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

Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifidum complexed with LNB-thiazoline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.1: 12 residues within 4Å: Chain A: C.168, C.170, Q.171, E.197, N.240, H.244, D.301, W.446, P.447, D.448, L.555 Ligands: NGT.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.171, A:N.240, A:D.301, A:D.448 Water bridges: A:E.197, A:H.244, A:N.246 GAL.7: 12 residues within 4Å: Chain B: C.168, C.170, Q.171, E.197, N.240, H.244, D.301, W.446, P.447, D.448, L.555 Ligands: NGT.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.171, B:N.240, B:H.244, B:D.301, B:D.448, B:D.448 Water bridges: B:E.197, B:E.197, B:N.246

2 x NGT: 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL(Non-covalent)

NGT.2: 9 residues within 4Å: Chain A: D.301, E.302, W.354, W.375, Y.400, Y.408, W.446, D.448 Ligands: GAL.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.301, A:W.354 Hydrogen bonds: A:D.448 Water bridges: A:Y.408 NGT.8: 10 residues within 4Å: Chain B: H.244, D.301, E.302, W.354, W.375, Y.400, Y.408, W.446, D.448 Ligands: GAL.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.301, B:W.354, B:W.375

7 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: 2 residues within 4Å: Chain A: F.549, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.171, A:N.246, A:N.267 SO4.9: 3 residues within 4Å: Chain B: Q.406, F.452, R.580 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.580 SO4.10: 2 residues within 4Å: Chain B: F.549, R.568 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.568 SO4.11: 3 residues within 4Å: Chain B: Q.171, N.246, N.267 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.171, B:N.246, B:N.267

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

Related Entries With Identical Sequence