data_3OD2 # _model_server_result.job_id kYAT1wYRIPaukomnlKS6HA _model_server_result.datetime_utc '2024-10-18 15:29:16' _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 3od2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":139}' # _entry.id 3OD2 # _exptl.entry_id 3OD2 _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 11 _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 120 _cell.entry_id 3OD2 _cell.length_a 50.735 _cell.length_b 50.735 _cell.length_c 183.114 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OD2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N 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 metalc ? metalc1 A O MET 1 A MET 1 1_555 D NI NI . A NI 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc2 A NE2 HIS 78 A HIS 78 1_555 F NI NI . A NI 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc3 A NE2 HIS 79 A HIS 79 1_555 G NI NI . A NI 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc4 A NE2 HIS 87 A HIS 87 1_555 C NI NI . A NI 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc5 A ND1 HIS 89 A HIS 89 1_555 C NI NI . A NI 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc6 A SG CYS 95 A CYS 95 1_555 C NI NI . A NI 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc7 A NE2 HIS 110 A HIS 110 1_555 F NI NI . A NI 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc8 A OD2 ASP 114 A ASP 114 1_555 F NI NI . A NI 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc9 A NE2 HIS 123 A HIS 123 1_555 H NI NI . A NI 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc10 A NE2 HIS 125 A HIS 125 1_555 E NI NI . A NI 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc11 D NI NI . A NI 135 1_555 O O HOH . A HOH 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc12 D NI NI . A NI 135 1_555 O O HOH . A HOH 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc13 D NI NI . A NI 135 1_555 P O HOH . B HOH 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc14 D NI NI . A NI 135 1_555 P O HOH . B HOH 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc15 E NI NI . A NI 136 1_555 O O HOH . A HOH 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc16 E NI NI . A NI 136 1_555 O O HOH . A HOH 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc17 E NI NI . A NI 136 1_555 B NE2 HIS 125 B HIS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc18 G NI NI . A NI 138 1_555 O O HOH . A HOH 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc19 G NI NI . A NI 138 1_555 O O HOH . A HOH 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc20 G NI NI . A NI 138 1_555 O O HOH . A HOH 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.855 ? metalc ? metalc21 H NI NI . A NI 139 1_555 O O HOH . A HOH 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc22 H NI NI . A NI 139 1_555 O O HOH . A HOH 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc23 H NI NI . A NI 139 1_555 P O HOH . B HOH 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc24 O O HOH . A HOH 157 1_555 N NI NI . B NI 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc25 O O HOH . A HOH 158 1_555 N NI NI . B NI 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc26 O O HOH . A HOH 160 1_555 L NI NI . B NI 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc27 O O HOH . A HOH 165 1_555 L NI NI . B NI 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc28 B O MET 1 B MET 1 1_555 N NI NI . B NI 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc29 B N MET 1 B MET 1 1_555 N NI NI . B NI 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc30 B NE2 HIS 78 B HIS 78 1_555 K NI NI . B NI 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc31 B NE2 HIS 79 B HIS 79 1_555 M NI NI . B NI 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc32 B NE2 HIS 87 B HIS 87 1_555 J NI NI . B NI 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc33 B ND1 HIS 89 B HIS 89 1_555 J NI NI . B NI 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.864 ? metalc ? metalc34 B SG CYS 95 B CYS 95 1_555 J NI NI . B NI 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc35 B NE2 HIS 110 B HIS 110 1_555 K NI NI . B NI 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc36 B OD2 ASP 114 B ASP 114 1_555 K NI NI . B NI 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc37 B NE2 HIS 123 B HIS 123 1_555 L NI NI . B NI 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc38 K NI NI . B NI 136 1_555 P O HOH . B HOH 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? metalc ? metalc39 K NI NI . B NI 136 1_555 P O HOH . B HOH 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc40 K NI NI . B NI 136 1_555 P O HOH . B HOH 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc41 L NI NI . B NI 137 1_555 P O HOH . B HOH 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc42 L NI NI . B NI 137 1_555 P O HOH . B HOH 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc43 M NI NI . B NI 138 1_555 P O HOH . B HOH 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc44 M NI NI . B NI 138 1_555 P O HOH . B HOH 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc45 M NI NI . B NI 138 1_555 P O HOH . B HOH 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc46 M NI NI . B NI 138 1_555 P O HOH . B HOH 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc47 N NI NI . B NI 139 1_555 P O HOH . B HOH 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc48 N NI NI . B NI 139 1_555 P O HOH . B HOH 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? # _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 3OD2 _atom_sites.fract_transf_matrix[1][1] 0.01971 _atom_sites.fract_transf_matrix[1][2] 0.01138 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022759 _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] 0.005461 _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 C 2 NI A 1 134 2 NI NI . D 2 NI A 1 135 4 NI NI . E 2 NI A 1 136 5 NI NI . F 2 NI A 1 137 7 NI NI . G 2 NI A 1 138 8 NI NI . H 2 NI A 1 139 10 NI NI . I 3 3CM B 1 134 1 3CM 3CM . J 2 NI B 1 135 1 NI NI . K 2 NI B 1 136 3 NI NI . L 2 NI B 1 137 6 NI NI . M 2 NI B 1 138 9 NI NI . N 2 NI B 1 139 11 NI NI . O 4 HOH A 1 140 2 HOH HOH . O 4 HOH A 2 141 3 HOH HOH . O 4 HOH A 3 142 4 HOH HOH . O 4 HOH A 4 143 5 HOH HOH . O 4 HOH A 5 144 6 HOH HOH . O 4 HOH A 6 145 7 HOH HOH . O 4 HOH A 7 146 8 HOH HOH . O 4 HOH A 8 147 10 HOH HOH . O 4 HOH A 9 148 11 HOH HOH . O 4 HOH A 10 149 17 HOH HOH . O 4 HOH A 11 150 18 HOH HOH . O 4 HOH A 12 152 23 HOH HOH . O 4 HOH A 13 153 25 HOH HOH . O 4 HOH A 14 154 31 HOH HOH . O 4 HOH A 15 155 32 HOH HOH . O 4 HOH A 16 156 34 HOH HOH . O 4 HOH A 17 157 35 HOH HOH . O 4 HOH A 18 158 38 HOH HOH . O 4 HOH A 19 159 44 HOH HOH . O 4 HOH A 20 160 45 HOH HOH . O 4 HOH A 21 161 46 HOH HOH . O 4 HOH A 22 162 47 HOH HOH . O 4 HOH A 23 163 48 HOH HOH . O 4 HOH A 24 164 50 HOH HOH . O 4 HOH A 25 165 55 HOH HOH . O 4 HOH A 26 166 57 HOH HOH . O 4 HOH A 27 167 58 HOH HOH . O 4 HOH A 28 168 59 HOH HOH . O 4 HOH A 29 169 60 HOH HOH . O 4 HOH A 30 170 61 HOH HOH . O 4 HOH A 31 171 62 HOH HOH . P 4 HOH B 1 140 1 HOH HOH . P 4 HOH B 2 141 9 HOH HOH . P 4 HOH B 3 142 12 HOH HOH . P 4 HOH B 4 143 13 HOH HOH . P 4 HOH B 5 144 14 HOH HOH . P 4 HOH B 6 145 15 HOH HOH . P 4 HOH B 7 146 16 HOH HOH . P 4 HOH B 8 147 20 HOH HOH . P 4 HOH B 9 148 21 HOH HOH . P 4 HOH B 10 149 22 HOH HOH . P 4 HOH B 11 150 24 HOH HOH . P 4 HOH B 12 151 19 HOH HOH . P 4 HOH B 13 152 27 HOH HOH . P 4 HOH B 14 153 28 HOH HOH . P 4 HOH B 15 154 29 HOH HOH . P 4 HOH B 16 155 30 HOH HOH . P 4 HOH B 17 156 33 HOH HOH . P 4 HOH B 18 157 36 HOH HOH . P 4 HOH B 19 158 37 HOH HOH . P 4 HOH B 20 159 39 HOH HOH . P 4 HOH B 21 160 40 HOH HOH . P 4 HOH B 22 161 41 HOH HOH . P 4 HOH B 23 162 42 HOH HOH . P 4 HOH B 24 163 43 HOH HOH . P 4 HOH B 25 164 49 HOH HOH . P 4 HOH B 26 165 51 HOH HOH . P 4 HOH B 27 166 52 HOH HOH . P 4 HOH B 28 167 53 HOH HOH . P 4 HOH B 29 168 54 HOH HOH . P 4 HOH B 30 169 56 HOH HOH . P 4 HOH B 31 170 26 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 H _atom_site.label_entity_id 2 _atom_site.Cartn_x -2.457 _atom_site.Cartn_y 30.75 _atom_site.Cartn_z 6.028 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 176.56 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 139 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #