data_5LU3 # _model_server_result.job_id su-BHi0af1BmItyeq1pPRA _model_server_result.datetime_utc '2025-02-17 08:53:07' _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 5lu3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":104}' # _entry.id 5LU3 # _exptl.entry_id 5LU3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 1 _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 5LU3 _cell.length_a 56.703 _cell.length_b 56.703 _cell.length_c 66.738 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LU3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A OD1 ASP 7 A ASP 7 1_555 D CA CA . A CA 103 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.246 ? metalc ? metalc2 A OD1 ASP 23 A ASP 23 1_555 D CA CA . A CA 103 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.417 ? metalc ? metalc3 A OD1 ASP 24 A ASP 24 1_555 D CA CA . A CA 103 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.732 ? metalc ? metalc4 A OD1 ASP 24 A ASP 24 1_555 D CA CA . A CA 103 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.565 ? metalc ? metalc5 A OD2 ASP 24 A ASP 24 1_555 D CA CA . A CA 103 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.733 ? metalc ? metalc6 D CA CA . A CA 103 1_555 G O HOH . A HOH 231 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.168 ? metalc ? metalc7 D CA CA . A CA 103 1_555 G O HOH . A HOH 231 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc8 D CA CA . A CA 103 1_555 G O HOH . A HOH 249 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.189 ? metalc ? metalc9 D CA CA . A CA 103 1_555 G O HOH . A HOH 249 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc10 D CA CA . A CA 103 1_555 G O HOH . A HOH 270 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc11 D CA CA . A CA 103 1_555 G O HOH . A HOH 270 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.285 ? # _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 5LU3 _atom_sites.fract_transf_matrix[1][1] 0.017636 _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] 0.017636 _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] 0.014984 _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 2NV A 1 101 2 2NV 2NV . C 3 SSN A 1 102 3 SSN SSN . D 4 CA A 1 103 1 CA CA . E 5 NI A 1 104 1 NI NI . F 6 FMT A 1 105 2 FMT FMT . G 7 HOH A 1 201 45 HOH HOH . G 7 HOH A 2 202 57 HOH HOH . G 7 HOH A 3 203 124 HOH HOH . G 7 HOH A 4 204 196 HOH HOH . G 7 HOH A 5 205 96 HOH HOH . G 7 HOH A 6 206 71 HOH HOH . G 7 HOH A 7 207 201 HOH HOH . G 7 HOH A 8 208 3 HOH HOH . G 7 HOH A 9 209 38 HOH HOH . G 7 HOH A 10 210 202 HOH HOH . G 7 HOH A 11 211 24 HOH HOH . G 7 HOH A 12 212 18 HOH HOH . G 7 HOH A 13 213 64 HOH HOH . G 7 HOH A 14 214 42 HOH HOH . G 7 HOH A 15 215 198 HOH HOH . G 7 HOH A 16 216 76 HOH HOH . G 7 HOH A 17 217 22 HOH HOH . G 7 HOH A 18 218 99 HOH HOH . G 7 HOH A 19 219 61 HOH HOH . G 7 HOH A 20 220 143 HOH HOH . G 7 HOH A 21 221 197 HOH HOH . G 7 HOH A 22 222 27 HOH HOH . G 7 HOH A 23 223 87 HOH HOH . G 7 HOH A 24 224 101 HOH HOH . G 7 HOH A 25 225 82 HOH HOH . G 7 HOH A 26 226 73 HOH HOH . G 7 HOH A 27 227 157 HOH HOH . G 7 HOH A 28 228 203 HOH HOH . G 7 HOH A 29 229 65 HOH HOH . G 7 HOH A 30 230 8 HOH HOH . G 7 HOH A 31 231 156 HOH HOH . G 7 HOH A 32 232 9 HOH HOH . G 7 HOH A 33 233 11 HOH HOH . G 7 HOH A 34 234 47 HOH HOH . G 7 HOH A 35 235 74 HOH HOH . G 7 HOH A 36 236 23 HOH HOH . G 7 HOH A 37 237 10 HOH HOH . G 7 HOH A 38 238 66 HOH HOH . G 7 HOH A 39 239 28 HOH HOH . G 7 HOH A 40 240 2 HOH HOH . G 7 HOH A 41 241 13 HOH HOH . G 7 HOH A 42 242 142 HOH HOH . G 7 HOH A 43 243 206 HOH HOH . G 7 HOH A 44 244 175 HOH HOH . G 7 HOH A 45 245 121 HOH HOH . G 7 HOH A 46 246 4 HOH HOH . G 7 HOH A 47 247 191 HOH HOH . G 7 HOH A 48 248 33 HOH HOH . G 7 HOH A 49 249 188 HOH HOH . G 7 HOH A 50 250 30 HOH HOH . G 7 HOH A 51 251 208 HOH HOH . G 7 HOH A 52 252 204 HOH HOH . G 7 HOH A 53 253 48 HOH HOH . G 7 HOH A 54 254 25 HOH HOH . G 7 HOH A 55 255 153 HOH HOH . G 7 HOH A 56 256 14 HOH HOH . G 7 HOH A 57 257 145 HOH HOH . G 7 HOH A 58 258 32 HOH HOH . G 7 HOH A 59 259 12 HOH HOH . G 7 HOH A 60 260 207 HOH HOH . G 7 HOH A 61 261 50 HOH HOH . G 7 HOH A 62 262 200 HOH HOH . G 7 HOH A 63 263 15 HOH HOH . G 7 HOH A 64 264 205 HOH HOH . G 7 HOH A 65 265 49 HOH HOH . G 7 HOH A 66 266 36 HOH HOH . G 7 HOH A 67 267 81 HOH HOH . G 7 HOH A 68 268 88 HOH HOH . G 7 HOH A 69 269 167 HOH HOH . G 7 HOH A 70 270 189 HOH HOH . G 7 HOH A 71 271 114 HOH HOH . G 7 HOH A 72 272 19 HOH HOH . G 7 HOH A 73 273 131 HOH HOH . G 7 HOH A 74 274 166 HOH HOH . G 7 HOH A 75 275 94 HOH HOH . G 7 HOH A 76 276 190 HOH HOH . G 7 HOH A 77 277 209 HOH HOH . G 7 HOH A 78 278 199 HOH HOH . G 7 HOH A 79 279 192 HOH HOH . G 7 HOH A 80 280 115 HOH HOH . G 7 HOH A 81 281 63 HOH HOH . G 7 HOH A 82 282 165 HOH HOH . G 7 HOH A 83 283 95 HOH HOH . G 7 HOH A 84 284 182 HOH HOH . G 7 HOH A 85 285 75 HOH HOH . G 7 HOH A 86 286 194 HOH HOH . G 7 HOH A 87 287 193 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 E _atom_site.label_entity_id 5 _atom_site.Cartn_x -23.019 _atom_site.Cartn_y -33.976 _atom_site.Cartn_z -16.788 _atom_site.occupancy 0.24 _atom_site.B_iso_or_equiv 20.74 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 104 _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 22 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 1 #