data_3HDP # _model_server_result.job_id rTBMBfR5ZBzt1CfCf5qCIQ _model_server_result.datetime_utc '2025-02-05 13:01:31' _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 3hdp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":129}' # _entry.id 3HDP # _exptl.entry_id 3HDP _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 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 3HDP _cell.length_a 70.269 _cell.length_b 70.269 _cell.length_c 66.589 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HDP _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 NE2 HIS 10 A HIS 5 1_555 B NI NI . A NI 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc2 A OE1 GLU 57 A GLU 52 1_555 B NI NI . A NI 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc3 A NE2 HIS 80 A HIS 75 1_555 B NI NI . A NI 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc4 A OE2 GLU 129 A GLU 124 1_555 B NI NI . A NI 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc5 B NI NI . A NI 129 1_555 C O HOH . A HOH 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc6 B NI NI . A NI 129 1_555 C O HOH . A HOH 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? # _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 3HDP _atom_sites.fract_transf_matrix[1][1] 0.014231 _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] 0.014231 _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] 0.015017 _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 1 129 129 NI NI . C 3 HOH A 1 1 1 HOH HOH . C 3 HOH A 2 130 130 HOH HOH . C 3 HOH A 3 132 132 HOH HOH . C 3 HOH A 4 133 133 HOH HOH . C 3 HOH A 5 134 134 HOH HOH . C 3 HOH A 6 135 135 HOH HOH . C 3 HOH A 7 137 137 HOH HOH . C 3 HOH A 8 138 138 HOH HOH . C 3 HOH A 9 139 139 HOH HOH . C 3 HOH A 10 140 140 HOH HOH . C 3 HOH A 11 141 141 HOH HOH . C 3 HOH A 12 143 143 HOH HOH . C 3 HOH A 13 144 144 HOH HOH . C 3 HOH A 14 145 145 HOH HOH . C 3 HOH A 15 146 146 HOH HOH . C 3 HOH A 16 147 147 HOH HOH . C 3 HOH A 17 149 149 HOH HOH . C 3 HOH A 18 150 150 HOH HOH . C 3 HOH A 19 151 151 HOH HOH . C 3 HOH A 20 152 152 HOH HOH . C 3 HOH A 21 153 153 HOH HOH . C 3 HOH A 22 154 154 HOH HOH . C 3 HOH A 23 155 155 HOH HOH . C 3 HOH A 24 156 156 HOH HOH . C 3 HOH A 25 157 157 HOH HOH . C 3 HOH A 26 158 158 HOH HOH . C 3 HOH A 27 159 159 HOH HOH . C 3 HOH A 28 160 160 HOH HOH . C 3 HOH A 29 161 161 HOH HOH . C 3 HOH A 30 162 162 HOH HOH . C 3 HOH A 31 163 163 HOH HOH . C 3 HOH A 32 164 164 HOH HOH . C 3 HOH A 33 165 165 HOH HOH . C 3 HOH A 34 166 166 HOH HOH . C 3 HOH A 35 167 167 HOH HOH . C 3 HOH A 36 168 168 HOH HOH . C 3 HOH A 37 169 169 HOH HOH . C 3 HOH A 38 170 170 HOH HOH . C 3 HOH A 39 171 171 HOH HOH . C 3 HOH A 40 172 172 HOH HOH . C 3 HOH A 41 173 173 HOH HOH . C 3 HOH A 42 174 174 HOH HOH . C 3 HOH A 43 175 175 HOH HOH . C 3 HOH A 44 176 176 HOH HOH . C 3 HOH A 45 177 177 HOH HOH . C 3 HOH A 46 178 178 HOH HOH . C 3 HOH A 47 179 179 HOH HOH . C 3 HOH A 48 180 180 HOH HOH . C 3 HOH A 49 181 181 HOH HOH . C 3 HOH A 50 182 182 HOH HOH . C 3 HOH A 51 183 183 HOH HOH . C 3 HOH A 52 184 184 HOH HOH . C 3 HOH A 53 185 185 HOH HOH . C 3 HOH A 54 186 186 HOH HOH . C 3 HOH A 55 187 187 HOH HOH . C 3 HOH A 56 188 188 HOH HOH . C 3 HOH A 57 190 190 HOH HOH . C 3 HOH A 58 191 191 HOH HOH . C 3 HOH A 59 194 194 HOH HOH . C 3 HOH A 60 195 195 HOH HOH . C 3 HOH A 61 196 196 HOH HOH . C 3 HOH A 62 197 197 HOH HOH . C 3 HOH A 63 198 198 HOH HOH . C 3 HOH A 64 199 199 HOH HOH . C 3 HOH A 65 200 200 HOH HOH . C 3 HOH A 66 201 201 HOH HOH . C 3 HOH A 67 202 202 HOH HOH . C 3 HOH A 68 203 203 HOH HOH . C 3 HOH A 69 204 204 HOH HOH . C 3 HOH A 70 205 205 HOH HOH . C 3 HOH A 71 206 206 HOH HOH . C 3 HOH A 72 207 207 HOH HOH . C 3 HOH A 73 208 208 HOH HOH . C 3 HOH A 74 209 209 HOH HOH . C 3 HOH A 75 210 210 HOH HOH . C 3 HOH A 76 211 211 HOH HOH . C 3 HOH A 77 212 212 HOH HOH . C 3 HOH A 78 213 213 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 B _atom_site.label_entity_id 2 _atom_site.Cartn_x 1.762 _atom_site.Cartn_y 16.025 _atom_site.Cartn_z -3.406 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 28.03 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 129 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #