SMTL ID : 1kwk.1

Crystal structure of Thermus thermophilus A4 beta-galactosidase in complex with galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

3 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.1: 12 residues within 4Å: Chain A: F.36, R.102, N.140, E.141, N.241, D.264, Y.266, E.312, W.320, F.350, E.360, H.363 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.102, A:R.102, A:N.140, A:E.141, A:N.241, A:D.264, A:Y.266, A:W.320, A:E.360 Water bridges: A:Y.7, A:R.32 Salt bridges: A:R.102 GAL.8: 12 residues within 4Å: Chain B: F.36, R.102, N.140, E.141, N.241, D.264, Y.266, E.312, W.320, F.350, E.360, H.363 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.102, B:R.102, B:N.140, B:E.141, B:N.241, B:D.264, B:Y.266, B:W.320, B:E.360 Water bridges: B:Y.7, B:R.32 Salt bridges: B:R.102 GAL.15: 12 residues within 4Å: Chain C: F.36, R.102, N.140, E.141, N.241, D.264, Y.266, E.312, W.320, F.350, E.360, H.363 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:R.102, C:R.102, C:N.140, C:E.141, C:N.241, C:D.264, C:Y.266, C:W.320, C:E.360 Water bridges: C:Y.7, C:R.32 Salt bridges: C:R.102

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

CL.2: 6 residues within 4Å: Chain A: Y.6, Y.7, W.11, R.351, W.352, R.353 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: Y.6, Y.7, W.11, R.351, W.352, R.353 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain C: Y.6, Y.7, W.11, R.351, W.352, R.353 Ligand excluded by PLIP

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: L.522, G.535, S.572 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.535 Water bridges: A:P.571 ACT.4: 3 residues within 4Å: Chain A: L.548, R.560, A.582 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.548 Salt bridges: A:R.560 ACT.10: 3 residues within 4Å: Chain B: L.522, G.535, S.572 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.535 Water bridges: B:P.571 ACT.11: 3 residues within 4Å: Chain B: L.548, R.560, A.582 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.548 Salt bridges: B:R.560 ACT.17: 3 residues within 4Å: Chain C: L.522, G.535, S.572 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.535 Water bridges: C:P.571 ACT.18: 3 residues within 4Å: Chain C: L.548, R.560, A.582 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.548 Salt bridges: C:R.560

3 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: C.106, C.150, C.152 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.106, A:C.150, A:C.152 ZN.12: 3 residues within 4Å: Chain B: C.106, C.150, C.152 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.106, B:C.150, B:C.152 ZN.19: 3 residues within 4Å: Chain C: C.106, C.150, C.152 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.106, C:C.150, C:C.152

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 5 residues within 4Å: Chain A: F.245, P.275, L.424, G.425, Y.428 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.245, A:L.424, A:Y.428 MPD.7: 4 residues within 4Å: Chain A: A.433, R.436, P.573, E.574 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.433, A:P.573 MPD.13: 5 residues within 4Å: Chain B: F.245, P.275, L.424, G.425, Y.428 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.245, B:L.424, B:Y.428 MPD.14: 4 residues within 4Å: Chain B: A.433, R.436, P.573, E.574 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.433, B:P.573 MPD.20: 5 residues within 4Å: Chain C: F.245, P.275, L.424, G.425, Y.428 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.245, C:L.424, C:Y.428 MPD.21: 4 residues within 4Å: Chain C: A.433, R.436, P.573, E.574 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.433, C:P.573

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hidaka, M. et al., Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. J.Mol.Biol. (2002)

Release Date

2002-10-02

Peptides

BETA-GALACTOSIDASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

BETA-GALACTOSIDASE

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