data_3DI5 # _model_server_result.job_id GpwBeHDbGsQp2KTHKcjtpw _model_server_result.datetime_utc '2024-10-20 00:37:21' _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 3di5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":168}' # _entry.id 3DI5 # _exptl.entry_id 3DI5 _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 3DI5 _cell.length_a 78.12 _cell.length_b 84.19 _cell.length_c 50.32 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DI5 _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 _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 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 covale ? covale1 A C MSE 2 A MSE 1 1_555 A N TYR 3 A TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 A C LYS 22 A LYS 21 1_555 A N MSE 23 A MSE 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C MSE 23 A MSE 22 1_555 A N LEU 24 A LEU 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale4 A C PRO 115 A PRO 114 1_555 A N MSE 116 A MSE 115 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C PRO 115 A PRO 114 1_555 A N MSE 116 A MSE 115 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 116 A MSE 115 1_555 A N PRO 117 A PRO 116 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale7 A C MSE 116 A MSE 115 1_555 A N PRO 117 A PRO 116 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale8 A C LEU 122 A LEU 121 1_555 A N MSE 123 A MSE 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale9 A C MSE 123 A MSE 122 1_555 A N THR 124 A THR 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C GLN 135 A GLN 134 1_555 A N MSE 136 A MSE 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale11 A C MSE 136 A MSE 135 1_555 A N THR 137 A THR 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale12 A C LEU 139 A LEU 138 1_555 A N MSE 140 A MSE 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 A C MSE 140 A MSE 139 1_555 A N ARG 141 A ARG 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A NE2 HIS 49 A HIS 48 1_555 B NI NI . A NI 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc2 A NE2 HIS 128 A HIS 127 1_555 B NI NI . A NI 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc3 A NE2 HIS 132 A HIS 131 1_555 B NI NI . A NI 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc4 B NI NI . A NI 168 1_555 C O HOH . A HOH 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc5 B NI NI . A NI 168 1_555 C O HOH . A HOH 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc6 B NI NI . A NI 168 1_555 C O HOH . A HOH 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? # _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 3DI5 _atom_sites.fract_transf_matrix[1][1] 0.012801 _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] 0.011878 _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] 0.019873 _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 1 168 1 NI NI . C 3 HOH A 1 169 2 HOH HOH . C 3 HOH A 2 170 3 HOH HOH . C 3 HOH A 3 171 4 HOH HOH . C 3 HOH A 4 172 5 HOH HOH . C 3 HOH A 5 173 6 HOH HOH . C 3 HOH A 6 174 7 HOH HOH . C 3 HOH A 7 175 8 HOH HOH . C 3 HOH A 8 176 9 HOH HOH . C 3 HOH A 9 177 10 HOH HOH . C 3 HOH A 10 178 11 HOH HOH . C 3 HOH A 11 179 12 HOH HOH . C 3 HOH A 12 180 13 HOH HOH . C 3 HOH A 13 181 14 HOH HOH . C 3 HOH A 14 182 15 HOH HOH . C 3 HOH A 15 183 16 HOH HOH . C 3 HOH A 16 184 17 HOH HOH . C 3 HOH A 17 185 18 HOH HOH . C 3 HOH A 18 186 19 HOH HOH . C 3 HOH A 19 187 20 HOH HOH . C 3 HOH A 20 188 21 HOH HOH . C 3 HOH A 21 189 22 HOH HOH . C 3 HOH A 22 190 23 HOH HOH . C 3 HOH A 23 191 24 HOH HOH . C 3 HOH A 24 192 25 HOH HOH . C 3 HOH A 25 193 26 HOH HOH . C 3 HOH A 26 194 27 HOH HOH . C 3 HOH A 27 195 28 HOH HOH . C 3 HOH A 28 196 29 HOH HOH . C 3 HOH A 29 197 30 HOH HOH . C 3 HOH A 30 198 31 HOH HOH . C 3 HOH A 31 199 32 HOH HOH . C 3 HOH A 32 200 33 HOH HOH . C 3 HOH A 33 201 34 HOH HOH . C 3 HOH A 34 202 35 HOH HOH . C 3 HOH A 35 203 36 HOH HOH . C 3 HOH A 36 204 37 HOH HOH . C 3 HOH A 37 205 38 HOH HOH . C 3 HOH A 38 206 39 HOH HOH . C 3 HOH A 39 207 40 HOH HOH . C 3 HOH A 40 208 41 HOH HOH . C 3 HOH A 41 209 42 HOH HOH . C 3 HOH A 42 210 43 HOH HOH . C 3 HOH A 43 211 44 HOH HOH . C 3 HOH A 44 212 45 HOH HOH . C 3 HOH A 45 213 46 HOH HOH . C 3 HOH A 46 214 47 HOH HOH . C 3 HOH A 47 215 48 HOH HOH . C 3 HOH A 48 216 49 HOH HOH . C 3 HOH A 49 217 50 HOH HOH . C 3 HOH A 50 218 51 HOH HOH . C 3 HOH A 51 219 52 HOH HOH . C 3 HOH A 52 220 53 HOH HOH . C 3 HOH A 53 221 54 HOH HOH . C 3 HOH A 54 222 55 HOH HOH . C 3 HOH A 55 223 56 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 26.305 _atom_site.Cartn_y 3.807 _atom_site.Cartn_z 15.121 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 54.28 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 168 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #