data_3DE9
#
_model_server_result.job_id            NqGT-A0pwX3UTSrijfbCIA 
_model_server_result.datetime_utc      '2024-11-24 22:43:05' 
_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          3de9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":109}' 
#
_entry.id    3DE9 
#
_exptl.entry_id    3DE9 
_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         120 
_cell.entry_id            3DE9 
_cell.length_a            51.042 
_cell.length_b            51.042 
_cell.length_c            121.971 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DE9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -25.521 -44.203669 0 
3 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 25.521 -44.203669 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
metalc ? metalc1 A N ALA 1 A ALA 1 1_555 D NI NI . A NI 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc2 A O ALA 1 A ALA 1 1_555 D NI NI . A NI 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc3 A SD MET 7 A MET 7 1_555 E FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc4 A NE2 HIS 59 A HIS 59 1_555 B NI NI . A NI 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc5 A NE2 HIS 63 A HIS 63 1_555 B NI NI . A NI 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc6 A NE2 HIS 73 A HIS 73 1_555 C NI NI . A NI 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc7 A NE2 HIS 77 A HIS 77 1_555 C NI NI . A NI 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc8 A NE2 HIS 102 A HIS 102 1_555 E FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
#
_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                     3DE9 
_atom_sites.fract_transf_matrix[1][1]    0.019592 
_atom_sites.fract_transf_matrix[1][2]    0.011311 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022623 
_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]    0.008199 
_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 1 107 1 NI NI . 
C 2 NI A 1 108 2 NI NI . 
D 2 NI A 1 109 3 NI NI . 
E 3 HEM A 1 150 150 HEM HEM . 
F 4 HOH A 1 151 1 HOH HOH . 
F 4 HOH A 2 152 2 HOH HOH . 
F 4 HOH A 3 153 3 HOH HOH . 
F 4 HOH A 4 154 4 HOH HOH . 
F 4 HOH A 5 155 5 HOH HOH . 
F 4 HOH A 6 156 6 HOH HOH . 
F 4 HOH A 7 157 7 HOH HOH . 
F 4 HOH A 8 158 8 HOH HOH . 
F 4 HOH A 9 159 9 HOH HOH . 
F 4 HOH A 10 160 10 HOH HOH . 
F 4 HOH A 11 161 11 HOH HOH . 
F 4 HOH A 12 162 12 HOH HOH . 
F 4 HOH A 13 163 13 HOH HOH . 
F 4 HOH A 14 164 14 HOH HOH . 
F 4 HOH A 15 165 15 HOH HOH . 
F 4 HOH A 16 166 16 HOH HOH . 
F 4 HOH A 17 167 17 HOH HOH . 
F 4 HOH A 18 168 18 HOH HOH . 
F 4 HOH A 19 169 19 HOH HOH . 
F 4 HOH A 20 170 20 HOH HOH . 
F 4 HOH A 21 171 21 HOH HOH . 
F 4 HOH A 22 172 22 HOH HOH . 
F 4 HOH A 23 173 23 HOH HOH . 
F 4 HOH A 24 174 24 HOH HOH . 
F 4 HOH A 25 175 25 HOH HOH . 
F 4 HOH A 26 176 26 HOH HOH . 
F 4 HOH A 27 177 27 HOH HOH . 
F 4 HOH A 28 178 28 HOH HOH . 
F 4 HOH A 29 179 29 HOH HOH . 
F 4 HOH A 30 180 30 HOH HOH . 
F 4 HOH A 31 181 31 HOH HOH . 
F 4 HOH A 32 182 32 HOH HOH . 
F 4 HOH A 33 183 33 HOH HOH . 
F 4 HOH A 34 184 34 HOH HOH . 
F 4 HOH A 35 185 35 HOH HOH . 
F 4 HOH A 36 186 36 HOH HOH . 
F 4 HOH A 37 187 37 HOH HOH . 
F 4 HOH A 38 188 38 HOH HOH . 
F 4 HOH A 39 189 39 HOH HOH . 
F 4 HOH A 40 190 40 HOH HOH . 
F 4 HOH A 41 191 41 HOH HOH . 
F 4 HOH A 42 192 42 HOH HOH . 
F 4 HOH A 43 193 43 HOH HOH . 
F 4 HOH A 44 194 44 HOH HOH . 
F 4 HOH A 45 195 45 HOH HOH . 
F 4 HOH A 46 196 46 HOH HOH . 
F 4 HOH A 47 197 47 HOH HOH . 
F 4 HOH A 48 198 48 HOH HOH . 
F 4 HOH A 49 199 49 HOH HOH . 
F 4 HOH A 50 200 50 HOH HOH . 
F 4 HOH A 51 201 51 HOH HOH . 
F 4 HOH A 52 202 52 HOH HOH . 
F 4 HOH A 53 203 53 HOH HOH . 
F 4 HOH A 54 204 54 HOH HOH . 
F 4 HOH A 55 205 55 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               -13.08 
_atom_site.Cartn_y               -13.613 
_atom_site.Cartn_z               -3.541 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        67.02 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           109 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           213 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#