data_6KH5 # _model_server_result.job_id 3MtEVWm84CNXbyY6qg_jdg _model_server_result.datetime_utc '2024-10-10 10:21:45' _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 6kh5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 6KH5 # _exptl.entry_id 6KH5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _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 90 _cell.entry_id 6KH5 _cell.length_a 118.533 _cell.length_b 118.533 _cell.length_c 118.533 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 207 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _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 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24 # 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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 118.533 118.533 0 3 'crystal symmetry operation' 3_654 -x+1,y,-z-1 -1 0 0 0 1 0 0 0 -1 118.533 0 -118.533 4 'crystal symmetry operation' 4_564 x,-y+1,-z-1 1 0 0 0 -1 0 0 0 -1 0 118.533 -118.533 5 'crystal symmetry operation' 5_654 z+1,x,y-1 0 0 1 1 0 0 0 1 0 118.533 0 -118.533 6 'crystal symmetry operation' 6_665 z+1,-x+1,-y 0 0 1 -1 0 0 0 -1 0 118.533 118.533 0 7 'crystal symmetry operation' 7_564 -z,-x+1,y-1 0 0 -1 -1 0 0 0 1 0 0 118.533 -118.533 8 'crystal symmetry operation' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 9 'crystal symmetry operation' 9_564 y,z+1,x-1 0 1 0 0 0 1 1 0 0 0 118.533 -118.533 10 'crystal symmetry operation' 10_665 -y+1,z+1,-x 0 -1 0 0 0 1 -1 0 0 118.533 118.533 0 11 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 12 'crystal symmetry operation' 12_654 -y+1,-z,x-1 0 -1 0 0 0 -1 1 0 0 118.533 0 -118.533 13 'crystal symmetry operation' 13_554 y,x,-z-1 0 1 0 1 0 0 0 0 -1 0 0 -118.533 14 'crystal symmetry operation' 14_664 -y+1,-x+1,-z-1 0 -1 0 -1 0 0 0 0 -1 118.533 118.533 -118.533 15 'crystal symmetry operation' 15_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 118.533 0 16 'crystal symmetry operation' 16_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 118.533 0 0 17 'crystal symmetry operation' 17_565 x,z+1,-y 1 0 0 0 0 1 0 -1 0 0 118.533 0 18 'crystal symmetry operation' 18_664 -x+1,z+1,y-1 -1 0 0 0 0 1 0 1 0 118.533 118.533 -118.533 19 'crystal symmetry operation' 19_655 -x+1,-z,-y -1 0 0 0 0 -1 0 -1 0 118.533 0 0 20 'crystal symmetry operation' 20_554 x,-z,y-1 1 0 0 0 0 -1 0 1 0 0 0 -118.533 21 'crystal symmetry operation' 21_655 z+1,y,-x 0 0 1 0 1 0 -1 0 0 118.533 0 0 22 'crystal symmetry operation' 22_664 z+1,-y+1,x-1 0 0 1 0 -1 0 1 0 0 118.533 118.533 -118.533 23 'crystal symmetry operation' 23_554 -z,y,x-1 0 0 -1 0 1 0 1 0 0 0 0 -118.533 24 'crystal symmetry operation' 24_565 -z,-y+1,-x 0 0 -1 0 -1 0 -1 0 0 0 118.533 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E 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 OE1 GLU 23 A GLU 24 1_555 B FE FE . A FE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc2 A OE1 GLU 58 A GLU 60 1_555 B FE FE . A FE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc3 A OE2 GLU 58 A GLU 60 1_555 B FE FE . A FE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc4 A OE2 GLU 136 A GLU 139 1_555 D NI NI . A NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc5 A OG SER 140 A SER 143 1_555 D NI NI . A NI 203 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc6 A ND1 HIS 157 A HIS 160 1_555 C NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc7 A NE2 HIS 157 A HIS 160 1_555 E NI NI . A NI 204 4_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc8 A O HIS 158 A HIS 161 1_555 E NI NI . A NI 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? # _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 6KH5 _atom_sites.fract_transf_matrix[1][1] 0.008436 _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] 0.008436 _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] 0.008436 _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 FE A 1 201 1 FE FE . C 3 NI A 1 202 1 NI NI . D 3 NI A 1 203 2 NI NI . E 3 NI A 1 204 3 NI NI . F 4 HOH A 1 301 47 HOH HOH . F 4 HOH A 2 302 11 HOH HOH . F 4 HOH A 3 303 15 HOH HOH . F 4 HOH A 4 304 18 HOH HOH . F 4 HOH A 5 305 17 HOH HOH . F 4 HOH A 6 306 23 HOH HOH . F 4 HOH A 7 307 29 HOH HOH . F 4 HOH A 8 308 52 HOH HOH . F 4 HOH A 9 309 12 HOH HOH . F 4 HOH A 10 310 54 HOH HOH . F 4 HOH A 11 311 44 HOH HOH . F 4 HOH A 12 312 2 HOH HOH . F 4 HOH A 13 313 16 HOH HOH . F 4 HOH A 14 314 1 HOH HOH . F 4 HOH A 15 315 48 HOH HOH . F 4 HOH A 16 316 9 HOH HOH . F 4 HOH A 17 317 13 HOH HOH . F 4 HOH A 18 318 19 HOH HOH . F 4 HOH A 19 319 22 HOH HOH . F 4 HOH A 20 320 21 HOH HOH . F 4 HOH A 21 321 7 HOH HOH . F 4 HOH A 22 322 53 HOH HOH . F 4 HOH A 23 323 24 HOH HOH . F 4 HOH A 24 324 31 HOH HOH . F 4 HOH A 25 325 3 HOH HOH . F 4 HOH A 26 326 27 HOH HOH . F 4 HOH A 27 327 6 HOH HOH . F 4 HOH A 28 328 43 HOH HOH . F 4 HOH A 29 329 10 HOH HOH . F 4 HOH A 30 330 20 HOH HOH . F 4 HOH A 31 331 42 HOH HOH . F 4 HOH A 32 332 40 HOH HOH . F 4 HOH A 33 333 28 HOH HOH . F 4 HOH A 34 334 8 HOH HOH . F 4 HOH A 35 335 14 HOH HOH . F 4 HOH A 36 336 46 HOH HOH . F 4 HOH A 37 337 26 HOH HOH . F 4 HOH A 38 338 33 HOH HOH . F 4 HOH A 39 339 37 HOH HOH . F 4 HOH A 40 340 39 HOH HOH . F 4 HOH A 41 341 5 HOH HOH . F 4 HOH A 42 342 49 HOH HOH . F 4 HOH A 43 343 36 HOH HOH . F 4 HOH A 44 344 50 HOH HOH . F 4 HOH A 45 345 25 HOH HOH . F 4 HOH A 46 346 41 HOH HOH . F 4 HOH A 47 347 51 HOH HOH . F 4 HOH A 48 348 45 HOH HOH . F 4 HOH A 49 349 57 HOH HOH . F 4 HOH A 50 350 58 HOH HOH . F 4 HOH A 51 351 34 HOH HOH . F 4 HOH A 52 352 35 HOH HOH . F 4 HOH A 53 353 56 HOH HOH . F 4 HOH A 54 354 38 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 3 _atom_site.Cartn_x 34.966 _atom_site.Cartn_y 48.238 _atom_site.Cartn_z -21.686 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 115.27 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 203 _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 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #