data_1NYI # _model_server_result.job_id jcDl95PvTz22RNCs_V3Zzw _model_server_result.datetime_utc '2025-02-27 08:15:49' _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 1nyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2}' # _entry.id 1NYI # _exptl.entry_id 1NYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.933 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'COBALT (II) ION' _entity.pdbx_number_of_molecules 4 _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 1NYI _cell.length_a 65.639 _cell.length_b 65.639 _cell.length_c 137.475 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NYI _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 ? 3 C N N ? 3 E N N ? 3 F N N ? 3 G 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 covale ? covale1 A P G 1 A G 11 1_555 D O5' 5GP . A 5GP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.579 ? metalc ? metalc1 A O4 U 10 A U 20 1_555 G CO CO . B CO 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc2 G CO CO . B CO 4 1_555 B O2' U 18 B U 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.784 ? hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 11 1_555 B N3 C 24 B C 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 11 1_555 B O2 C 24 B C 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 11 1_555 B N4 C 24 B C 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 U 2 A U 12 1_555 B N1 A 23 B A 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 U 2 A U 12 1_555 B N6 A 23 B A 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 G 3 A G 13 1_555 B N3 C 22 B C 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 G 3 A G 13 1_555 B O2 C 22 B C 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 G 3 A G 13 1_555 B N4 C 22 B C 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 G 4 A G 14 1_555 B N3 C 21 B C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 G 4 A G 14 1_555 B O2 C 21 B C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 G 4 A G 14 1_555 B N4 C 21 B C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 U 5 A U 15 1_555 B N1 A 20 B A 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O4 U 5 A U 15 1_555 B N6 A 20 B A 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-C MISPAIR' hydrog14 A N3 C 6 A C 16 1_555 B N4 C 19 B C 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog15 A O2 U 10 A U 20 1_555 B N6 A 6 B A 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog16 A N2 G 11 A G 21 1_555 B N7 A 5 B A 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog17 A N3 G 11 A G 21 1_555 B N6 A 5 B A 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog18 A N6 A 12 A A 22 1_555 B N3 G 4 B G 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog19 A N7 A 12 A A 22 1_555 B N2 G 4 B G 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 G 13 A G 23 1_555 B N3 C 3 B C 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 G 13 A G 23 1_555 B O2 C 3 B C 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 G 13 A G 23 1_555 B N4 C 3 B C 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 G 14 A G 24 1_555 B N3 C 2 B C 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N2 G 14 A G 24 1_555 B O2 C 2 B C 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A O6 G 14 A G 24 1_555 B N4 C 2 B C 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N3 C 15 A C 25 1_555 B N1 G 1 B G 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N4 C 15 A C 25 1_555 B O6 G 1 B G 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O2 C 15 A C 25 1_555 B N2 G 1 B G 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog29 B N6 A 7 B A 108 1_555 B O4 U 18 B U 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N3 C 8 B C 109 1_555 B N1 G 17 B G 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N4 C 8 B C 109 1_555 B O6 G 17 B G 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B O2 C 8 B C 109 1_555 B N2 G 17 B G 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N3 U 9 B U 110 1_555 B N1 A 16 B A 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B O4 U 9 B U 110 1_555 B N6 A 16 B A 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N3 C 10 B C 111 1_555 B N1 G 15 B G 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B N4 C 10 B C 111 1_555 B O6 G 15 B G 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B O2 C 10 B C 111 1_555 B N2 G 15 B G 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog38 B N2 G 11 B G 112 1_555 B N7 A 14 B A 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Co 2' _chem_comp.formula_weight 58.933 _chem_comp.id CO _chem_comp.mon_nstd_flag . _chem_comp.name 'COBALT (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1NYI _atom_sites.fract_transf_matrix[1][1] 0.015235 _atom_sites.fract_transf_matrix[1][2] 0.008796 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017592 _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] 0.007274 _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 CO A 1 2 2 CO CO . D 4 5GP A 1 500 500 5GP GUA . E 3 CO B 1 1 1 CO CO . F 3 CO B 1 3 3 CO CO . G 3 CO B 1 4 4 CO CO . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CO _atom_site.label_atom_id CO _atom_site.label_comp_id CO _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 37.939 _atom_site.Cartn_y 6.13 _atom_site.Cartn_z 21.129 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 72.82 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CO _atom_site.auth_comp_id CO _atom_site.auth_seq_id 2 _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 16 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #