SMTL ID : 9e6q.1

Cryo-EM structure of the Pyrobaculum calidifontis 50S ribosomal subunit in complex with Dri

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

46 x SPM: SPERMINE(Non-covalent)(Non-functional Binders)

SPM.1: 8 residues within 4Å: Chain A: C.781, G.782, C.951, A.1062, G.1063, G.1064 Chain O: G.19, W.20 Ligand excluded by PLIP SPM.2: 9 residues within 4Å: Chain A: G.167, G.168, G.169, G.170, G.186, C.415 Chain K: N.120 Chain P: T.92, W.94 Ligand excluded by PLIP SPM.3: 11 residues within 4Å: Chain A: U.1907, G.1908, U.1963, G.1964, G.2093, G.2094, A.2095, U.2096, C.2704, C.2705 Chain D: R.190 Ligand excluded by PLIP SPM.4: 9 residues within 4Å: Chain A: U.183, A.185, G.186, G.227, G.228, U.416, U.417, G.419, U.420 Ligand excluded by PLIP SPM.5: 13 residues within 4Å: Chain A: G.24, G.336, A.337, A.358, C.505, U.506, G.507, A.508, A.531, C.539, C.1337, G.1363, A.1364 Ligand excluded by PLIP SPM.6: 10 residues within 4Å: Chain A: U.979, A.980, G.981, A.982, A.1029, U.1032, G.1035, G.2377, A.2378, A.2379 Ligand excluded by PLIP SPM.7: 10 residues within 4Å: Chain A: G.2755, G.2756, G.2757, A.2759, C.2880 Chain J: I.71, S.72, W.74, R.75, P.85 Ligand excluded by PLIP SPM.8: 9 residues within 4Å: Chain A: G.351, A.352, G.353, G.354, G.355, U.356, A.360 Chain F: Y.220, E.222 Ligand excluded by PLIP SPM.9: 12 residues within 4Å: Chain A: U.1394, A.1395, C.1800, G.2125, G.2126, C.2127, C.2128, G.2168, A.2169, C.2170, A.2728 Chain W: K.82 Ligand excluded by PLIP SPM.10: 10 residues within 4Å: Chain A: A.644, C.645, A.654, C.655, C.657, G.658, G.2178, A.2179, G.2616, A.2617 Ligand excluded by PLIP SPM.11: 10 residues within 4Å: Chain A: C.1124, C.1125, C.1126, U.1145, C.1260, A.1261, G.1262, G.1263, G.1264, A.1265 Ligand excluded by PLIP SPM.12: 9 residues within 4Å: Chain A: C.935, G.936, U.1316, A.1317, G.1318, G.1319, G.1320, G.1321 Chain O: Y.11 Ligand excluded by PLIP SPM.13: 9 residues within 4Å: Chain A: A.2954, U.2955, G.2956, G.2957, G.2958, G.2959, G.2960, C.3004, U.3005 Ligand excluded by PLIP SPM.14: 10 residues within 4Å: Chain 6: M.7, H.10 Chain A: G.494, U.495, G.496, U.803, A.906, A.907, C.1754, G.1755 Ligand excluded by PLIP SPM.15: 7 residues within 4Å: Chain A: G.226, G.227, G.228, C.230, U.420, U.422, A.2522 Ligand excluded by PLIP SPM.16: 9 residues within 4Å: Chain A: G.866, C.867, A.868, U.1454, C.1757 Chain W: M.144, P.145, R.146, A.147 Ligand excluded by PLIP SPM.17: 9 residues within 4Å: Chain A: G.43, U.111, G.112, C.144, G.145, G.155, G.156, G.157, C.158 Ligand excluded by PLIP SPM.18: 8 residues within 4Å: Chain A: G.854, G.855, G.856, G.1750, G.1761, G.1762, U.1763, C.1765 Ligand excluded by PLIP SPM.19: 7 residues within 4Å: Chain A: A.1938, G.1939, C.1940, G.1948, G.1949, U.1950, G.1951 Ligand excluded by PLIP SPM.20: 7 residues within 4Å: Chain A: G.2760, G.2761, U.2762, C.2787, G.2788, C.2789 Chain E: R.60 Ligand excluded by PLIP SPM.21: 11 residues within 4Å: Chain A: A.177, A.178, C.179, C.230, G.231, U.2188, A.2508, A.2546 Chain O: H.41, K.42, Y.61 Ligand excluded by PLIP SPM.22: 8 residues within 4Å: Chain A: C.1806, C.1807, U.2802, G.2803, C.2829, G.2830, G.2831, G.2832 Ligand excluded by PLIP SPM.23: 7 residues within 4Å: Chain A: C.849, G.1825, G.1826, C.1827, G.1843, A.1898, G.1899 Ligand excluded by PLIP SPM.24: 8 residues within 4Å: Chain A: U.1850, G.1851, C.1852, G.1885, G.1886, U.1887, G.1889, G.1892 Ligand excluded by PLIP SPM.25: 7 residues within 4Å: Chain A: A.650, G.1068, G.1069, G.1070, C.1083, C.1084, C.2612 Ligand excluded by PLIP SPM.26: 8 residues within 4Å: Chain A: A.1398, G.1793, G.1795, U.1796, G.1797, G.2124, G.2125, G.2126 Ligand excluded by PLIP SPM.27: 8 residues within 4Å: Chain A: A.1588, G.1589, U.1614, A.1615, C.1663, G.1664, G.1665, G.1666 Ligand excluded by PLIP SPM.28: 9 residues within 4Å: Chain A: C.2621, G.2622, U.2623, G.2688, U.2689, G.2690, A.2693, U.2694 Chain E: G.2 Ligand excluded by PLIP SPM.29: 10 residues within 4Å: Chain A: G.200, G.201, A.202, A.454, A.455, G.456, G.457, C.458, U.459 Chain K: R.105 Ligand excluded by PLIP SPM.30: 8 residues within 4Å: Chain A: G.2661, G.2662, A.2680, G.2681, G.2682, G.2683 Chain E: K.4, N.6 Ligand excluded by PLIP SPM.31: 10 residues within 4Å: Chain A: G.589, A.590, A.591, G.592, G.593, G.613, U.614, A.615, C.616, G.617 Ligand excluded by PLIP SPM.32: 10 residues within 4Å: Chain 4: W.60 Chain A: U.642, U.643, A.1096, C.1097, A.1102, C.1103, A.1104, C.2156, C.2157 Ligand excluded by PLIP SPM.33: 8 residues within 4Å: Chain A: U.121, G.122, C.123, C.138, C.139, C.1740, C.1741 Chain X: T.30 Ligand excluded by PLIP SPM.34: 10 residues within 4Å: Chain A: G.791, G.916, G.917, U.918, G.919, A.920 Chain F: K.82, E.83, C.86, F.111 Ligand excluded by PLIP SPM.35: 7 residues within 4Å: Chain A: C.1400, A.1402, A.1403, A.1430, C.1787, G.1789, C.1790 Ligand excluded by PLIP SPM.36: 9 residues within 4Å: Chain A: U.857, U.858, A.1920, A.1921, G.2103, G.2104, U.2105, G.2721, G.2722 Ligand excluded by PLIP SPM.37: 11 residues within 4Å: Chain A: C.808, C.809, C.810, U.811, G.812, G.813, U.885, G.886, G.887, G.888, G.889 Ligand excluded by PLIP SPM.38: 6 residues within 4Å: Chain A: G.1428, G.1770, G.1771, G.1772, U.1773, G.1774 Ligand excluded by PLIP SPM.39: 9 residues within 4Å: Chain 6: M.1 Chain A: G.856, U.857, U.858, U.871, G.873, U.874, A.1916, A.1917 Ligand excluded by PLIP SPM.40: 8 residues within 4Å: Chain A: U.2468, G.2469, A.2475, A.2476, G.2477, G.2478, G.2479, G.2480 Ligand excluded by PLIP SPM.41: 9 residues within 4Å: Chain A: C.516, C.517, C.518, G.519, G.523, G.524, G.525, G.526, G.527 Ligand excluded by PLIP SPM.42: 12 residues within 4Å: Chain A: U.1710, G.1711, A.1712, A.1713 Chain D: W.22, K.23, D.25, L.44, H.45, E.46 Chain b: L.52, I.56 Ligand excluded by PLIP SPM.43: 10 residues within 4Å: Chain A: C.2115, C.2116, C.2117, G.2118 Chain E: T.222, I.223, P.225, W.227, H.234 Chain L: R.54 Ligand excluded by PLIP SPM.44: 12 residues within 4Å: Chain A: G.413, G.414, C.2201, C.2343, A.2344 Chain a: K.43, L.44, K.45, G.46, Y.47, G.48, S.49 Ligand excluded by PLIP SPM.214: 8 residues within 4Å: Chain A: A.716, G.766, A.2508, C.2509 Chain O: E.53, W.58, K.63, H.64 Ligand excluded by PLIP SPM.217: 13 residues within 4Å: Chain A: U.1492, A.1493, G.2341, G.2342 Chain P: L.67, I.68, R.69, P.71, N.73, V.88, Y.89, W.97, R.104 Ligand excluded by PLIP

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

MG.45: 3 residues within 4Å: Chain A: C.2618, U.2620, A.2686 No protein-ligand interaction detected (PLIP) MG.46: 1 residues within 4Å: Chain A: G.2349 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain A: G.1908, C.1910 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain A: U.2194, G.2350 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain A: A.1808, G.1811 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain A: G.2711, A.2712 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain A: A.948, G.949 No protein-ligand interaction detected (PLIP) MG.52: 1 residues within 4Å: Chain A: C.1924 No protein-ligand interaction detected (PLIP) MG.53: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.54: 1 residues within 4Å: Chain A: U.925 No protein-ligand interaction detected (PLIP) MG.55: 1 residues within 4Å: Chain A: A.173 No protein-ligand interaction detected (PLIP) MG.56: 2 residues within 4Å: Chain A: G.481, C.484 No protein-ligand interaction detected (PLIP) MG.57: 1 residues within 4Å: Chain A: G.186 No protein-ligand interaction detected (PLIP) MG.58: 1 residues within 4Å: Chain A: G.2089 No protein-ligand interaction detected (PLIP) MG.59: 3 residues within 4Å: Chain A: A.1916, C.1918, A.1919 No protein-ligand interaction detected (PLIP) MG.60: 3 residues within 4Å: Chain A: U.857, A.1919, A.1920 No protein-ligand interaction detected (PLIP) MG.61: 3 residues within 4Å: Chain A: U.2186, C.2359, U.2360 No protein-ligand interaction detected (PLIP) MG.62: 3 residues within 4Å: Chain A: A.868, A.869, A.1756 No protein-ligand interaction detected (PLIP) MG.63: 2 residues within 4Å: Chain A: A.2632, A.2655 No protein-ligand interaction detected (PLIP) MG.64: 2 residues within 4Å: Chain A: G.1082, G.2149 No protein-ligand interaction detected (PLIP) MG.65: 1 residues within 4Å: Chain A: G.2154 No protein-ligand interaction detected (PLIP) MG.66: 1 residues within 4Å: Chain A: G.843 No protein-ligand interaction detected (PLIP) MG.67: 4 residues within 4Å: Chain A: G.842, C.1582, G.1583, A.1641 No protein-ligand interaction detected (PLIP) MG.68: 1 residues within 4Å: Chain A: G.199 No protein-ligand interaction detected (PLIP) MG.69: 2 residues within 4Å: Chain A: A.198, A.461 No protein-ligand interaction detected (PLIP) MG.70: 3 residues within 4Å: Chain A: G.894, A.911, G.912 No protein-ligand interaction detected (PLIP) MG.71: 4 residues within 4Å: Chain A: C.795, G.894, A.2191, G.2192 No protein-ligand interaction detected (PLIP) MG.72: 3 residues within 4Å: Chain A: A.173, G.2353, U.2354 No protein-ligand interaction detected (PLIP) MG.73: 4 residues within 4Å: Chain A: A.178, C.179, G.2189, G.2190 No protein-ligand interaction detected (PLIP) MG.74: 3 residues within 4Å: Chain A: A.176, A.178, C.179 No protein-ligand interaction detected (PLIP) MG.75: 3 residues within 4Å: Chain A: G.902, G.2702, A.2703 No protein-ligand interaction detected (PLIP) MG.76: 4 residues within 4Å: Chain A: A.901, G.902, G.2702, A.2703 No protein-ligand interaction detected (PLIP) MG.77: 2 residues within 4Å: Chain A: C.905, U.908 No protein-ligand interaction detected (PLIP) MG.78: 2 residues within 4Å: Chain A: G.2560, G.2616 No protein-ligand interaction detected (PLIP) MG.79: 3 residues within 4Å: Chain A: G.481, G.483 Chain F: G.118 No protein-ligand interaction detected (PLIP) MG.80: 1 residues within 4Å: Chain A: C.648 No protein-ligand interaction detected (PLIP) MG.81: 2 residues within 4Å: Chain A: U.1442, C.1463 No protein-ligand interaction detected (PLIP) MG.82: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.83: 2 residues within 4Å: Chain A: C.1814, U.1815 No protein-ligand interaction detected (PLIP) MG.84: 4 residues within 4Å: Chain A: A.1813, C.1814, U.1815, G.2664 No protein-ligand interaction detected (PLIP) MG.85: 2 residues within 4Å: Chain A: C.1425, C.1782 No protein-ligand interaction detected (PLIP) MG.86: 2 residues within 4Å: Chain A: A.2824, G.2827 No protein-ligand interaction detected (PLIP) MG.87: 2 residues within 4Å: Chain A: C.1426, C.1782 No protein-ligand interaction detected (PLIP) MG.88: 4 residues within 4Å: Chain A: A.2022, G.2023, G.2024, U.2092 No protein-ligand interaction detected (PLIP) MG.89: 3 residues within 4Å: Chain A: U.1143, G.1144, C.1260 No protein-ligand interaction detected (PLIP) MG.90: 1 residues within 4Å: Chain A: G.1433 No protein-ligand interaction detected (PLIP) MG.91: 5 residues within 4Å: Chain A: A.1751, G.1758, C.1759, C.1790, U.1791 No protein-ligand interaction detected (PLIP) MG.92: 3 residues within 4Å: Chain A: G.861, U.2694 Chain E: K.229 No protein-ligand interaction detected (PLIP) MG.93: 2 residues within 4Å: Chain A: G.797, G.894 No protein-ligand interaction detected (PLIP) MG.94: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.95: 1 residues within 4Å: Chain A: A.2091 No protein-ligand interaction detected (PLIP) MG.96: 1 residues within 4Å: Chain A: G.2094 No protein-ligand interaction detected (PLIP) MG.97: 1 residues within 4Å: Chain A: G.2093 No protein-ligand interaction detected (PLIP) MG.98: 2 residues within 4Å: Chain A: C.2056, G.2061 No protein-ligand interaction detected (PLIP) MG.99: 2 residues within 4Å: Chain A: C.1479, G.1507 No protein-ligand interaction detected (PLIP) MG.100: 2 residues within 4Å: Chain 1: T.24 Chain A: G.1108 5 PLIP interactions: 1 interactions with chain 1, 4 Ligand-Water interactions Metal complexes: 1:T.24, H2O.28, H2O.154, H2O.163, H2O.296 MG.101: 2 residues within 4Å: Chain A: U.928, G.1380 No protein-ligand interaction detected (PLIP) MG.102: 2 residues within 4Å: Chain A: G.2181, G.2616 No protein-ligand interaction detected (PLIP) MG.103: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.104: 1 residues within 4Å: Chain A: G.981 No protein-ligand interaction detected (PLIP) MG.105: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.106: 2 residues within 4Å: Chain A: A.1784, G.1785 No protein-ligand interaction detected (PLIP) MG.107: 2 residues within 4Å: Chain A: G.1100, A.1102 No protein-ligand interaction detected (PLIP) MG.108: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.109: 2 residues within 4Å: Chain A: G.1511, G.1513 No protein-ligand interaction detected (PLIP) MG.110: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.111: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.112: 4 residues within 4Å: Chain A: C.655, A.656, C.2175, C.2613 No protein-ligand interaction detected (PLIP) MG.113: 3 residues within 4Å: Chain A: A.656, C.657, C.2618 No protein-ligand interaction detected (PLIP) MG.114: 2 residues within 4Å: Chain A: A.110, U.111 No protein-ligand interaction detected (PLIP) MG.115: 3 residues within 4Å: Chain A: G.651, A.2562, C.2613 No protein-ligand interaction detected (PLIP) MG.116: 3 residues within 4Å: Chain 4: D.53 Chain A: U.647, A.652 4 PLIP interactions: 1 interactions with chain 4, 3 Ligand-Water interactions Metal complexes: 4:D.53, H2O.31, H2O.47, H2O.299 MG.117: 2 residues within 4Å: Chain A: U.2438, G.2504 No protein-ligand interaction detected (PLIP) MG.118: 1 residues within 4Å: Chain A: G.2382 No protein-ligand interaction detected (PLIP) MG.119: 3 residues within 4Å: Chain A: A.1471, U.1744 Chain X: T.51 No protein-ligand interaction detected (PLIP) MG.120: 1 residues within 4Å: Chain A: U.2096 No protein-ligand interaction detected (PLIP) MG.121: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.122: 1 residues within 4Å: Chain A: C.365 No protein-ligand interaction detected (PLIP) MG.123: 1 residues within 4Å: Chain A: A.1820 No protein-ligand interaction detected (PLIP) MG.124: 3 residues within 4Å: Chain A: G.23, G.24, C.1366 No protein-ligand interaction detected (PLIP) MG.125: 2 residues within 4Å: Chain A: C.2372, G.2469 No protein-ligand interaction detected (PLIP) MG.126: 3 residues within 4Å: Chain A: C.2359, G.2366, G.2367 No protein-ligand interaction detected (PLIP) MG.127: 1 residues within 4Å: Chain A: G.2709 No protein-ligand interaction detected (PLIP) MG.128: 2 residues within 4Å: Chain A: A.1778, G.1779 No protein-ligand interaction detected (PLIP) MG.129: 2 residues within 4Å: Chain A: A.1965, A.1966 No protein-ligand interaction detected (PLIP) MG.130: 3 residues within 4Å: Chain A: U.860, G.861, U.863 No protein-ligand interaction detected (PLIP) MG.131: 2 residues within 4Å: Chain A: G.864, C.2726 No protein-ligand interaction detected (PLIP) MG.132: 3 residues within 4Å: Chain A: C.847, C.848, A.879 No protein-ligand interaction detected (PLIP) MG.133: 1 residues within 4Å: Chain A: G.659 No protein-ligand interaction detected (PLIP) MG.134: 1 residues within 4Å: Chain A: U.803 No protein-ligand interaction detected (PLIP) MG.135: 2 residues within 4Å: Chain A: A.2522, C.2523 No protein-ligand interaction detected (PLIP) MG.136: 2 residues within 4Å: Chain A: A.2380, A.2381 No protein-ligand interaction detected (PLIP) MG.137: 3 residues within 4Å: Chain A: C.1128, A.1129, A.1130 No protein-ligand interaction detected (PLIP) MG.138: 2 residues within 4Å: Chain A: G.1396, G.2126 No protein-ligand interaction detected (PLIP) MG.139: 1 residues within 4Å: Chain A: G.2619 No protein-ligand interaction detected (PLIP) MG.140: 4 residues within 4Å: Chain A: C.2175, G.2176, C.2618, G.2619 No protein-ligand interaction detected (PLIP) MG.141: 1 residues within 4Å: Chain A: A.2728 No protein-ligand interaction detected (PLIP) MG.142: 1 residues within 4Å: Chain A: A.1897 No protein-ligand interaction detected (PLIP) MG.143: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.144: 3 residues within 4Å: Chain A: G.223, G.235 Chain K: E.137 4 PLIP interactions: 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:E.137, H2O.94, H2O.97, H2O.274 MG.145: 2 residues within 4Å: Chain A: G.941, G.942 No protein-ligand interaction detected (PLIP) MG.146: 2 residues within 4Å: Chain A: G.2619, G.2690 No protein-ligand interaction detected (PLIP) MG.147: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.148: 3 residues within 4Å: Chain A: A.802, U.803, C.804 No protein-ligand interaction detected (PLIP) MG.149: 1 residues within 4Å: Chain A: C.1754 No protein-ligand interaction detected (PLIP) MG.150: 3 residues within 4Å: Chain A: U.2689, G.2690, A.2691 No protein-ligand interaction detected (PLIP) MG.151: 1 residues within 4Å: Chain A: A.2448 No protein-ligand interaction detected (PLIP) MG.152: 1 residues within 4Å: Chain A: U.1391 No protein-ligand interaction detected (PLIP) MG.153: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.154: 3 residues within 4Å: Chain A: U.1443, C.1444, G.1461 No protein-ligand interaction detected (PLIP) MG.155: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.156: 2 residues within 4Å: Chain 4: D.53 Chain A: A.652 No protein-ligand interaction detected (PLIP) MG.157: 2 residues within 4Å: Chain A: G.404, A.454 No protein-ligand interaction detected (PLIP) MG.158: 3 residues within 4Å: Chain A: A.2544, G.2545 Chain O: H.41 4 PLIP interactions: 2 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:H.41, O:H.41, H2O.278, H2O.279 MG.159: 3 residues within 4Å: Chain A: U.944, C.2543, A.2544 No protein-ligand interaction detected (PLIP) MG.160: 1 residues within 4Å: Chain A: C.947 No protein-ligand interaction detected (PLIP) MG.161: 3 residues within 4Å: Chain A: A.2162, G.2889, A.2890 No protein-ligand interaction detected (PLIP) MG.162: 4 residues within 4Å: Chain A: A.1524, U.1525, A.1526, C.1746 No protein-ligand interaction detected (PLIP) MG.163: 5 residues within 4Å: Chain A: A.2561, A.2562, A.2611, C.2612, C.2613 No protein-ligand interaction detected (PLIP) MG.164: 1 residues within 4Å: Chain A: G.1404 No protein-ligand interaction detected (PLIP) MG.165: 1 residues within 4Å: Chain A: G.784 No protein-ligand interaction detected (PLIP) MG.166: 4 residues within 4Å: Chain A: C.538, C.539, U.540, G.541 No protein-ligand interaction detected (PLIP) MG.167: 4 residues within 4Å: Chain A: G.571, A.572, A.573, G.575 No protein-ligand interaction detected (PLIP) MG.168: 2 residues within 4Å: Chain A: G.575, G.576 No protein-ligand interaction detected (PLIP) MG.169: 1 residues within 4Å: Chain A: G.2697 No protein-ligand interaction detected (PLIP) MG.170: 2 residues within 4Å: Chain A: U.2811, G.2812 No protein-ligand interaction detected (PLIP) MG.171: 3 residues within 4Å: Chain A: C.2183, C.2184 Chain C: T.224 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.224, H2O.88, H2O.90, H2O.259 MG.172: 2 residues within 4Å: Chain A: G.2803, G.2832 No protein-ligand interaction detected (PLIP) MG.173: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.174: 3 residues within 4Å: Chain A: A.7, A.8, G.9 No protein-ligand interaction detected (PLIP) MG.175: 4 residues within 4Å: Chain A: U.1525, A.1526, A.1745, C.1746 No protein-ligand interaction detected (PLIP) MG.176: 2 residues within 4Å: Chain A: G.778 Chain F: E.132 No protein-ligand interaction detected (PLIP) MG.177: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.178: 2 residues within 4Å: Chain A: G.2051, G.2089 No protein-ligand interaction detected (PLIP) MG.179: 1 residues within 4Å: Chain A: A.1028 No protein-ligand interaction detected (PLIP) MG.180: 1 residues within 4Å: Chain A: G.2125 No protein-ligand interaction detected (PLIP) MG.181: 1 residues within 4Å: Chain A: G.1371 No protein-ligand interaction detected (PLIP) MG.182: 2 residues within 4Å: Chain A: G.2181, U.2182 No protein-ligand interaction detected (PLIP) MG.183: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.184: 2 residues within 4Å: Chain A: G.936, G.1315 No protein-ligand interaction detected (PLIP) MG.185: 1 residues within 4Å: Chain A: G.2582 No protein-ligand interaction detected (PLIP) MG.186: 1 residues within 4Å: Chain A: G.2601 No protein-ligand interaction detected (PLIP) MG.187: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.188: 1 residues within 4Å: Chain A: A.2819 No protein-ligand interaction detected (PLIP) MG.189: 2 residues within 4Å: Chain A: U.860, U.2723 No protein-ligand interaction detected (PLIP) MG.190: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.191: 1 residues within 4Å: Chain A: G.2532 No protein-ligand interaction detected (PLIP) MG.192: 4 residues within 4Å: Chain A: G.2480, G.2499, C.2500, C.2501 No protein-ligand interaction detected (PLIP) MG.193: 3 residues within 4Å: Chain A: C.849, G.850, A.879 No protein-ligand interaction detected (PLIP) MG.194: 2 residues within 4Å: Chain A: G.972, G.973 No protein-ligand interaction detected (PLIP) MG.195: 3 residues within 4Å: Chain A: G.285, U.286, G.287 No protein-ligand interaction detected (PLIP) MG.196: 2 residues within 4Å: Chain A: G.1512, A.1576 No protein-ligand interaction detected (PLIP) MG.197: 2 residues within 4Å: Chain A: G.1314, G.1315 No protein-ligand interaction detected (PLIP) MG.198: 2 residues within 4Å: Chain A: G.325, G.366 No protein-ligand interaction detected (PLIP) MG.199: 1 residues within 4Å: Chain A: G.46 No protein-ligand interaction detected (PLIP) MG.200: 1 residues within 4Å: Chain A: C.2575 No protein-ligand interaction detected (PLIP) MG.201: 3 residues within 4Å: Chain A: C.2687, G.2688, U.2689 No protein-ligand interaction detected (PLIP) MG.202: 1 residues within 4Å: Chain A: C.2700 No protein-ligand interaction detected (PLIP) MG.203: 2 residues within 4Å: Chain A: A.2059, C.2078 No protein-ligand interaction detected (PLIP) MG.204: 3 residues within 4Å: Chain A: G.2695, G.2696, G.2697 No protein-ligand interaction detected (PLIP) MG.205: 3 residues within 4Å: Chain A: A.2470, A.2471, C.2472 No protein-ligand interaction detected (PLIP) MG.206: 1 residues within 4Å: Chain A: A.2338 No protein-ligand interaction detected (PLIP) MG.207: 2 residues within 4Å: Chain A: C.1425, C.1426 No protein-ligand interaction detected (PLIP) MG.208: 2 residues within 4Å: Chain A: G.1066, G.1067 No protein-ligand interaction detected (PLIP) MG.209: 2 residues within 4Å: Chain A: G.1912, A.2102 No protein-ligand interaction detected (PLIP) MG.210: 1 residues within 4Å: Chain A: U.2052 No protein-ligand interaction detected (PLIP) MG.211: 1 residues within 4Å: Chain A: A.194 No protein-ligand interaction detected (PLIP) MG.212: 1 residues within 4Å: Chain A: G.2504 No protein-ligand interaction detected (PLIP) MG.213: 3 residues within 4Å: Chain D: Q.16, K.182, W.184 No protein-ligand interaction detected (PLIP) MG.215: 2 residues within 4Å: Chain A: G.1064 Chain O: G.24 No protein-ligand interaction detected (PLIP) MG.216: 1 residues within 4Å: Chain O: Q.25 No protein-ligand interaction detected (PLIP) MG.218: 3 residues within 4Å: Chain A: G.1075, G.1078 Chain Q: K.13 5 PLIP interactions: 1 interactions with chain Q, 4 Ligand-Water interactions Metal complexes: Q:K.13, H2O.63, H2O.90, H2O.138, H2O.283 MG.219: 3 residues within 4Å: Chain A: G.2133 Chain W: M.40, E.156 5 PLIP interactions: 1 interactions with chain W, 4 Ligand-Water interactions Metal complexes: W:E.156, H2O.70, H2O.106, H2O.290, H2O.291

