SMTL ID : 1dp0.1

E. COLI BETA-GALACTOSIDASE AT 1.7 ANGSTROM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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.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.6 MG.2: 7 residues within 4Å: Chain A: D.15, W.16, N.18, V.21, Y.161, 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.3: 2 residues within 4Å: Chain A: Q.718 Ligands: DMS.32 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: DMS.15 No protein-ligand interaction detected (PLIP) MG.38: 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.45, H2O.48, H2O.51 MG.39: 5 residues within 4Å: Chain B: D.15, N.18, V.21, Q.163, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193, B:D.193 MG.40: 1 residues within 4Å: Chain B: Q.718 No protein-ligand interaction detected (PLIP) MG.73: 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.88, H2O.91, H2O.94 MG.74: 6 residues within 4Å: Chain C: D.15, N.18, V.21, Y.161, Q.163, D.193 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193 MG.75: 3 residues within 4Å: Chain C: H.622, Q.718, T.911 No protein-ligand interaction detected (PLIP) MG.76: 1 residues within 4Å: Chain C: Q.49 No protein-ligand interaction detected (PLIP) MG.77: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.111: 3 residues within 4Å: Chain D: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.416, D:H.418, D:E.461, H2O.130, H2O.132, H2O.135 MG.112: 5 residues within 4Å: Chain D: D.15, N.18, V.21, Q.163, D.193 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.15, D:N.18, D:V.21, D:D.193, D:D.193 MG.113: 2 residues within 4Å: Chain D: Q.718, T.911 No protein-ligand interaction detected (PLIP) MG.114: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.5: 4 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.6: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.8: 4 residues within 4Å: Chain A: S.647, E.650, L.670 Ligands: DMS.31 Ligand excluded by PLIP NA.9: 2 residues within 4Å: Chain A: N.597, E.797 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.42: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.43: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.44: 4 residues within 4Å: Chain B: S.647, E.650, L.670 Ligands: DMS.66 Ligand excluded by PLIP NA.45: 1 residues within 4Å: Chain B: N.597 Ligand excluded by PLIP NA.78: 4 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.79: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.80: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.81: 4 residues within 4Å: Chain C: S.647, E.650, L.670 Ligands: DMS.103 Ligand excluded by PLIP NA.82: 2 residues within 4Å: Chain C: N.597, E.797 Ligand excluded by PLIP NA.115: 4 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.116: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.117: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.118: 6 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.140 Ligand excluded by PLIP NA.119: 2 residues within 4Å: Chain D: N.597, E.797 Ligand excluded by PLIP

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

DMS.10: 9 residues within 4Å: Chain A: V.227, T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.13: 7 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, A.327 Ligands: DMS.33 Ligand excluded by PLIP DMS.14: 3 residues within 4Å: Chain A: T.271, L.291, R.292 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: E.314, H.316, G.320, L.322 Ligands: MG.4 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain A: E.334, V.335, P.480 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain A: P.106, P.115, W.191 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.21: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain A: G.593, D.594, T.595 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.24: 2 residues within 4Å: Chain A: K.621, W.717 Ligand excluded by PLIP DMS.25: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain A: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain A: D.428, P.430 Chain D: R.448, V.478 Ligand excluded by PLIP DMS.29: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain A: Y.926, Y.962, R.973, H.974, L.976 Ligand excluded by PLIP DMS.31: 7 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.8 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain A: W.695, Q.719, W.720, R.721 Ligands: MG.3 Ligand excluded by PLIP DMS.33: 7 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.13 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain A: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain A: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.37: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.46: 8 residues within 4Å: Chain B: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.47: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.49: 6 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.50: 3 residues within 4Å: Chain B: T.271, L.291, R.292 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain B: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain B: P.106, P.115, W.191 Ligands: DMS.58 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain B: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain B: G.593, D.594, T.595 Ligands: DMS.55 Ligand excluded by PLIP DMS.59: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.60: 2 residues within 4Å: Chain B: K.621, W.717 Ligand excluded by PLIP DMS.61: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.63: 2 residues within 4Å: Chain B: D.428 Chain C: V.478 Ligand excluded by PLIP DMS.64: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain B: Y.926, P.928, Y.962, R.973 Ligand excluded by PLIP DMS.66: 7 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.44 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain B: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain B: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.69: 4 residues within 4Å: Chain B: R.37, S.132, W.133, H.216 Ligand excluded by PLIP DMS.70: 3 residues within 4Å: Chain B: N.102, D.598, F.601 Ligand excluded by PLIP DMS.71: 5 residues within 4Å: Chain B: S.923, Y.926, R.961, Y.962, A.978 Ligand excluded by PLIP DMS.72: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.83: 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 PLIP DMS.84: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.85: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.86: 7 residues within 4Å: Chain C: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain C: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.88: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain C: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.90: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.91: 3 residues within 4Å: Chain C: P.106, P.115, W.191 Ligand excluded by PLIP DMS.92: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.93: 5 residues within 4Å: Chain C: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.94: 3 residues within 4Å: Chain C: G.593, D.594, T.595 Ligand excluded by PLIP DMS.95: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.96: 3 residues within 4Å: Chain C: K.621, I.714, W.717 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.98: 6 residues within 4Å: Chain C: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.99: 5 residues within 4Å: Chain C: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.100: 3 residues within 4Å: Chain B: W.474 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.101: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.102: 5 residues within 4Å: Chain C: Y.926, P.928, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.103: 7 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.81 Ligand excluded by PLIP DMS.104: 4 residues within 4Å: Chain C: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.105: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.106: 4 residues within 4Å: Chain C: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.107: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.108: 4 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.109: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.110: 3 residues within 4Å: Chain C: Q.266, V.267, A.268 Ligand excluded by PLIP DMS.120: 8 residues within 4Å: Chain D: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.121: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.122: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.123: 8 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.142 Ligand excluded by PLIP DMS.124: 3 residues within 4Å: Chain D: T.271, L.291, R.292 Ligand excluded by PLIP DMS.125: 4 residues within 4Å: Chain D: E.314, H.316, G.320 Ligands: DMS.146 Ligand excluded by PLIP DMS.126: 4 residues within 4Å: Chain D: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.127: 5 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.128: 4 residues within 4Å: Chain D: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.129: 3 residues within 4Å: Chain D: P.106, P.115, W.191 Ligand excluded by PLIP DMS.130: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.131: 6 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.132: 3 residues within 4Å: Chain D: G.593, D.594, T.595 Ligand excluded by PLIP DMS.133: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.134: 3 residues within 4Å: Chain D: K.621, I.714, W.717 Ligand excluded by PLIP DMS.135: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.136: 6 residues within 4Å: Chain D: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.137: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.138: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.139: 4 residues within 4Å: Chain D: Y.926, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.140: 7 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.118 Ligand excluded by PLIP DMS.141: 4 residues within 4Å: Chain D: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.142: 6 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.123 Ligand excluded by PLIP DMS.143: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.144: 4 residues within 4Å: Chain D: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.145: 4 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP DMS.146: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.125 Ligand excluded by PLIP DMS.147: 5 residues within 4Å: Chain D: Q.49, Q.50, D.130, S.132, W.133 Ligand excluded by PLIP DMS.148: 6 residues within 4Å: Chain D: W.133, L.134, Q.135, E.136, G.137, S.174 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juers, D.H. et al., High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation. Protein Sci. (2000)

Release Date

2001-02-21

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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