SMTL ID : 5okg.1 (1 other biounit)

Non-conservatively refined structure of Gan1D-E170Q, a catalytic mutant of a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with cellobiose-6-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

1 x BG6: 6-O-phosphono-beta-D-glucopyranose(Non-covalent)

BG6.1: 12 residues within 4Å: Chain A: Q.30, H.131, Q.177, I.180, W.359, E.385, W.432, S.439, W.440, N.442, K.446, Y.448 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.30, A:Q.30, A:H.131, A:Q.177, A:Q.177, A:Q.177, A:Y.448, A:Y.448, A:Y.448 Water bridges: A:N.306, A:S.439, A:W.440, A:W.440 Salt bridges: A:K.446

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Y.270, P.271, Q.272, W.275, W.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.270, A:Q.272 Water bridges: A:W.275 GOL.3: 7 residues within 4Å: Chain A: W.267, M.269 Chain B: W.267, R.376, Y.377, Q.378 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.376, B:Q.378 GOL.4: 6 residues within 4Å: Chain A: W.267, R.376, Y.377, Q.378 Chain B: W.267 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.376, A:Q.378 GOL.5: 6 residues within 4Å: Chain A: F.56, W.357, F.391, N.442, Q.445, K.446 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.357 Water bridges: A:S.439, A:D.457 GOL.6: 7 residues within 4Å: Chain A: N.252, A.273, L.343 Chain B: R.11, R.367, R.371, D.422 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:N.252, A:E.255, A:N.276, B:T.421 Hydrogen bonds: B:R.367, B:R.371, B:D.422 GOL.9: 5 residues within 4Å: Chain B: Y.270, P.271, Q.272, W.275, W.292 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.270, B:Q.272 Water bridges: B:Q.272, B:W.275

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 2 residues within 4Å: Chain A: D.66, E.460 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.460 IMD.10: 2 residues within 4Å: Chain B: Q.163, R.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.163 Water bridges: B:R.164, B:R.168

1 x BGC- BG6: 6-O-phosphono-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-BG6.8: 14 residues within 4Å: Chain B: Q.30, H.131, Q.177, F.184, A.233, Y.308, W.359, E.385, W.432, S.439, W.440, N.442, K.446, Y.448 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.30, B:Q.30, B:H.131, B:Q.177, B:Q.177, B:S.439, B:N.442, B:Y.448 Water bridges: B:N.176, B:W.440, B:W.440, B:N.306, B:Q.309 Salt bridges: B:K.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lansky, S. et al., Structural basis for enzyme bifunctionality - the case of Gan1D from Geobacillus stearothermophilus. FEBS J. (2017)

Release Date

2017-10-18

Peptides

Putative 6-phospho-beta-galactobiosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Putative 6-phospho-beta-galactobiosidase

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