data_5KD8 # _model_server_result.job_id 5Py-j-Y54vGDy21I2sk2PA _model_server_result.datetime_utc '2024-10-12 06:20:26' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5kd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":903}' # _entry.id 5KD8 # _exptl.entry_id 5KD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5KD8 _cell.length_a 87.45 _cell.length_b 88.23 _cell.length_c 98.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KD8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 G OG SER . A SER 906 1_555 H C1 A2G . A A2G 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? metalc ? metalc1 A OE1 GLU 29 A GLU 327 1_555 F NA NA . A NA 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc2 A OE2 GLU 29 A GLU 327 1_555 F NA NA . A NA 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc3 A NE2 HIS 140 A HIS 438 1_555 C NI NI . A NI 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc4 A OD1 ASP 153 A ASP 451 1_555 E NA NA . A NA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc5 A OD2 ASP 153 A ASP 451 1_555 E NA NA . A NA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc6 A OE1 GLU 156 A GLU 454 1_555 F NA NA . A NA 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc7 A NE2 HIS 276 A HIS 574 1_555 B ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc8 A NE2 HIS 280 A HIS 578 1_555 B ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc9 A OE1 GLU 293 A GLU 591 1_555 B ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? metalc ? metalc10 A OE2 GLU 293 A GLU 591 1_555 B ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc11 A OE2 GLU 410 A GLU 708 1_555 D NI NI . A NI 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc12 A OE1 GLU 416 A GLU 714 1_555 D NI NI . A NI 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc13 B ZN ZN . A ZN 901 1_555 G OXT SER . A SER 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc14 C NI NI . A NI 902 1_555 I O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc15 C NI NI . A NI 902 1_555 I O HOH . A HOH 1139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc16 C NI NI . A NI 902 1_555 I O HOH . A HOH 1142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc17 C NI NI . A NI 902 1_555 I O HOH . A HOH 1146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc18 D NI NI . A NI 903 1_555 I O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc19 D NI NI . A NI 903 1_555 I O HOH . A HOH 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc20 D NI NI . A NI 903 1_555 I O HOH . A HOH 1083 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc21 E NA NA . A NA 904 1_555 I O HOH . A HOH 1124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc22 E NA NA . A NA 904 1_555 I O HOH . A HOH 1144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc23 F NA NA . A NA 905 1_555 I O HOH . A HOH 1071 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? # _chem_comp.formula 'Ni 2' _chem_comp.formula_weight 58.693 _chem_comp.id NI _chem_comp.mon_nstd_flag . _chem_comp.name 'NICKEL (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5KD8 _atom_sites.fract_transf_matrix[1][1] 0.011435 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011334 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010137 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 ZN A 1 901 1 ZN ZN . C 3 NI A 1 902 1 NI NI . D 3 NI A 1 903 2 NI NI . E 4 NA A 1 904 1 NA NA . F 4 NA A 1 905 2 NA NA . G 5 SER A 1 906 1 SER TNR . H 6 A2G A 1 907 1 A2G TNR . I 7 HOH A 1 1001 37 HOH HOH . I 7 HOH A 2 1002 122 HOH HOH . I 7 HOH A 3 1003 7 HOH HOH . I 7 HOH A 4 1004 154 HOH HOH . I 7 HOH A 5 1005 121 HOH HOH . I 7 HOH A 6 1006 117 HOH HOH . I 7 HOH A 7 1007 72 HOH HOH . I 7 HOH A 8 1008 44 HOH HOH . I 7 HOH A 9 1009 48 HOH HOH . I 7 HOH A 10 1010 78 HOH HOH . I 7 HOH A 11 1011 166 HOH HOH . I 7 HOH A 12 1012 118 HOH HOH . I 7 HOH A 13 1013 80 HOH HOH . I 7 HOH A 14 1014 52 HOH HOH . I 7 HOH A 15 1015 94 HOH HOH . I 7 HOH A 16 1016 35 HOH HOH . I 7 HOH A 17 1017 18 HOH HOH . I 7 HOH A 18 1018 68 HOH HOH . I 7 HOH A 19 1019 61 HOH HOH . I 7 HOH A 20 1020 43 HOH HOH . I 7 HOH A 21 1021 99 HOH HOH . I 7 HOH A 22 1022 25 HOH HOH . I 7 HOH A 23 1023 147 HOH HOH . I 7 HOH A 24 1024 34 HOH HOH . I 7 HOH A 25 1025 38 HOH HOH . I 7 HOH A 26 1026 42 HOH HOH . I 7 HOH A 27 1027 11 HOH HOH . I 7 HOH A 28 1028 33 HOH HOH . I 7 HOH A 29 1029 73 HOH HOH . I 7 HOH A 30 1030 17 HOH HOH . I 7 HOH A 31 1031 50 HOH HOH . I 7 HOH A 32 1032 39 HOH HOH . I 7 HOH A 33 1033 130 HOH HOH . I 7 HOH A 34 1034 27 HOH HOH . I 7 HOH A 35 1035 20 HOH HOH . I 7 HOH A 36 1036 57 HOH HOH . I 7 HOH A 37 1037 64 HOH HOH . I 7 HOH A 38 1038 86 HOH HOH . I 7 HOH A 39 1039 36 HOH HOH . I 7 HOH A 40 1040 84 HOH HOH . I 7 HOH A 41 1041 31 HOH HOH . I 7 HOH A 42 1042 135 HOH HOH . I 7 HOH A 43 1043 143 HOH HOH . I 7 HOH A 44 1044 10 HOH HOH . I 7 HOH A 45 1045 66 HOH HOH . I 7 HOH A 46 1046 28 HOH HOH . I 7 HOH A 47 1047 88 HOH HOH . I 7 HOH A 48 1048 29 HOH HOH . I 7 HOH A 49 1049 146 HOH HOH . I 7 HOH A 50 1050 15 HOH HOH . I 7 HOH A 51 1051 12 HOH HOH . I 7 HOH A 52 1052 9 HOH HOH . I 7 HOH A 53 1053 67 HOH HOH . I 7 HOH A 54 1054 128 HOH HOH . I 7 HOH A 55 1055 163 HOH HOH . I 7 HOH A 56 1056 93 HOH HOH . I 7 HOH A 57 1057 112 HOH HOH . I 7 HOH A 58 1058 41 HOH HOH . I 7 HOH A 59 1059 110 HOH HOH . I 7 HOH A 60 1060 92 HOH HOH . I 7 HOH A 61 1061 74 HOH HOH . I 7 HOH A 62 1062 108 HOH HOH . I 7 HOH A 63 1063 81 HOH HOH . I 7 HOH A 64 1064 60 HOH HOH . I 7 HOH A 65 1065 54 HOH HOH . I 7 HOH A 66 1066 129 HOH HOH . I 7 HOH A 67 1067 19 HOH HOH . I 7 HOH A 68 1068 113 HOH HOH . I 7 HOH A 69 1069 23 HOH HOH . I 7 HOH A 70 1070 59 HOH HOH . I 7 HOH A 71 1071 162 HOH HOH . I 7 HOH A 72 1072 30 HOH HOH . I 7 HOH A 73 1073 157 HOH HOH . I 7 HOH A 74 1074 24 HOH HOH . I 7 HOH A 75 1075 62 HOH HOH . I 7 HOH A 76 1076 104 HOH HOH . I 7 HOH A 