data_7NJC # _model_server_result.job_id Yb1L0YuejYGbFZJOFfamOw _model_server_result.datetime_utc '2024-11-13 04:52:07' _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 7njc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":101}' # _entry.id 7NJC # _exptl.entry_id 7NJC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 281.268 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-methyladenosine _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 114.679 _cell.angle_beta 100.702 _cell.angle_gamma 97.653 _cell.entry_id 7NJC _cell.length_a 32.442 _cell.length_b 35.153 _cell.length_c 38.35 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NJC _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id P _struct_conn.ptnr1_label_comp_id C _struct_conn.ptnr1_label_seq_id 4 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id C _struct_conn.ptnr1_auth_seq_id 2 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id O3' _struct_conn.ptnr2_label_comp_id 6MD _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id 6MD _struct_conn.ptnr2_auth_seq_id 101 _struct_conn.ptnr2_symmetry 1_555 _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 1.55 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C11 H15 N5 O4' _chem_comp.formula_weight 281.268 _chem_comp.id 6MD _chem_comp.mon_nstd_flag . _chem_comp.name N-methyladenosine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C2 N1 6MD doub 1 n y C2 N3 6MD sing 2 n y N1 C6 6MD sing 3 n y N3 C4 6MD doub 4 n y CZ N6 6MD sing 5 n n C6 N6 6MD sing 6 n n C6 C5 6MD doub 7 n y C4 C5 6MD sing 8 n y C4 N9 6MD sing 9 n y C4' O4' 6MD sing 10 n n C4' C5' 6MD sing 11 n n C4' C3' 6MD sing 12 n n O4' C1' 6MD sing 13 n n C5 N7 6MD sing 14 n y C5' O5' 6MD sing 15 n n O3' C3' 6MD sing 16 n n C1' N9 6MD sing 17 n n C1' C2' 6MD sing 18 n n N9 C8 6MD sing 19 n y C3' C2' 6MD sing 20 n n C2' O2' 6MD sing 21 n n N7 C8 6MD doub 22 n y O5' H1 6MD sing 23 n n C5' H2 6MD sing 24 n n C5' H3 6MD sing 25 n n C4' H4 6MD sing 26 n n C3' H5 6MD sing 27 n n O3' H6 6MD sing 28 n n C2' H7 6MD sing 29 n n O2' H8 6MD sing 30 n n C1' H9 6MD sing 31 n n C8 H10 6MD sing 32 n n N6 H11 6MD sing 33 n n C2 H12 6MD sing 34 n n CZ H13 6MD sing 35 n n CZ H14 6MD sing 36 n n CZ H15 6MD sing 37 n n # _atom_sites.entry_id 7NJC _atom_sites.fract_transf_matrix[1][1] 0.030824 _atom_sites.fract_transf_matrix[1][2] 0.004142 _atom_sites.fract_transf_matrix[1][3] 0.00865 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028703 _atom_sites.fract_transf_matrix[2][3] 0.014631 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.029786 _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 TOE A 1 600 600 TOE PG4 . D 4 6MD B 1 101 1 6MD 6MD . E 5 HOH A 1 701 12 HOH HOH . E 5 HOH A 2 702 10 HOH HOH . E 5 HOH A 3 703 50 HOH HOH . E 5 HOH A 4 704 35 HOH HOH . E 5 HOH A 5 705 26 HOH HOH . E 5 HOH A 6 706 37 HOH HOH . E 5 HOH A 7 707 29 HOH HOH . E 5 HOH A 8 708 25 HOH HOH . E 5 HOH A 9 709 54 HOH HOH . E 5 HOH A 10 710 61 HOH HOH . E 5 HOH A 11 711 32 HOH HOH . E 5 HOH A 12 712 38 HOH HOH . E 5 HOH A 13 713 4 HOH HOH . E 5 HOH A 14 714 9 HOH HOH . E 5 HOH A 15 715 19 HOH HOH . E 5 HOH A 16 716 15 HOH HOH . E 5 HOH A 17 717 42 HOH HOH . E 5 HOH A 18 718 62 HOH HOH . E 5 HOH A 19 719 31 HOH HOH . E 5 HOH A 20 720 2 HOH HOH . E 5 HOH A 21 721 24 HOH HOH . E 5 HOH A 22 722 8 HOH HOH . E 5 HOH A 23 723 6 HOH HOH . E 5 HOH A 24 724 44 HOH HOH . E 5 HOH A 25 725 18 HOH HOH . E 5 HOH A 26 726 45 HOH HOH . E 5 HOH A 27 727 58 HOH HOH . E 5 HOH A 28 728 56 HOH HOH . E 5 HOH A 29 729 1 HOH HOH . E 5 HOH A 30 730 14 HOH HOH . E 5 HOH A 31 731 30 HOH HOH . E 5 HOH A 32 732 22 HOH HOH . E 5 HOH A 33 733 39 HOH HOH . E 5 HOH A 34 734 49 HOH HOH . E 5 HOH A 35 735 43 HOH HOH . E 5 HOH A 36 736 16 HOH HOH . E 5 HOH A 37 737 51 HOH HOH . E 5 HOH A 38 738 60 HOH HOH . E 5 HOH A 39 739 47 HOH HOH . E 5 HOH A 40 740 27 HOH HOH . E 5 HOH A 41 741 23 HOH HOH . E 5 HOH A 42 742 33 HOH HOH . E 5 HOH A 43 743 46 HOH HOH . E 5 HOH A 44 744 48 HOH HOH . E 5 HOH A 45 745 3 HOH HOH . E 5 HOH A 46 746 57 HOH HOH . E 5 HOH A 47 747 7 HOH HOH . E 5 HOH A 48 748 28 HOH HOH . E 5 HOH A 49 749 55 HOH HOH . E 5 HOH A 50 750 52 HOH HOH . E 5 HOH A 51 751 20 HOH HOH . E 5 HOH A 52 752 59 HOH HOH . E 5 HOH A 53 753 34 HOH HOH . E 5 HOH A 54 754 11 HOH HOH . E 5 HOH A 55 755 5 HOH HOH . E 5 HOH A 56 756 53 HOH HOH . E 5 HOH A 57 757 41 HOH HOH . E 5 HOH A 58 758 17 HOH HOH . E 5 HOH A 59 759 21 HOH HOH . E 5 HOH A 60 760 36 HOH HOH . E 5 HOH A 61 761 40 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O5' 6MD . . . D 4 -12.734 2.834 15.003 1 31.17 ? O5' 6MD 101 B 1 HETATM 2 C C5' 6MD . . . D 4 -12.621 3.807 16.044 1 20.52 ? C5' 6MD 101 B 1 HETATM 3 C C4' 6MD . . . D 4 -11.474 3.472 16.966 1 14.55 ? C4' 6MD 101 B 1 HETATM 4 O O4' 6MD . . . D 4 -10.22 3.781 16.332 1 15.68 ? O4' 6MD 101 B 1 HETATM 5 C C3' 6MD . . . D 4 -11.394 4.181 18.271 1 14.06 ? C3' 6MD 101 B 1 HETATM 6 O O3' 6MD . . . D 4 -12.333 3.916 19.254 1 15.23 ? O3' 6MD 101 B 1 HETATM 7 C C2' 6MD . . . D 4 -9.968 4.137 18.634 1 13.54 ? C2' 6MD 101 B 1 HETATM 8 O O2' 6MD . . . D 4 -9.5 3.642 19.84 1 15.99 ? O2' 6MD 101 B 1 HETATM 9 C C1' 6MD . . . D 4 -9.228 3.886 17.337 1 13.24 ? C1' 6MD 101 B 1 HETATM 10 N N9 6MD . . . D 4 -8.223 4.847 16.879 1 12.28 ? N9 6MD 101 B 1 HETATM 11 C C8 6MD . . . D 4 -8.446 5.979 16.366 1 11.86 ? C8 6MD 101 B 1 HETATM 12 N N7 6MD . . . D 4 -7.236 6.474 15.967 1 10.93 ? N7 6MD 101 B 1 HETATM 13 C C5 6MD . . . D 4 -6.287 5.513 16.261 1 11.31 ? C5 6MD 101 B 1 HETATM 14 C C6 6MD . . . D 4 -4.859 5.363 16.125 1 11.27 ? C6 6MD 101 B 1 HETATM 15 N N6 6MD . . . D 4 -4.016 6.432 15.527 1 10.59 ? N6 6MD 101 B 1 HETATM 16 N N1 6MD . . . D 4 -4.264 4.247 16.534 1 10.65 ? N1 6MD 101 B 1 HETATM 17 C C2 6MD . . . D 4 -4.986 3.242 17.089 1 11.87 ? C2 6MD 101 B 1 HETATM 18 N N3 6MD . . . D 4 -6.323 3.35 17.242 1 12.08 ? N3 6MD 101 B 1 HETATM 19 C C4 6MD . . . D 4 -7.001 4.449 16.838 1 11.55 ? C4 6MD 101 B 1 HETATM 20 C CZ 6MD . . . D 4 -2.646 6.14 15.269 1 11.56 ? CZ 6MD 101 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 20 #