SMTL ID : 1yq2.1

beta-galactosidase from Arthrobacter sp. C2-2 (isoenzyme C2-2-1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: A.526, G.528, G.530 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.526, A:G.528, A:G.530, H2O.8, H2O.30 MG.8: 3 residues within 4Å: Chain B: A.526, G.528, G.530 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.526, B:G.528, B:G.530, H2O.53, H2O.72 MG.15: 3 residues within 4Å: Chain C: A.526, G.528, G.530 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.526, C:G.528, C:G.530, H2O.92, H2O.122 MG.21: 3 residues within 4Å: Chain D: A.526, G.528, G.530 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.526, D:G.528, D:G.530, H2O.150, H2O.165 MG.28: 3 residues within 4Å: Chain E: A.526, G.528, G.530 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:A.526, E:G.528, E:G.530, H2O.172, H2O.202 MG.35: 3 residues within 4Å: Chain F: A.526, G.528, G.530 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:A.526, F:G.528, F:G.530, H2O.212, H2O.221

12 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: Y.99, D.202, W.553, F.586, D.589 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.99 Water bridges: A:D.589 NA.3: 5 residues within 4Å: Chain A: T.100, N.101, D.200, Q.201, W.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.100, A:Q.201 Water bridges: A:Q.203 NA.9: 5 residues within 4Å: Chain B: Y.99, D.202, W.553, F.586, D.589 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.99, B:D.589 NA.10: 5 residues within 4Å: Chain B: T.100, N.101, D.200, Q.201, W.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.201 Water bridges: B:Q.203 NA.16: 5 residues within 4Å: Chain C: Y.99, D.202, W.553, F.586, D.589 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.99, C:F.586 NA.17: 5 residues within 4Å: Chain C: T.100, N.101, D.200, Q.201, W.205 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.100 Water bridges: C:Q.203 NA.22: 5 residues within 4Å: Chain D: Y.99, D.202, W.553, F.586, D.589 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.553 Water bridges: D:D.589 NA.23: 5 residues within 4Å: Chain D: T.100, N.101, D.200, Q.201, W.205 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.100, D:T.100 Water bridges: D:Q.203 NA.29: 5 residues within 4Å: Chain E: Y.99, D.202, W.553, F.586, D.589 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:W.553 NA.30: 5 residues within 4Å: Chain E: T.100, N.101, D.200, Q.201, W.205 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.100, E:T.100 Water bridges: E:Q.203 NA.36: 5 residues within 4Å: Chain F: Y.99, D.202, W.553, F.586, D.589 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.99, F:D.202 Water bridges: F:D.589 NA.37: 5 residues within 4Å: Chain F: T.100, N.101, D.200, Q.201, W.205 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.201 Water bridges: F:Q.203

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

CL.4: 3 residues within 4Å: Chain A: R.762, T.812, R.813 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: R.762, T.812, R.813 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: R.762, T.812, R.813 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: R.762, T.812, R.813 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain E: R.762, T.812, R.813 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain F: R.762, T.812, R.813 Ligand excluded by PLIP