77 1077 58 HOH HOH . I 7 HOH A 78 1078 105 HOH HOH . I 7 HOH A 79 1079 46 HOH HOH . I 7 HOH A 80 1080 65 HOH HOH . I 7 HOH A 81 1081 76 HOH HOH . I 7 HOH A 82 1082 98 HOH HOH . I 7 HOH A 83 1083 4 HOH HOH . I 7 HOH A 84 1084 49 HOH HOH . I 7 HOH A 85 1085 71 HOH HOH . I 7 HOH A 86 1086 53 HOH HOH . I 7 HOH A 87 1087 102 HOH HOH . I 7 HOH A 88 1088 16 HOH HOH . I 7 HOH A 89 1089 134 HOH HOH . I 7 HOH A 90 1090 91 HOH HOH . I 7 HOH A 91 1091 69 HOH HOH . I 7 HOH A 92 1092 63 HOH HOH . I 7 HOH A 93 1093 125 HOH HOH . I 7 HOH A 94 1094 132 HOH HOH . I 7 HOH A 95 1095 111 HOH HOH . I 7 HOH A 96 1096 14 HOH HOH . I 7 HOH A 97 1097 75 HOH HOH . I 7 HOH A 98 1098 55 HOH HOH . I 7 HOH A 99 1099 47 HOH HOH . I 7 HOH A 100 1100 131 HOH HOH . I 7 HOH A 101 1101 40 HOH HOH . I 7 HOH A 102 1102 151 HOH HOH . I 7 HOH A 103 1103 127 HOH HOH . I 7 HOH A 104 1104 79 HOH HOH . I 7 HOH A 105 1105 167 HOH HOH . I 7 HOH A 106 1106 144 HOH HOH . I 7 HOH A 107 1107 150 HOH HOH . I 7 HOH A 108 1108 56 HOH HOH . I 7 HOH A 109 1109 45 HOH HOH . I 7 HOH A 110 1110 115 HOH HOH . I 7 HOH A 111 1111 89 HOH HOH . I 7 HOH A 112 1112 145 HOH HOH . I 7 HOH A 113 1113 120 HOH HOH . I 7 HOH A 114 1114 87 HOH HOH . I 7 HOH A 115 1115 8 HOH HOH . I 7 HOH A 116 1116 26 HOH HOH . I 7 HOH A 117 1117 160 HOH HOH . I 7 HOH A 118 1118 100 HOH HOH . I 7 HOH A 119 1119 141 HOH HOH . I 7 HOH A 120 1120 133 HOH HOH . I 7 HOH A 121 1121 101 HOH HOH . I 7 HOH A 122 1122 21 HOH HOH . I 7 HOH A 123 1123 109 HOH HOH . I 7 HOH A 124 1124 5 HOH HOH . I 7 HOH A 125 1125 85 HOH HOH . I 7 HOH A 126 1126 22 HOH HOH . I 7 HOH A 127 1127 82 HOH HOH . I 7 HOH A 128 1128 137 HOH HOH . I 7 HOH A 129 1129 124 HOH HOH . I 7 HOH A 130 1130 90 HOH HOH . I 7 HOH A 131 1131 155 HOH HOH . I 7 HOH A 132 1132 13 HOH HOH . I 7 HOH A 133 1133 97 HOH HOH . I 7 HOH A 134 1134 123 HOH HOH . I 7 HOH A 135 1135 148 HOH HOH . I 7 HOH A 136 1136 95 HOH HOH . I 7 HOH A 137 1137 116 HOH HOH . I 7 HOH A 138 1138 126 HOH HOH . I 7 HOH A 139 1139 3 HOH HOH . I 7 HOH A 140 1140 153 HOH HOH . I 7 HOH A 141 1141 114 HOH HOH . I 7 HOH A 142 1142 2 HOH HOH . I 7 HOH A 143 1143 158 HOH HOH . I 7 HOH A 144 1144 6 HOH HOH . I 7 HOH A 145 1145 51 HOH HOH . I 7 HOH A 146 1146 1 HOH HOH . I 7 HOH A 147 1147 32 HOH HOH . I 7 HOH A 148 1148 161 HOH HOH . I 7 HOH A 149 1149 156 HOH HOH . I 7 HOH A 150 1150 70 HOH HOH . I 7 HOH A 151 1151 165 HOH HOH . I 7 HOH A 152 1152 96 HOH HOH . I 7 HOH A 153 1153 138 HOH HOH . I 7 HOH A 154 1154 152 HOH HOH . I 7 HOH A 155 1155 107 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NI _atom_site.label_atom_id NI _atom_site.label_comp_id NI _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x 11.516 _atom_site.Cartn_y 24.467 _atom_site.Cartn_z -20.038 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 54.82 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 903 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 1 #