SMTL ID : 3mv1.1

E.Coli (lacZ) beta-galactosidase (R599A) in complex with Guanidinium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

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.3, H2O.6 MG.2: 5 residues within 4Å: Chain A: D.44, N.47, V.50, 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: 2 residues within 4Å: Chain A: Q.747, T.940 No protein-ligand interaction detected (PLIP) MG.34: 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.34, H2O.36, H2O.39 MG.35: 5 residues within 4Å: Chain B: D.44, N.47, V.50, Q.192, D.222 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.44, B:N.47, B:V.50, B:D.222, B:D.222 MG.36: 3 residues within 4Å: Chain B: H.651, Q.747, T.940 No protein-ligand interaction detected (PLIP) MG.72: 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.72, H2O.74, H2O.77 MG.73: 6 residues within 4Å: Chain C: D.44, 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.74: 2 residues within 4Å: Chain C: Q.747, T.940 No protein-ligand interaction detected (PLIP) MG.108: 4 residues within 4Å: Chain D: N.131, 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.109, H2O.112, H2O.115 MG.109: 5 residues within 4Å: Chain D: D.44, N.47, V.50, 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.110: 2 residues within 4Å: Chain D: Q.747, T.940 No protein-ligand interaction detected (PLIP)

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

NA.4: 4 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.5: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.6: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.37: 4 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.38: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.39: 5 residues within 4Å: Chain B: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.40: 6 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, L.699 Ligands: DMS.58 Ligand excluded by PLIP NA.75: 4 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.76: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.77: 4 residues within 4Å: Chain C: F.960, P.961, L.996, T.999 Ligand excluded by PLIP NA.78: 5 residues within 4Å: Chain C: S.676, N.678, E.679, L.699 Ligands: DMS.96 Ligand excluded by PLIP NA.111: 4 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.112: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.113: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.114: 5 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP

4 x GAI: GUANIDINE(Non-covalent)

GAI.8: 5 residues within 4Å: Chain A: N.626, D.627, F.630, V.824, E.826 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.626, A:V.824 Salt bridges: A:D.627, A:E.826 GAI.41: 4 residues within 4Å: Chain B: D.627, F.630, V.824, E.826 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.627, B:E.826 GAI.79: 5 residues within 4Å: Chain C: D.627, F.630, V.824, S.825, E.826 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.627, C:D.627, C:V.824, C:V.824 Salt bridges: C:E.826 GAI.115: 5 residues within 4Å: Chain D: D.627, F.630, V.824, E.826 Ligands: DMS.141 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.626 Salt bridges: D:D.627, D:E.826

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

DMS.9: 8 residues within 4Å: Chain A: T.258, V.359, G.360, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.12: 8 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.22 Ligand excluded by PLIP DMS.13: 3 residues within 4Å: Chain A: T.300, L.320, R.321 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: R.534, E.537, P.1030, S.1031, V.1032 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: Y.134, P.135, I.136, T.137, P.625 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.22: 7 residues within 4Å: Chain A: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.12 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain A: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain A: R.66, Q.79, W.162, H.245 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain A: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain A: Y.501, T.523, T.525, D.526 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain A: R.659, S.661, T.664, E.666 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain A: I.766, H.768, E.779, L.780, G.781 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain A: T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.31: 3 residues within 4Å: Chain A: N.131, H.447, W.1028 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain A: L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain A: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.42: 8 residues within 4Å: Chain B: T.258, V.359, G.360, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.43: 5 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.45: 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.46: 3 residues within 4Å: Chain B: T.300, L.320, R.321 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: T.286, E.343, H.345, G.349 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain B: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.49: 3 residues within 4Å: Chain B: I.128, P.135, W.220 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain B: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.53: 3 residues within 4Å: Chain B: L.279, R.280, D.281 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: F.260, N.261, D.262, E.363, R.365 Ligand excluded by PLIP DMS.55: 3 residues within 4Å: Chain B: D.457, P.459 Chain C: V.507 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.57: 3 residues within 4Å: Chain B: Y.955, Y.991, R.1002 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain B: D.677, N.678, E.679 Ligands: NA.40 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain B: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain B: S.952, R.990, Y.991, A.1007 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain B: V.296, N.323, V.324, E.325 Ligand excluded by PLIP DMS.62: 4 residues within 4Å: Chain B: E.398, L.426, L.430, R.433 Ligand excluded by PLIP DMS.63: 2 residues within 4Å: Chain B: R.433, Y.434 Ligand excluded by PLIP DMS.64: 3 residues within 4Å: Chain B: I.334, P.335, N.336 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain B: L.406, T.735, W.737, S.738, E.739 Ligand excluded by PLIP DMS.66: 4 residues within 4Å: Chain B: R.659, S.661, T.664, E.666 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain B: Y.134, P.135, I.136, T.137 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain B: A.63, W.65, D.74, R.75, S.77 Ligand excluded by PLIP DMS.69: 3 residues within 4Å: Chain B: N.131, H.447, W.1028 Ligand excluded by PLIP DMS.70: 2 residues within 4Å: Chain B: E.70, Q.78 Ligand excluded by PLIP DMS.71: 6 residues within 4Å: Chain B: L.83, N.84, G.85, E.86, L.154, F.156 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: 5 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657 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: 8 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.97 Ligand excluded by PLIP DMS.84: 3 residues within 4Å: Chain C: T.300, 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: 4 residues within 4Å: Chain C: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.87: 3 residues within 4Å: Chain C: I.128, P.135, W.220 Ligand excluded by PLIP DMS.88: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.90: 3 residues within 4Å: Chain C: V.113, V.114, H.122 Ligand excluded by PLIP DMS.91: 4 residues within 4Å: Chain C: K.650, I.743, W.746 Ligands: DMS.105 Ligand excluded by PLIP DMS.92: 3 residues within 4Å: Chain C: L.279, R.280, D.281 Ligand excluded by PLIP DMS.93: 4 residues within 4Å: Chain B: Q.474, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.94: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.95: 4 residues within 4Å: Chain C: Y.955, Y.991, R.1002, H.1003 Ligand excluded by PLIP DMS.96: 6 residues within 4Å: Chain C: D.677, N.678, E.679, P.732, N.733 Ligands: NA.78 Ligand excluded by PLIP DMS.97: 7 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.83 Ligand excluded by PLIP DMS.98: 3 residues within 4Å: Chain C: Q.295, V.296, A.297 Ligand excluded by PLIP DMS.99: 4 residues within 4Å: Chain C: Y.134, P.135, I.136, T.137 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain C: R.659, S.661, T.664, E.666 Ligand excluded by PLIP DMS.101: 5 residues within 4Å: Chain C: T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.102: 3 residues within 4Å: Chain C: R.433, Y.434, A.736 Ligand excluded by PLIP DMS.103: 3 residues within 4Å: Chain C: E.343, H.345, G.349 Ligand excluded by PLIP DMS.104: 6 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.105: 3 residues within 4Å: Chain C: I.743, W.746 Ligands: DMS.91 Ligand excluded by PLIP DMS.106: 3 residues within 4Å: Chain C: N.131, H.447, E.490 Ligand excluded by PLIP DMS.107: 5 residues within 4Å: Chain C: L.83, N.84, G.85, E.86, L.154 Ligand excluded by PLIP DMS.116: 7 residues within 4Å: Chain D: T.258, V.359, G.360, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.117: 6 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.118: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.119: 7 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.131 Ligand excluded by PLIP DMS.120: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.121: 4 residues within 4Å: Chain D: T.286, E.343, H.345, G.349 Ligand excluded by PLIP DMS.122: 5 residues within 4Å: Chain D: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.123: 4 residues within 4Å: Chain D: P.135, P.144, E.146, W.220 Ligand excluded by PLIP DMS.124: 4 residues within 4Å: Chain D: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.125: 5 residues within 4Å: Chain D: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.126: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.127: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.128: 4 residues within 4Å: Chain D: Y.134, P.135, I.136, T.137 Ligand excluded by PLIP DMS.129: 3 residues within 4Å: Chain D: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.130: 4 residues within 4Å: Chain D: Y.955, Y.991, R.1002, L.1005 Ligand excluded by PLIP DMS.131: 6 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76 Ligands: DMS.119 Ligand excluded by PLIP DMS.132: 3 residues within 4Å: Chain D: F.658, Q.747, W.749 Ligand excluded by PLIP DMS.133: 4 residues within 4Å: Chain D: S.952, Y.955, R.990, Y.991 Ligand excluded by PLIP DMS.134: 5 residues within 4Å: Chain D: L.163, Q.164, E.165, G.166, S.203 Ligand excluded by PLIP DMS.135: 6 residues within 4Å: Chain D: A.765, I.766, H.768, E.779, L.780, G.781 Ligand excluded by PLIP DMS.136: 2 residues within 4Å: Chain D: K.650, W.746 Ligand excluded by PLIP DMS.137: 4 residues within 4Å: Chain D: R.659, S.661, T.664, E.666 Ligand excluded by PLIP DMS.138: 5 residues within 4Å: Chain D: L.406, T.735, A.736, W.737, S.738 Ligand excluded by PLIP DMS.139: 3 residues within 4Å: Chain D: N.131, W.1028 Ligands: DMS.141 Ligand excluded by PLIP DMS.140: 4 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.141: 6 residues within 4Å: Chain D: N.131, D.627, F.630, V.824 Ligands: GAI.115, DMS.139 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dugdale, M.L. et al., Importance of Arg-599 of b-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop. Biochem.Cell Biol. (2010)

Release Date

2011-03-16

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

Beta-galactosidase

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