SMTL ID : 7sf2.1 (1 other biounit)

Crystal Structure of Beta-Galactosidase from Bacteroides cellulosilyticus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.113, D.157, Q.169, V.181 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.113, A:D.157, A:V.181, H2O.2, H2O.3 MG.21: 4 residues within 4Å: Chain B: D.113, D.157, Q.169, V.181 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.113, B:D.157, B:V.181, H2O.12, H2O.12 MG.43: 4 residues within 4Å: Chain C: D.113, D.157, Q.169, V.181 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.113, C:D.157, C:V.181, H2O.24, H2O.24

36 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: L.267, T.269, Y.287, Q.368 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: I.203, P.205, A.288, A.289, R.291, S.420, P.422 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: W.119, D.122, R.150, V.152 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: W.39, K.40, N.41 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: S.222, T.223 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: E.28, R.361 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: Y.29, Q.35, R.36, N.37 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: R.36, P.192, V.193, A.194, V.281, D.282 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: D.160, R.161, G.162, P.163, D.381 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: N.37, D.38, W.39 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: T.14, K.15, W.16, D.564, R.565, K.566 Ligand excluded by PLIP EDO.15: 1 residues within 4Å: Chain A: K.258 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: S.264, P.265, F.266 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: T.140, P.141 Chain B: S.224 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: I.203, P.205, A.288, A.289, R.291, S.420, P.422 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: R.36, K.103, P.192, V.193, A.194, V.281, D.282 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: D.539, R.540 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: T.14, K.15, W.16, D.564, R.565, K.566 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: N.37, D.38, W.39 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: W.39, K.40, N.41 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: I.57, W.119, D.122, R.150 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: Q.104, T.140, P.141 Chain C: T.223 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: L.267, T.269, Y.287, Q.368 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: P.32, R.361, T.364, Y.365, Q.368 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: S.264, P.265, F.266 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain B: T.295, R.297, V.303 Ligands: EDO.36 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: T.295, R.296, R.297 Ligands: EDO.35 Ligand excluded by PLIP EDO.37: 1 residues within 4Å: Chain B: K.258 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain B: S.261, L.307, E.310 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain C: Y.48, G.63, Q.64, G.77 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain C: I.203, P.205, A.288, A.289, R.291, S.420, P.422 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain C: K.438, T.439, V.440, E.441 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain C: P.27, W.39, K.40, N.41 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain C: W.119, D.122, V.152 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain C: P.134, E.358, A.360, C.417, L.418, Y.421 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain C: D.539, R.540 Ligand excluded by PLIP

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: D.225, V.227, S.243, I.244, G.246 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: Q.387, N.388, R.389, K.390 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: P.97, S.98, A.99 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: W.100, G.102, K.103 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: V.227, S.243, I.244, G.246 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain B: W.100, R.101, G.102, K.103 Ligand excluded by PLIP CL.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain C: I.244, G.246 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain C: K.215, E.217, L.218, N.221 Ligand excluded by PLIP

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 12 residues within 4Å: Chain A: K.168, I.176, Y.178, L.318, Q.320, H.354, W.434, Y.475, E.493, Y.514, T.548, E.556 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.168, A:Y.178, A:Q.320, A:H.354, A:E.493, A:N.558 TRS.26: 13 residues within 4Å: Chain B: K.168, I.176, Y.178, L.318, Q.320, H.354, W.434, Y.475, E.493, Y.514, T.548, E.556, N.558 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.168, B:Y.178, B:Q.320, B:H.354, B:Y.514, B:N.558 TRS.47: 13 residues within 4Å: Chain C: K.168, I.176, Y.178, L.318, Q.320, H.354, N.431, W.434, Y.475, E.493, Y.514, T.548, E.556 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:K.168, C:Y.178, C:Y.178, C:Q.320, C:H.354, C:N.431, C:Y.475, C:Y.514

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.38: 2 residues within 4Å: Chain B: S.222, T.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.223, B:T.223

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.40: 3 residues within 4Å: Chain B: P.97, S.98, A.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.98, B:A.99 PO4.52: 3 residues within 4Å: Chain C: P.97, S.98, A.99 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.98, C:S.98, C:A.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Beta-Galactosidase from Bacteroides cellulosilyticus. To Be Published

Release Date

2021-11-03

Peptides

Glycosyl hydrolase family 2, sugar binding domain protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Glycosyl hydrolase family 2, sugar binding domain protein

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