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: R.229, T.230, R.315, S.462, S.463 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.230, A:S.462 Water bridges: A:R.229, A:R.312, A:R.312, A:S.463 Salt bridges: A:R.229, A:R.315 SO4.6: 10 residues within 4Å: Chain A: W.227, L.228, R.229, T.230, R.312, K.430, N.431, H.432, P.433, R.464 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.230 Water bridges: A:T.230, A:G.310, A:R.312, A:R.312, A:S.463 Salt bridges: A:R.312, A:R.464 SO4.12: 4 residues within 4Å: Chain B: R.229, R.315, S.462, S.463 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.312, B:S.463 Salt bridges: B:R.229, B:R.315 SO4.13: 10 residues within 4Å: Chain B: W.227, L.228, R.229, T.230, R.312, K.430, N.431, H.432, P.433, R.464 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:L.228, B:T.230 Water bridges: B:R.312, B:R.312, B:R.312, B:S.463 Salt bridges: B:R.312, B:R.464 SO4.19: 10 residues within 4Å: Chain C: W.227, L.228, R.229, T.230, R.312, K.430, N.431, H.432, P.433, R.464 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.230, C:T.230, C:K.430 Water bridges: C:T.230, C:T.230, C:R.312, C:R.312, C:S.463 Salt bridges: C:R.312, C:R.464 SO4.25: 4 residues within 4Å: Chain D: R.229, R.315, S.462, S.463 6 PLIP interactions: 6 interactions with chain D Water bridges: D:R.312, D:V.314, D:S.463, D:S.463 Salt bridges: D:R.229, D:R.315 SO4.26: 10 residues within 4Å: Chain D: W.227, L.228, R.229, T.230, R.312, K.430, N.431, H.432, P.433, R.464 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:L.228, D:T.230 Water bridges: D:T.230, D:T.230, D:R.312, D:R.312, D:R.312, D:S.463 Salt bridges: D:R.312, D:R.464 SO4.32: 5 residues within 4Å: Chain E: R.229, T.230, R.315, S.462, S.463 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:T.230, E:S.462 Water bridges: E:R.312, E:S.463 Salt bridges: E:R.229, E:R.315 SO4.33: 10 residues within 4Å: Chain E: W.227, L.228, R.229, T.230, R.312, K.430, N.431, H.432, P.433, R.464 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:T.230, E:T.230, E:K.430 Water bridges: E:R.312, E:S.463, E:S.463 Salt bridges: E:R.312, E:R.464 SO4.39: 4 residues within 4Å: Chain F: R.229, T.230, R.315, S.463 7 PLIP interactions: 7 interactions with chain F Water bridges: F:R.312, F:R.312, F:V.314, F:R.315, F:S.463 Salt bridges: F:R.229, F:R.315 SO4.40: 10 residues within 4Å: Chain F: L.228, R.229, T.230, G.310, R.312, K.430, N.431, H.432, P.433, R.464 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:T.230, F:N.431 Water bridges: F:T.230, F:T.230, F:R.312, F:R.312, F:S.463, F:R.464, F:R.464 Salt bridges: F:R.312, F:R.464

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

PEG.7: 12 residues within 4Å: Chain A: Q.203, W.204, L.206, H.336, T.338, H.339, P.340, G.343, R.344, H.558, G.559, I.560 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.204, A:H.336, A:H.339, A:R.344, A:H.558 PEG.14: 12 residues within 4Å: Chain B: Q.203, W.204, L.206, H.336, T.338, H.339, P.340, G.343, R.344, H.558, G.559, I.560 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.204, B:H.336, B:H.339, B:R.344, B:H.558 PEG.20: 12 residues within 4Å: Chain C: Q.203, W.204, L.206, H.336, T.338, H.339, P.340, G.343, R.344, H.558, G.559, I.560 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:W.204, C:H.336, C:T.338, C:H.339, C:R.344, C:G.559 Water bridges: C:G.559 PEG.27: 12 residues within 4Å: Chain D: Q.203, W.204, L.206, H.336, T.338, H.339, P.340, G.343, R.344, H.558, G.559, I.560 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:W.204, D:H.336, D:H.339, D:R.344, D:H.558 PEG.34: 12 residues within 4Å: Chain E: Q.203, W.204, L.206, H.336, T.338, H.339, P.340, G.343, R.344, H.558, G.559, I.560 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:W.204, E:H.336, E:H.339, E:R.344, E:H.558 PEG.41: 13 residues within 4Å: Chain F: Q.203, W.204, L.206, H.336, E.337, T.338, H.339, P.340, G.343, R.344, H.558, G.559, I.560 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:W.204, F:H.336, F:T.338, F:H.339, F:R.344, F:H.558

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skalova, T. et al., Cold-active beta-Galactosidase from Arthrobacter sp. C2-2 Forms Compact 660kDa Hexamers: Crystal Structure at 1.9A Resolution. J.Mol.Biol. (2005)

Release Date

2005-10-04

Peptides

beta-galactosidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

beta-galactosidase