SMTL ID : 4uoz.1

beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 nucleophile mutant E324A in complex with galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.1: 12 residues within 4Å: Chain A: F.59, R.125, N.163, E.164, N.266, D.291, Y.293, A.324, W.332, F.362, E.372, H.375 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.28, A:R.125, A:R.125, A:N.163, A:E.164, A:N.266, A:D.291, A:Y.293, A:W.332, A:E.372 GLA.5: 12 residues within 4Å: Chain B: F.59, R.125, N.163, E.164, N.266, D.291, Y.293, A.324, W.332, F.362, E.372, H.375 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.125, B:R.125, B:N.163, B:E.164, B:N.266, B:D.291, B:W.332, B:E.372 Water bridges: B:N.163 GLA.8: 12 residues within 4Å: Chain C: F.59, R.125, N.163, E.164, N.266, D.291, Y.293, A.324, W.332, F.362, E.372, H.375 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.28, C:R.125, C:R.125, C:N.163, C:E.164, C:N.266, C:D.291, C:D.291, C:W.332 Water bridges: C:E.372, C:E.372

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.118 Chain B: H.118 Chain C: H.118 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:H.118, B:H.118, C:H.118

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 4 residues within 4Å: Chain A: T.295, W.299, W.442, L.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.272 PGE.4: 4 residues within 4Å: Chain A: T.572, V.593, P.595, A.623 No protein-ligand interaction detected (PLIP) PGE.6: 7 residues within 4Å: Chain B: S.272, T.295, W.299, W.442, T.443, L.446 Chain C: F.542 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.272 PGE.7: 5 residues within 4Å: Chain B: V.593, A.622, A.623, L.624, G.625 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.624 PGE.9: 6 residues within 4Å: Chain C: S.272, T.295, W.299, W.442, T.443, L.446 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.272, C:S.272 PGE.10: 4 residues within 4Å: Chain C: T.572, V.593, A.622, A.623 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viborg, A.H. et al., A beta 1-6/ beta 1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of beta-galactoside catabolism within Bifidobacterium. Mol. Microbiol. (2014)

Release Date

2014-10-15

Peptides

BETA-GALACTOSIDASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

BETA-GALACTOSIDASE

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