5 x ZN: ZINC ION(Non-covalent)

ZN.220: 4 residues within 4Å: Chain Z: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.6, Z:C.9, Z:C.32, Z:C.36 ZN.221: 4 residues within 4Å: Chain 6: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.19, 6:C.22, 6:C.34, 6:C.37 ZN.222: 4 residues within 4Å: Chain 9: C.23, C.26, C.37, C.40 4 PLIP interactions: 4 interactions with chain 9 Metal complexes: 9:C.23, 9:C.26, 9:C.37, 9:C.40 ZN.223: 4 residues within 4Å: Chain a: C.11, C.14, C.71, C.74 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:C.11, a:C.14, a:C.71, a:C.74 ZN.224: 4 residues within 4Å: Chain b: C.40, C.43, C.59, C.62 4 PLIP interactions: 4 interactions with chain b Metal complexes: b:C.40, b:C.43, b:C.59, b:C.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nissley, A.J. et al., Structure of an Archaeal Ribosome with a Divergent Active Site. To Be Published

Release Date

2024-11-20

Peptides

Putative signal-transduction protein with CBS domains: C
Large ribosomal subunit protein uL2: D
Large ribosomal subunit protein uL3: E
Large ribosomal subunit protein uL4: F
Large ribosomal subunit protein uL5: G
Large ribosomal subunit protein uL6: H
Large ribosomal subunit protein eL8: I
Large ribosomal subunit protein uL13: J
Large ribosomal subunit protein eL13: K
Large ribosomal subunit protein uL14: L
eL14: MN
Large ribosomal subunit protein uL15: O
50S ribosomal protein L15e: P
Large ribosomal subunit protein uL16: Q
Large ribosomal subunit protein uL18: R
Large ribosomal subunit protein eL18: S
Large ribosomal subunit protein eL19: T
Large ribosomal subunit protein eL20: U
Large ribosomal subunit protein eL21: V
Large ribosomal subunit protein uL22: W
Large ribosomal subunit protein uL23: X
Large ribosomal subunit protein uL24: Y
Large ribosomal subunit protein eL24: Z
Large ribosomal subunit protein uL29: 0
Large ribosomal subunit protein uL30: 1
Large ribosomal subunit protein eL30: 2
Large ribosomal subunit protein eL31: 3
Large ribosomal subunit protein eL32: 4
Large ribosomal subunit protein eL34: 5
Large ribosomal subunit protein eL37: 6
LSU ribosomal protein L38E: 7
Large ribosomal subunit protein eL39: 8
Large ribosomal subunit protein eL40: 9
eL42: a
Large ribosomal subunit protein eL43: b
DJ-1/PfpI domain-containing protein: c
PaREP1 domain containing protein: d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
3

D
AA

E
AB

F
AC

G
AD

H
AE

I
AF

J
AG

K
AH

L
AI

M
AJ

N
AK

O
AL

P
AM

Q
AN

R
AO

S
AP

T
AQ

U
AR

V
AS

W
AT

X
AU

Y
AV

Z
AW

0
AX

1
AY

2
AZ

3
Aa

4
Ab

5
Ac

6
Ad

7
Ae

8
Af

9
Ag

a
Ah

b
Ai

c
Aj

d
Ak

Putative signal-transduction protein with CBS domains

Large ribosomal subunit protein uL2

Large ribosomal subunit protein uL3

Large ribosomal subunit protein uL4

Large ribosomal subunit protein uL5

Large ribosomal subunit protein uL6

Large ribosomal subunit protein eL8

Large ribosomal subunit protein uL13

Large ribosomal subunit protein eL13

Large ribosomal subunit protein uL14

eL14

Large ribosomal subunit protein uL15

50S ribosomal protein L15e

Large ribosomal subunit protein uL16

Large ribosomal subunit protein uL18

Large ribosomal subunit protein eL18

Large ribosomal subunit protein eL19

Large ribosomal subunit protein eL20

Large ribosomal subunit protein eL21

Large ribosomal subunit protein uL22

Large ribosomal subunit protein uL23

Large ribosomal subunit protein uL24

Large ribosomal subunit protein eL24

Large ribosomal subunit protein uL29

Large ribosomal subunit protein uL30

Large ribosomal subunit protein eL30

Large ribosomal subunit protein eL31

Large ribosomal subunit protein eL32

Large ribosomal subunit protein eL34

Large ribosomal subunit protein eL37

LSU ribosomal protein L38E

Large ribosomal subunit protein eL39

Large ribosomal subunit protein eL40

eL42

Large ribosomal subunit protein eL43

DJ-1/PfpI domain-containing protein

PaREP1 domain containing protein