- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x 149: D-galactonolactone(Non-covalent)
- 7 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 4 residues within 4Å:- Chain A: N.102, E.416, H.418, E.461
6 PLIP interactions:3 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:E.416, A:H.418, A:E.461, H2O.1, H2O.3, H2O.22
MG.3: 5 residues within 4Å:- Chain A: D.15, N.18, V.21, Q.163, D.193
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.15, A:N.18, A:V.21, A:D.193, A:D.193
MG.33: 3 residues within 4Å:- Chain B: E.416, H.418, E.461
6 PLIP interactions:3 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:E.416, B:H.418, B:E.461, H2O.26, H2O.28, H2O.31
MG.34: 6 residues within 4Å:- Chain B: D.15, W.16, N.18, V.21, Q.163, D.193
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193
MG.35: 1 residues within 4Å:- Chain B: E.369
No protein-ligand interaction detected (PLIP)MG.67: 3 residues within 4Å:- Chain C: E.416, H.418, E.461
6 PLIP interactions:3 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:E.416, C:H.418, C:E.461, H2O.52, H2O.54, H2O.57
MG.68: 6 residues within 4Å:- Chain C: D.15, N.18, V.21, Y.161, Q.163, D.193
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193, C:D.193
- 12 x NA: SODIUM ION(Non-functional Binders)
NA.4: 5 residues within 4Å:- Chain A: Y.100, D.201, F.601, N.604
- Ligands: 149.1
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.201, A:N.604
NA.5: 4 residues within 4Å:- Chain A: F.556, Y.559, P.560, L.562
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:P.560, A:L.562
NA.6: 5 residues within 4Å:- Chain A: F.931, P.932, L.967, M.968, T.970
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.970
NA.7: 5 residues within 4Å:- Chain A: S.647, D.648, N.649, E.650, L.670
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.647, A:E.650
NA.36: 5 residues within 4Å:- Chain B: Y.100, D.201, F.601, N.604
- Ligands: 149.32
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.201, B:N.604
NA.37: 4 residues within 4Å:- Chain B: F.556, Y.559, P.560, L.562
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:F.556, B:L.562
NA.38: 5 residues within 4Å:- Chain B: F.931, P.932, L.967, M.968, T.970
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:T.970
NA.39: 6 residues within 4Å:- Chain B: S.647, D.648, N.649, E.650, L.670
- Ligands: DMS.55
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.647, B:E.650
NA.69: 4 residues within 4Å:- Chain C: D.201, F.601, N.604
- Ligands: 149.66
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:W.568, C:N.604
NA.70: 4 residues within 4Å:- Chain C: F.556, Y.559, P.560, L.562
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:P.560, C:L.562
NA.71: 5 residues within 4Å:- Chain C: F.931, P.932, L.967, M.968, T.970
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:M.968
NA.72: 5 residues within 4Å:- Chain C: S.647, D.648, N.649, E.650, L.670
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:E.650, C:E.650
- 69 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.8: 9 residues within 4Å:- Chain A: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482
Ligand excluded by PLIPDMS.9: 6 residues within 4Å:- Chain A: R.557, H.622, Q.623, Q.625, Q.628, Q.718
Ligand excluded by PLIPDMS.10: 6 residues within 4Å:- Chain A: K.380, N.383, F.384, F.626, Y.642, W.708
Ligand excluded by PLIPDMS.11: 8 residues within 4Å:- Chain A: P.32, F.33, A.34, W.36, D.45, R.310, A.327
- Ligands: DMS.22
Ligand excluded by PLIPDMS.12: 4 residues within 4Å:- Chain A: G.270, T.271, R.292, L.293
Ligand excluded by PLIPDMS.13: 6 residues within 4Å:- Chain A: R.505, E.508, P.1001, S.1002, V.1003, Q.1008
Ligand excluded by PLIPDMS.14: 4 residues within 4Å:- Chain A: L.54, N.55, L.125, F.127
Ligand excluded by PLIPDMS.15: 4 residues within 4Å:- Chain A: E.334, V.335, R.336, P.480
Ligand excluded by PLIPDMS.16: 5 residues within 4Å:- Chain A: I.99, P.106, I.107, P.115, W.191
Ligand excluded by PLIPDMS.17: 5 residues within 4Å:- Chain A: I.576, P.584, W.585, S.586, R.973
Ligand excluded by PLIPDMS.18: 5 residues within 4Å:- Chain A: G.275, G.276, E.277, V.289, T.290
Ligand excluded by PLIPDMS.19: 3 residues within 4Å:- Chain A: G.593, D.594, T.595
Ligand excluded by PLIPDMS.20: 4 residues within 4Å:- Chain A: K.621, R.699, I.714, W.717
Ligand excluded by PLIPDMS.21: 3 residues within 4Å:- Chain A: H.93, G.94, Y.95
Ligand excluded by PLIPDMS.22: 5 residues within 4Å:- Chain A: A.34, W.36, D.45, R.46
- Ligands: DMS.11
Ligand excluded by PLIPDMS.23: 5 residues within 4Å:- Chain A: E.57, W.58, R.59, L.125, T.126
Ligand excluded by PLIPDMS.24: 4 residues within 4Å:- Chain A: Q.266, V.267, A.268, S.269
Ligand excluded by PLIPDMS.25: 5 residues within 4Å:- Chain A: N.102, H.418, F.601, W.999
- Ligands: 149.1
Ligand excluded by PLIPDMS.26: 5 residues within 4Å:- Chain A: T.257, E.314, H.316, G.320, L.322
Ligand excluded by PLIPDMS.27: 3 residues within 4Å:- Chain A: I.107, T.108, P.596
Ligand excluded by PLIPDMS.28: 7 residues within 4Å:- Chain A: F.60, A.61, W.62, E.80, A.81, D.82, Y.95
Ligand excluded by PLIPDMS.29: 5 residues within 4Å:- Chain A: R.37, S.132, W.133, E.136, H.216
Ligand excluded by PLIPDMS.30: 5 residues within 4Å:- Chain A: R.282, G.283, G.284, A.286
- Chain C: V.421
Ligand excluded by PLIPDMS.31: 7 residues within 4Å:- Chain A: H.226, Q.445, R.448, W.474, V.478
- Chain C: D.428, P.430
Ligand excluded by PLIPDMS.40: 8 residues within 4Å:- Chain B: V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482
Ligand excluded by PLIPDMS.41: 6 residues within 4Å:- Chain B: R.557, H.622, Q.623, Q.625, Q.628, Q.718
Ligand excluded by PLIPDMS.42: 6 residues within 4Å:- Chain B: K.380, N.383, F.384, F.626, Y.642, W.708
Ligand excluded by PLIPDMS.43: 9 residues within 4Å:- Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327
- Ligands: DMS.56, DMS.59
Ligand excluded by PLIPDMS.44: 5 residues within 4Å:- Chain B: G.270, T.271, L.291, R.292, L.293
Ligand excluded by PLIPDMS.45: 6 residues within 4Å:- Chain B: T.257, E.314, H.316, G.320, T.321, L.322
Ligand excluded by PLIPDMS.46: 5 residues within 4Å:- Chain B: R.505, E.508, P.1001, S.1002, V.1003
Ligand excluded by PLIPDMS.47: 5 residues within 4Å:- Chain B: S.53, L.54, N.55, E.57, L.125
Ligand excluded by PLIPDMS.48: 4 residues within 4Å:- Chain B: E.334, V.335, R.336, P.480
Ligand excluded by PLIPDMS.49: 3 residues within 4Å:- Chain B: I.99, P.106, I.107
Ligand excluded by PLIPDMS.50: 4 residues within 4Å:- Chain B: P.584, W.585, S.586, R.973
Ligand excluded by PLIPDMS.51: 5 residues within 4Å:- Chain B: G.275, E.277, V.289, T.290, R.292
Ligand excluded by PLIPDMS.52: 3 residues within 4Å:- Chain B: G.593, D.594, T.595
Ligand excluded by PLIPDMS.53: 2 residues within 4Å:- Chain B: D.428, P.430
Ligand excluded by PLIPDMS.54: 3 residues within 4Å:- Chain B: H.93, G.94, Y.95
Ligand excluded by PLIPDMS.55: 5 residues within 4Å:- Chain B: D.648, N.649, E.650, P.703
- Ligands: NA.39
Ligand excluded by PLIPDMS.56: 6 residues within 4Å:- Chain B: W.36, D.45, R.46, P.47, S.48
- Ligands: DMS.43
Ligand excluded by PLIPDMS.57: 6 residues within 4Å:- Chain B: E.57, W.58, R.59, S.124, L.125, T.126
Ligand excluded by PLIPDMS.58: 6 residues within 4Å:- Chain B: N.102, V.103, H.418, S.796, W.999
- Ligands: 149.32
Ligand excluded by PLIPDMS.59: 4 residues within 4Å:- Chain B: P.396, L.397, T.400
- Ligands: DMS.43
Ligand excluded by PLIPDMS.60: 2 residues within 4Å:- Chain B: S.53, N.55
Ligand excluded by PLIPDMS.61: 2 residues within 4Å:- Chain B: S.923, Y.962
Ligand excluded by PLIPDMS.62: 3 residues within 4Å:- Chain B: I.305, P.306, N.307
Ligand excluded by PLIPDMS.63: 6 residues within 4Å:- Chain B: F.60, A.61, W.62, E.80, A.81, D.82
Ligand excluded by PLIPDMS.64: 2 residues within 4Å:- Chain B: E.41, P.47
Ligand excluded by PLIPDMS.65: 6 residues within 4Å:- Chain B: L.377, T.706, A.707, W.708, S.709, E.710
Ligand excluded by PLIPDMS.73: 6 residues within 4Å:- Chain A: D.428, P.430, A.466
- Chain C: Q.445, W.474, V.478
Ligand excluded by PLIPDMS.74: 9 residues within 4Å:- Chain C: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482
Ligand excluded by PLIPDMS.75: 6 residues within 4Å:- Chain C: R.557, H.622, Q.623, Q.625, Q.628, Q.718
Ligand excluded by PLIPDMS.76: 6 residues within 4Å:- Chain C: K.380, N.383, F.384, F.626, Y.642, W.708
Ligand excluded by PLIPDMS.77: 8 residues within 4Å:- Chain C: P.32, F.33, A.34, W.36, D.45, R.310, A.327
- Ligands: DMS.88
Ligand excluded by PLIPDMS.78: 4 residues within 4Å:- Chain C: G.270, T.271, R.292, L.293
Ligand excluded by PLIPDMS.79: 4 residues within 4Å:- Chain C: R.505, E.508, P.1001, V.1003
Ligand excluded by PLIPDMS.80: 5 residues within 4Å:- Chain C: S.53, L.54, N.55, G.56, L.125
Ligand excluded by PLIPDMS.81: 4 residues within 4Å:- Chain C: E.334, V.335, R.336, P.480
Ligand excluded by PLIPDMS.82: 3 residues within 4Å:- Chain C: P.106, P.115, E.117
Ligand excluded by PLIPDMS.83: 5 residues within 4Å:- Chain C: I.576, P.584, W.585, S.586, R.973
Ligand excluded by PLIPDMS.84: 5 residues within 4Å:- Chain C: G.275, G.276, E.277, V.289, T.290
Ligand excluded by PLIPDMS.85: 3 residues within 4Å:- Chain C: V.84, V.85, H.93
Ligand excluded by PLIPDMS.86: 4 residues within 4Å:- Chain C: K.621, R.699, I.714, W.717
Ligand excluded by PLIPDMS.87: 4 residues within 4Å:- Chain C: F.231, N.232, D.233, E.334
Ligand excluded by PLIPDMS.88: 5 residues within 4Å:- Chain C: D.45, R.46, P.47, L.51
- Ligands: DMS.77
Ligand excluded by PLIPDMS.89: 5 residues within 4Å:- Chain C: H.418, E.461, S.796, W.999
- Ligands: 149.66
Ligand excluded by PLIPDMS.90: 4 residues within 4Å:- Chain C: Y.472, T.494, T.496, D.497
Ligand excluded by PLIPDMS.91: 3 residues within 4Å:- Chain C: L.341, G.346, P.348
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kappelhoff, J.C. et al., Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-beta-Galactosidase (E. coli) as Examples. Protein J. (2009)
- Release Date
- 2009-04-07
- Peptides
- Beta-galactosidase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x 149: D-galactonolactone(Non-covalent)
- 7 x MG: MAGNESIUM ION(Non-covalent)
- 12 x NA: SODIUM ION(Non-functional Binders)
- 69 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kappelhoff, J.C. et al., Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-beta-Galactosidase (E. coli) as Examples. Protein J. (2009)
- Release Date
- 2009-04-07
- Peptides
- Beta-galactosidase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
D