SMTL ID : 3t2o.1

E. coli (lacZ) beta-galactosidase (S796D)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.445, A:H.447, A:E.490, H2O.1, H2O.35, H2O.39 MG.2: 7 residues within 4Å: Chain A: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.44, A:N.47, A:V.50, A:D.222 MG.3: 1 residues within 4Å: Chain A: Q.747 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: DMS.15 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain B: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.445, B:H.447, B:E.490, H2O.48, H2O.92, H2O.93 MG.37: 7 residues within 4Å: Chain B: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.44, B:N.47, B:V.50, B:D.222 MG.38: 1 residues within 4Å: Chain B: Q.747 No protein-ligand interaction detected (PLIP) MG.71: 3 residues within 4Å: Chain C: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.445, C:H.447, C:E.490, H2O.95, H2O.131, H2O.137 MG.72: 7 residues within 4Å: Chain C: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.44, C:N.47, C:V.50, C:D.222 MG.73: 1 residues within 4Å: Chain C: Q.747 No protein-ligand interaction detected (PLIP) MG.74: 1 residues within 4Å: Chain C: Q.78 No protein-ligand interaction detected (PLIP) MG.75: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.111: 3 residues within 4Å: Chain D: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.445, D:H.447, D:E.490, H2O.140, H2O.173, H2O.182 MG.112: 7 residues within 4Å: Chain D: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.44, D:N.47, D:V.50, D:D.222 MG.113: 1 residues within 4Å: Chain D: Q.747 No protein-ligand interaction detected (PLIP)

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

NA.6: 4 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.7: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: S.676, E.679, L.699 Ligands: DMS.28 Ligand excluded by PLIP NA.39: 4 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.40: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.41: 5 residues within 4Å: Chain B: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.42: 5 residues within 4Å: Chain B: S.676, D.677, E.679, L.699 Ligands: DMS.61 Ligand excluded by PLIP NA.76: 4 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.77: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.78: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.79: 4 residues within 4Å: Chain C: S.676, E.679, L.699 Ligands: DMS.99 Ligand excluded by PLIP NA.114: 4 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.115: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.116: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.117: 5 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP

112 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 9 residues within 4Å: Chain A: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.13: 8 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.30 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: E.343, H.345, G.349, L.351 Ligands: MG.4 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: R.534, E.537, P.1030, S.1031, V.1032 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: P.135, P.144 Ligands: DMS.22, DMS.24 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.21: 6 residues within 4Å: Chain A: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain A: G.622, D.623, T.624 Ligands: DMS.19 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain A: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.24: 6 residues within 4Å: Chain A: Y.134, P.135, I.136, T.137, P.625 Ligands: DMS.19 Ligand excluded by PLIP DMS.25: 5 residues within 4Å: Chain A: D.457, P.459 Chain D: H.255, R.477, V.507 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain A: D.111, H.122, G.123, Y.124 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain A: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.28: 6 residues within 4Å: Chain A: S.676, D.677, N.678, E.679, N.733 Ligands: NA.9 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain A: W.724, Q.748, W.749, R.750 Ligand excluded by PLIP DMS.30: 7 residues within 4Å: Chain A: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.13 Ligand excluded by PLIP DMS.31: 5 residues within 4Å: Chain A: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain A: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.33: 6 residues within 4Å: Chain A: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.34: 3 residues within 4Å: Chain A: Q.295, V.296, A.297 Ligand excluded by PLIP DMS.35: 3 residues within 4Å: Chain A: I.334, P.335, N.336 Ligand excluded by PLIP DMS.43: 8 residues within 4Å: Chain B: T.258, V.359, G.360, R.362, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.44: 6 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.45: 5 residues within 4Å: Chain B: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.46: 7 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.49: 6 residues within 4Å: Chain B: L.83, N.84, G.85, E.86, L.154, F.156 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.52: 6 residues within 4Å: Chain B: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.53: 4 residues within 4Å: Chain B: I.128, P.135, P.144, W.220 Ligand excluded by PLIP DMS.54: 3 residues within 4Å: Chain B: V.113, V.114, H.122 Ligand excluded by PLIP DMS.55: 3 residues within 4Å: Chain B: K.650, I.743, W.746 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: L.279, R.280, D.281 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain B: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain B: D.457, P.459 Chain C: Q.474, W.503 Ligand excluded by PLIP DMS.59: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain B: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.61: 6 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, N.733 Ligands: NA.42 Ligand excluded by PLIP DMS.62: 4 residues within 4Å: Chain B: W.724, Q.748, W.749, R.750 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain B: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.64: 5 residues within 4Å: Chain B: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain B: N.131, D.627, F.630, V.824 Ligand excluded by PLIP DMS.66: 4 residues within 4Å: Chain B: S.952, Y.955, R.990, Y.991 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain B: V.296, N.323, V.324, E.325 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain B: F.658, R.659, L.660, Q.747, W.749 Ligand excluded by PLIP DMS.69: 6 residues within 4Å: Chain B: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.70: 6 residues within 4Å: Chain B: L.406, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.80: 9 residues within 4Å: Chain C: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.81: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.82: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.83: 7 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligand excluded by PLIP DMS.84: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.85: 4 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.86: 5 residues within 4Å: Chain C: L.83, N.84, G.85, E.86, L.154 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain C: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.88: 4 residues within 4Å: Chain C: P.135, P.144, W.220 Ligands: DMS.95 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.90: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.91: 3 residues within 4Å: Chain C: V.113, V.114, H.122 Ligand excluded by PLIP DMS.92: 3 residues within 4Å: Chain C: K.650, I.743, W.746 Ligand excluded by PLIP DMS.93: 3 residues within 4Å: Chain C: L.279, R.280, D.281 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain C: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.95: 6 residues within 4Å: Chain C: Y.134, P.135, I.136, T.137, P.625 Ligands: DMS.88 Ligand excluded by PLIP DMS.96: 4 residues within 4Å: Chain B: W.503, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.98: 3 residues within 4Å: Chain C: Y.955, Y.991, R.1002 Ligand excluded by PLIP DMS.99: 7 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, P.732, N.733 Ligands: NA.79 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain C: W.724, Q.748, W.749, R.750 Ligand excluded by PLIP DMS.101: 6 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligand excluded by PLIP DMS.102: 4 residues within 4Å: Chain C: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.103: 5 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.104: 4 residues within 4Å: Chain C: N.131, D.627, F.630, V.824 Ligand excluded by PLIP DMS.105: 4 residues within 4Å: Chain C: V.296, N.323, V.324, E.325 Ligand excluded by PLIP DMS.106: 3 residues within 4Å: Chain C: Q.295, V.296, A.297 Ligand excluded by PLIP DMS.107: 5 residues within 4Å: Chain C: Y.501, T.523, T.525, D.526, R.560 Ligand excluded by PLIP DMS.108: 5 residues within 4Å: Chain C: L.406, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.109: 6 residues within 4Å: Chain C: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.110: 2 residues within 4Å: Chain C: P.335, N.336 Ligand excluded by PLIP DMS.118: 9 residues within 4Å: Chain D: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.120: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.121: 6 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, A.356 Ligands: DMS.137 Ligand excluded by PLIP DMS.122: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.123: 6 residues within 4Å: Chain D: E.343, H.345, T.346, G.349, T.350 Ligands: DMS.140 Ligand excluded by PLIP DMS.124: 5 residues within 4Å: Chain D: L.83, N.84, G.85, E.86, L.154 Ligand excluded by PLIP DMS.125: 5 residues within 4Å: Chain D: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.126: 5 residues within 4Å: Chain D: I.128, P.135, P.144, W.220 Ligands: DMS.133 Ligand excluded by PLIP DMS.127: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.128: 6 residues within 4Å: Chain D: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.129: 3 residues within 4Å: Chain D: G.622, D.623, T.624 Ligand excluded by PLIP DMS.130: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.131: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.132: 6 residues within 4Å: Chain D: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.133: 6 residues within 4Å: Chain D: Y.134, P.135, I.136, T.137, P.625 Ligands: DMS.126 Ligand excluded by PLIP DMS.134: 3 residues within 4Å: Chain D: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.135: 3 residues within 4Å: Chain D: Y.955, Y.991, R.1002 Ligand excluded by PLIP DMS.136: 4 residues within 4Å: Chain D: W.724, Q.748, W.749, R.750 Ligand excluded by PLIP DMS.137: 7 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.121 Ligand excluded by PLIP DMS.138: 4 residues within 4Å: Chain D: N.131, D.627, F.630, V.824 Ligand excluded by PLIP DMS.139: 4 residues within 4Å: Chain D: S.952, Y.955, R.990, Y.991 Ligand excluded by PLIP DMS.140: 3 residues within 4Å: Chain D: G.349, L.351 Ligands: DMS.123 Ligand excluded by PLIP DMS.141: 5 residues within 4Å: Chain D: Q.78, Q.79, D.159, S.161, W.162 Ligand excluded by PLIP DMS.142: 6 residues within 4Å: Chain D: W.162, L.163, Q.164, E.165, G.166, S.203 Ligand excluded by PLIP DMS.143: 6 residues within 4Å: Chain D: L.406, Q.410, T.735, A.736, W.737, S.738 Ligand excluded by PLIP DMS.144: 2 residues within 4Å: Chain D: R.433, Y.434 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jancewicz, L.J. et al., Ser-796 of Beta-Galactosidase (E. coli) Plays a Key Role in Maintaining an Optimum Balance between the Opened and Closed Conformations of the Catalytically Important Active Site Loop. Arch.Biochem.Biophys. (2012)

Release Date

2012-01-18

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-galactosidase

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