: 3 residues within 4Å: Chain A: Q.171, N.246, N.267 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.171, A:N.246, A:N.267 Water bridges: A:Q.171, A:H.244, A:H.244 SO4.7: 3 residues within 4Å: Chain B: Q.406, F.452, R.580 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.580, B:R.580 Salt bridges: B:R.580 SO4.8: 1 residues within 4Å: Chain B: R.568 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.568 SO4.9: 3 residues within 4Å: Chain B: Q.171, N.246, N.267 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.171, B:N.246, B:N.267 Water bridges: B:H.244, B:H.244, B:H.244, B:L.555 SO4.10: 2 residues within 4Å: Chain B: K.381, R.429 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.381, B:R.429

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ito, T. et al., Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum. J.Biol.Chem. (2013)

Release Date

2013-03-20

Peptides

Lacto-N-biosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lacto-N-biosidase

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