SMTL ID : 4uoq.1

Nucleophile mutant (E324A) of beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

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

PG4.1: 5 residues within 4Å: Chain A: T.572, V.593, P.595, A.622, A.623 No protein-ligand interaction detected (PLIP) PG4.13: 7 residues within 4Å: Chain A: F.542 Chain C: S.272, T.295, W.299, W.442, T.443, L.446 No protein-ligand interaction detected (PLIP)

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

PGE.2: 6 residues within 4Å: Chain A: R.316, K.317, K.414, Q.467, T.470, Y.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.467, A:T.470 PGE.9: 7 residues within 4Å: Chain B: D.77, I.80, D.81, Y.84, H.149, N.153, P.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.149, B:N.153 PGE.15: 4 residues within 4Å: Chain C: V.593, P.595, A.622, A.623 No protein-ligand interaction detected (PLIP) PGE.17: 5 residues within 4Å: Chain C: D.77, D.81, Y.84, H.149, N.153 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.149, C:N.153

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: S.272, T.295, W.299, W.442, L.446 Chain B: F.542 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.272, A:W.299 PEG.4: 6 residues within 4Å: Chain A: G.525, D.526, V.530, A.566, I.567, A.568 No protein-ligand interaction detected (PLIP) PEG.5: 4 residues within 4Å: Chain A: G.406, L.408, R.409, Q.644 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.409, A:Q.644 PEG.6: 3 residues within 4Å: Chain A: T.137, Y.138, R.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.141 PEG.8: 6 residues within 4Å: Chain B: S.272, T.295, W.299, W.442, L.446 Chain C: F.542 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.272, B:W.299 PEG.10: 7 residues within 4Å: Chain B: G.525, G.529, V.530, R.531, A.566, I.567, A.568 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.569 PEG.11: 5 residues within 4Å: Chain B: S.298, N.454, R.610, R.656, T.657 No protein-ligand interaction detected (PLIP) PEG.12: 5 residues within 4Å: Chain B: S.272, N.274, E.426, E.430, R.440 No protein-ligand interaction detected (PLIP) PEG.14: 5 residues within 4Å: Chain C: G.525, V.530, R.531, A.566, I.567 No protein-ligand interaction detected (PLIP) PEG.16: 5 residues within 4Å: Chain C: H.107, T.134, T.137, Y.138, R.141 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.141

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain A: H.118 Chain B: H.118 Chain C: H.118 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.118, C:H.118, B:H.118, H2O.1

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

2014-10-22

Peptides

BETA-GALACTOSIDASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

BETA-GALACTOSIDASE

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