data_1SK3 # _model_server_result.job_id '_jcv9gYydfy6IbIFJSqLQg' _model_server_result.datetime_utc '2024-10-18 22:20:21' _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 1sk3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":21}' # _entry.id 1SK3 # _exptl.entry_id 1SK3 _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 2 _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 1SK3 _cell.length_a 102.632 _cell.length_b 102.632 _cell.length_c 41.496 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SK3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # 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 # 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 disulf ? disulf1 A SG CYS 2 A CYS 178 1_555 A SG CYS 124 A CYS 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 18 A CYS 194 1_555 A SG CYS 62 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 38 A CYS 214 1_555 A SG CYS 44 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc1 B NI NI . A NI 21 1_555 A O VAL 1 A VAL 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc2 B NI NI . A NI 21 1_555 A OD2 ASP 120 A ASP 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc3 B NI NI . A NI 21 1_555 E O HOH . A HOH 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc4 B NI NI . A NI 21 1_555 A N VAL 1 A VAL 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc5 B NI NI . A NI 21 1_555 A NE2 HIS 162 A HIS 338 6_764 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc6 C NI NI . A NI 22 1_555 A NE2 HIS 165 A HIS 341 6_764 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? # _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 1SK3 _atom_sites.fract_transf_matrix[1][1] 0.009744 _atom_sites.fract_transf_matrix[1][2] 0.005625 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011251 _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] 0.024099 _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 21 1 NI NI2 . C 2 NI A 1 22 2 NI NI2 . D 3 SO4 A 1 342 276 SO4 SO4 . E 4 HOH A 1 1 1 HOH HOH . E 4 HOH A 2 2 2 HOH HOH . E 4 HOH A 3 3 3 HOH HOH . E 4 HOH A 4 4 4 HOH HOH . E 4 HOH A 5 5 5 HOH HOH . E 4 HOH A 6 6 6 HOH HOH . E 4 HOH A 7 7 7 HOH HOH . E 4 HOH A 8 8 8 HOH HOH . E 4 HOH A 9 9 9 HOH HOH . E 4 HOH A 10 10 10 HOH HOH . E 4 HOH A 11 11 11 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 78.464 _atom_site.Cartn_y 48.447 _atom_site.Cartn_z 0.539 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 28.39 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 21 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #