data_4Q2D # _model_server_result.job_id 4Gj9g3oKCMnk1hcV7QZz6Q _model_server_result.datetime_utc '2025-07-17 22:27:08' _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 4q2d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1003}' # _entry.id 4Q2D # _exptl.entry_id 4Q2D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 3 _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 4Q2D _cell.length_a 105.684 _cell.length_b 211.63 _cell.length_c 104.272 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q2D _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 _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 ? 2 B N N ? 2 C N N ? 2 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 A C HIS 57 A HIS 52 1_555 A N MSE 58 A MSE 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 58 A MSE 53 1_555 A N LEU 59 A LEU 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C GLN 67 A GLN 62 1_555 A N MSE 68 A MSE 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 68 A MSE 63 1_555 A N TRP 69 A TRP 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C GLY 198 A GLY 193 1_555 A N MSE 199 A MSE 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C MSE 199 A MSE 194 1_555 A N TRP 200 A TRP 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C PHE 232 A PHE 227 1_555 A N MSE 233 A MSE 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C MSE 233 A MSE 228 1_555 A N LEU 234 A LEU 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 A C ALA 273 A ALA 268 1_555 A N MSE 274 A MSE 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 A C MSE 274 A MSE 269 1_555 A N ARG 275 A ARG 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 A C ALA 280 A ALA 275 1_555 A N MSE 281 A MSE 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 A C MSE 281 A MSE 276 1_555 A N ALA 282 A ALA 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale13 A C SER 295 A SER 290 1_555 A N MSE 296 A MSE 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 A C MSE 296 A MSE 291 1_555 A N ARG 297 A ARG 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale15 A C PRO 333 A PRO 328 1_555 A N MSE 334 A MSE 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale16 A C MSE 334 A MSE 329 1_555 A N GLY 335 A GLY 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale17 A C ALA 342 A ALA 337 1_555 A N MSE 343 A MSE 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 A C MSE 343 A MSE 338 1_555 A N LEU 344 A LEU 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale19 A C GLY 354 A GLY 349 1_555 A N MSE 355 A MSE 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale20 A C MSE 355 A MSE 350 1_555 A N SER 356 A SER 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale21 A C THR 364 A THR 359 1_555 A N MSE 365 A MSE 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale22 A C MSE 365 A MSE 360 1_555 A N ALA 366 A ALA 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale23 A C GLN 370 A GLN 365 1_555 A N MSE 371 A MSE 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale24 A C MSE 371 A MSE 366 1_555 A N PHE 372 A PHE 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale25 A C TYR 490 A TYR 485 1_555 A N MSE 491 A MSE 486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale26 A C MSE 491 A MSE 486 1_555 A N THR 492 A THR 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale27 A C GLY 626 A GLY 621 1_555 A N MSE 627 A MSE 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale28 A C MSE 627 A MSE 622 1_555 A N PRO 628 A PRO 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale29 A C LEU 681 A LEU 676 1_555 A N MSE 682 A MSE 677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale30 A C MSE 682 A MSE 677 1_555 A N VAL 683 A VAL 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale31 A C ARG 695 A ARG 690 1_555 A N MSE 696 A MSE 691 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale32 A C MSE 696 A MSE 691 1_555 A N GLY 697 A GLY 692 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale33 A C VAL 725 A VAL 720 1_555 A N MSE 726 A MSE 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale34 A C MSE 726 A MSE 721 1_555 A N GLY 727 A GLY 722 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale35 A C ALA 879 A ALA 874 1_555 A N MSE 880 A MSE 875 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale36 A C MSE 880 A MSE 875 1_555 A N ALA 881 A ALA 876 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale37 A C ALA 929 A ALA 924 1_555 A N MSE 930 A MSE 925 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale38 A C MSE 930 A MSE 925 1_555 A N VAL 931 A VAL 926 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A NE2 HIS 57 A HIS 52 1_555 B NI NI . A NI 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc2 A NE2 HIS 103 A HIS 98 1_555 B NI NI . A NI 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc3 A OD2 ASP 104 A ASP 99 1_555 B NI NI . A NI 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc4 A OD1 ASP 104 A ASP 99 1_555 C NI NI . A NI 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc5 A NE2 HIS 143 A HIS 138 1_555 C NI NI . A NI 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc6 A NE2 HIS 176 A HIS 171 1_555 C NI NI . A NI 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc7 A NE2 HIS 177 A HIS 172 1_555 C NI NI . A NI 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc8 A OD1 ASP 242 A ASP 237 1_555 B NI NI . A NI 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc9 E MG MG . A MG 1004 1_555 F O3G DTP . A DTP 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc10 E MG MG . A MG 1004 1_555 F O1B DTP . A DTP 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc11 E MG MG . A MG 1004 1_555 G O HOH . A HOH 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? # _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 4Q2D _atom_sites.fract_transf_matrix[1][1] 0.009462 _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] 0.004725 _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] 0.00959 _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 NI A 1 1001 1 NI NI . C 2 NI A 1 1002 2 NI NI . D 2 NI A 1 1003 3 NI NI . E 3 MG A 1 1004 5 MG MG . F 4 DTP A 1 1005 1 DTP DTP . G 5 HOH A 1 1101 1 HOH HOH . G 5 HOH A 2 1102 2 HOH HOH . G 5 HOH A 3 1103 3 HOH HOH . G 5 HOH A 4 1104 4 HOH HOH . G 5 HOH A 5 1105 5 HOH HOH . G 5 HOH A 6 1106 6 HOH HOH . G 5 HOH A 7 1107 7 HOH HOH . G 5 HOH A 8 1108 8 HOH HOH . G 5 HOH A 9 1109 9 HOH HOH . G 5 HOH A 10 1110 10 HOH HOH . G 5 HOH A 11 1111 11 HOH HOH . G 5 HOH A 12 1112 12 HOH HOH . G 5 HOH A 13 1113 13 HOH HOH . G 5 HOH A 14 1114 14 HOH HOH . G 5 HOH A 15 1115 15 HOH HOH . G 5 HOH A 16 1116 16 HOH HOH . G 5 HOH A 17 1117 17 HOH HOH . G 5 HOH A 18 1118 18 HOH HOH . G 5 HOH A 19 1119 19 HOH HOH . G 5 HOH A 20 1120 20 HOH HOH . G 5 HOH A 21 1121 21 HOH HOH . G 5 HOH A 22 1122 22 HOH HOH . G 5 HOH A 23 1123 23 HOH HOH . G 5 HOH A 24 1124 24 HOH HOH . G 5 HOH A 25 1125 25 HOH HOH . G 5 HOH A 26 1126 26 HOH HOH . G 5 HOH A 27 1127 28 HOH HOH . G 5 HOH A 28 1128 29 HOH HOH . G 5 HOH A 29 1129 30 HOH HOH . G 5 HOH A 30 1130 31 HOH HOH . G 5 HOH A 31 1131 32 HOH HOH . G 5 HOH A 32 1132 33 HOH HOH . G 5 HOH A 33 1133 34 HOH HOH . G 5 HOH A 34 1134 35 HOH HOH . G 5 HOH A 35 1135 36 HOH HOH . G 5 HOH A 36 1136 37 HOH HOH . G 5 HOH A 37 1137 38 HOH HOH . G 5 HOH A 38 1138 39 HOH HOH . G 5 HOH A 39 1139 40 HOH HOH . G 5 HOH A 40 1140 41 HOH HOH . G 5 HOH A 41 1141 42 HOH HOH . G 5 HOH A 42 1142 43 HOH HOH . G 5 HOH A 43 1143 44 HOH HOH . G 5 HOH A 44 1144 45 HOH HOH . G 5 HOH A 45 1145 46 HOH HOH . G 5 HOH A 46 1146 47 HOH HOH . G 5 HOH A 47 1147 48 HOH HOH . G 5 HOH A 48 1148 49 HOH HOH . G 5 HOH A 49 1149 50 HOH HOH . G 5 HOH A 50 1150 51 HOH HOH . G 5 HOH A 51 1151 52 HOH HOH . G 5 HOH A 52 1152 53 HOH HOH . G 5 HOH A 53 1153 54 HOH HOH . G 5 HOH A 54 1154 55 HOH HOH . G 5 HOH A 55 1155 56 HOH HOH . G 5 HOH A 56 1156 57 HOH HOH . G 5 HOH A 57 1157 58 HOH HOH . G 5 HOH A 58 1158 59 HOH HOH . G 5 HOH A 59 1159 60 HOH HOH . G 5 HOH A 60 1160 61 HOH HOH . G 5 HOH A 61 1161 62 HOH HOH . G 5 HOH A 62 1162 63 HOH HOH . G 5 HOH A 63 1163 64 HOH HOH . G 5 HOH A 64 1164 65 HOH HOH . G 5 HOH A 65 1165 66 HOH HOH . G 5 HOH A 66 1166 67 HOH HOH . G 5 HOH A 67 1167 68 HOH HOH . G 5 HOH A 68 1168 69 HOH HOH . G 5 HOH A 69 1169 70 HOH HOH . G 5 HOH A 70 1170 71 HOH HOH . G 5 HOH A 71 1171 72 HOH HOH . G 5 HOH A 72 1172 73 HOH HOH . G 5 HOH A 73 1173 75 HOH HOH . G 5 HOH A 74 1174 76 HOH HOH . G 5 HOH A 75 1175 77 HOH HOH . G 5 HOH A 76 1176 78 HOH HOH . G 5 HOH A 77 1177 79 HOH HOH . G 5 HOH A 78 1178 80 HOH HOH . G 5 HOH A 79 1179 81 HOH HOH . G 5 HOH A 80 1180 82 HOH HOH . G 5 HOH A 81 1181 83 HOH HOH . G 5 HOH A 82 1182 84 HOH HOH . G 5 HOH A 83 1183 85 HOH HOH . G 5 HOH A 84 1184 86 HOH HOH . G 5 HOH A 85 1185 87 HOH HOH . G 5 HOH A 86 1186 88 HOH HOH . G 5 HOH A 87 1187 89 HOH HOH . G 5 HOH A 88 1188 91 HOH HOH . G 5 HOH A 89 1189 93 HOH HOH . G 5 HOH A 90 1190 94 HOH HOH . G 5 HOH A 91 1191 95 HOH HOH . G 5 HOH A 92 1192 96 HOH HOH . G 5 HOH A 93 1193 97 HOH HOH . G 5 HOH A 94 1194 98 HOH HOH . G 5 HOH A 95 1195 99 HOH HOH . G 5 HOH A 96 1196 100 HOH HOH . G 5 HOH A 97 1197 101 HOH HOH . G 5 HOH A 98 1198 102 HOH HOH . G 5 HOH A 99 1199 103 HOH HOH . G 5 HOH A 100 1200 104 HOH HOH . G 5 HOH A 101 1201 105 HOH HOH . G 5 HOH A 102 1202 106 HOH HOH . G 5 HOH A 103 1203 107 HOH HOH . G 5 HOH A 104 1204 108 HOH HOH . G 5 HOH A 105 1205 109 HOH HOH . G 5 HOH A 106 1206 110 HOH HOH . G 5 HOH A 107 1207 111 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 2 _atom_site.Cartn_x -35.358 _atom_site.Cartn_y 45.251 _atom_site.Cartn_z 12.238 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 39.95 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 1003 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #