data_5YKO # _model_server_result.job_id bpVLtsQc-mBKQjXQEQx77g _model_server_result.datetime_utc '2024-11-05 00:19:19' _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 5yko # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":800}' # _entry.id 5YKO # _exptl.entry_id 5YKO _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 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 5YKO _cell.length_a 68.639 _cell.length_b 100.113 _cell.length_c 109.405 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YKO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 3 _struct_asym.id C _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 B C THR 3 P THR 3 1_555 B N M3L 4 P M3L 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 B C M3L 4 P M3L 4 1_555 B N GLN 5 P GLN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? metalc ? metalc1 A NE2 HIS 276 A HIS 309 1_555 C NI NI . A NI 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc2 A OE1 GLU 278 A GLU 311 1_555 C NI NI . A NI 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc3 A NE2 HIS 364 A HIS 397 1_555 C NI NI . A NI 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc4 A SG CYS 486 A CYS 519 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc5 A SG CYS 489 A CYS 522 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc6 A SG CYS 500 A CYS 533 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc7 A SG CYS 502 A CYS 535 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc8 A SG CYS 509 A CYS 542 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc9 A SG CYS 517 A CYS 550 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc10 C NI NI . A NI 800 1_555 F O2' OGA . A OGA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc11 C NI NI . A NI 800 1_555 F O1 OGA . A OGA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? # _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 5YKO _atom_sites.fract_transf_matrix[1][1] 0.014569 _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] 0.009989 _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] 0.00914 _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 3 NI A 1 800 800 NI NI . D 4 ZN A 1 801 801 ZN ZN . E 4 ZN A 1 802 802 ZN ZN . F 5 OGA A 1 803 803 OGA OGA . # _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 C _atom_site.label_entity_id 3 _atom_site.Cartn_x 27.081 _atom_site.Cartn_y -9.505 _atom_site.Cartn_z -14.625 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 73.85 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 800 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 1 #