data_9CVM # _model_server_result.job_id M1h_Leh_knNxOXYKUByORQ _model_server_result.datetime_utc '2025-08-02 19:21:39' _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 9cvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":805}' # _entry.id 9CVM # _exptl.entry_id 9CVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.293 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(2M)-4-methyl-5'-[(methylamino)methyl][2,3'-bipyridin]-6-amine" _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 9CVM _cell.length_a 48.462 _cell.length_b 113.007 _cell.length_c 162.788 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _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 metalc ? metalc1 A SG CYS 30 A CYS 326 1_555 E ZN ZN . A ZN 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc2 A SG CYS 30 A CYS 326 1_555 E ZN ZN . A ZN 804 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc3 A SG CYS 35 A CYS 331 1_555 E ZN ZN . A ZN 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc4 A SG CYS 35 A CYS 331 1_555 E ZN ZN . A ZN 804 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc5 A SG CYS 119 A CYS 415 1_555 B FE HEM . A HEM 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? # _chem_comp.formula 'C13 H16 N4' _chem_comp.formula_weight 228.293 _chem_comp.id A1A0E _chem_comp.mon_nstd_flag . _chem_comp.name "(2M)-4-methyl-5'-[(methylamino)methyl][2,3'-bipyridin]-6-amine" _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 C07 C04 A1A0E sing 1 n n C04 C05 A1A0E doub 2 n y C04 C03 A1A0E sing 3 n y C05 C06 A1A0E sing 4 n y C03 C02 A1A0E doub 5 n y C06 N01 A1A0E doub 6 n y C06 C13 A1A0E sing 7 n n C02 N01 A1A0E sing 8 n y C02 N02 A1A0E sing 9 n n C13 C12 A1A0E doub 10 n y C13 C14 A1A0E sing 11 n y C12 N11 A1A0E sing 12 n y C14 C16 A1A0E doub 13 n y N11 C15 A1A0E doub 14 n y C16 C15 A1A0E sing 15 n y C16 C17 A1A0E sing 16 n n C17 N18 A1A0E sing 17 n n N18 C19 A1A0E sing 18 n n C03 H1 A1A0E sing 19 n n C05 H2 A1A0E sing 20 n n C07 H3 A1A0E sing 21 n n C07 H4 A1A0E sing 22 n n C07 H5 A1A0E sing 23 n n C12 H6 A1A0E sing 24 n n C14 H7 A1A0E sing 25 n n C15 H8 A1A0E sing 26 n n C17 H9 A1A0E sing 27 n n C17 H10 A1A0E sing 28 n n C19 H11 A1A0E sing 29 n n C19 H12 A1A0E sing 30 n n C19 H13 A1A0E sing 31 n n N02 H14 A1A0E sing 32 n n N02 H15 A1A0E sing 33 n n N18 H16 A1A0E sing 34 n n # _atom_sites.entry_id 9CVM _atom_sites.fract_transf_matrix[1][1] 0.020635 _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] 0.008849 _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] 0.006143 _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 HEM A 1 801 750 HEM HEM . C 3 H4B A 1 802 760 H4B BH4 . D 4 ACT A 1 803 860 ACT ACT . E 5 ZN A 1 804 900 ZN ZN . F 6 A1A0E A 1 805 800 A1A0E 4V6 . G 7 HOH A 1 901 34 HOH HOH . G 7 HOH A 2 902 20 HOH HOH . G 7 HOH A 3 903 5 HOH HOH . G 7 HOH A 4 904 12 HOH HOH . G 7 HOH A 5 905 49 HOH HOH . G 7 HOH A 6 906 4 HOH HOH . G 7 HOH A 7 907 13 HOH HOH . G 7 HOH A 8 908 39 HOH HOH . G 7 HOH A 9 909 18 HOH HOH . G 7 HOH A 10 910 11 HOH HOH . G 7 HOH A 11 911 2 HOH HOH . G 7 HOH A 12 912 28 HOH HOH . G 7 HOH A 13 913 19 HOH HOH . G 7 HOH A 14 914 44 HOH HOH . G 7 HOH A 15 915 21 HOH HOH . G 7 HOH A 16 916 38 HOH HOH . G 7 HOH A 17 917 32 HOH HOH . G 7 HOH A 18 918 45 HOH HOH . G 7 HOH A 19 919 41 HOH HOH . G 7 HOH A 20 920 51 HOH HOH . G 7 HOH A 21 921 36 HOH HOH . G 7 HOH A 22 922 33 HOH HOH . G 7 HOH A 23 923 8 HOH HOH . G 7 HOH A 24 924 6 HOH HOH . G 7 HOH A 25 925 15 HOH HOH . G 7 HOH A 26 926 30 HOH HOH . G 7 HOH A 27 927 9 HOH HOH . G 7 HOH A 28 928 27 HOH HOH . G 7 HOH A 29 929 14 HOH HOH . G 7 HOH A 30 930 50 HOH HOH . G 7 HOH A 31 931 1 HOH HOH . G 7 HOH A 32 932 16 HOH HOH . G 7 HOH A 33 933 35 HOH HOH . G 7 HOH A 34 934 25 HOH HOH . G 7 HOH A 35 935 24 HOH HOH . G 7 HOH A 36 936 40 HOH HOH . G 7 HOH A 37 937 3 HOH HOH . G 7 HOH A 38 938 47 HOH HOH . G 7 HOH A 39 939 52 HOH HOH . G 7 HOH A 40 940 43 HOH HOH . G 7 HOH A 41 941 37 HOH HOH . G 7 HOH A 42 942 17 HOH HOH . G 7 HOH A 43 943 29 HOH HOH . G 7 HOH A 44 944 42 HOH HOH . G 7 HOH A 45 945 48 HOH HOH . G 7 HOH A 46 946 22 HOH HOH . G 7 HOH A 47 947 7 HOH HOH . G 7 HOH A 48 948 23 HOH HOH . G 7 HOH A 49 949 10 HOH HOH . G 7 HOH A 50 950 46 HOH HOH . G 7 HOH A 51 951 26 HOH HOH . G 7 HOH A 52 952 31 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 C C02 A1A0E . . . F 6 -25.556 0.245 23.111 1 54.9 ? C02 A1A0E 805 A 1 HETATM 2 C C03 A1A0E . . . F 6 -26.049 -0.58 22.103 1 57.65 ? C03 A1A0E 805 A 1 HETATM 3 C C04 A1A0E . . . F 6 -25.201 -1.512 21.52 1 58.58 ? C04 A1A0E 805 A 1 HETATM 4 C C05 A1A0E . . . F 6 -23.883 -1.606 21.956 1 57.3 ? C05 A1A0E 805 A 1 HETATM 5 C C06 A1A0E . . . F 6 -23.438 -0.772 22.982 1 55.19 ? C06 A1A0E 805 A 1 HETATM 6 C C07 A1A0E . . . F 6 -25.704 -2.422 20.431 1 51.85 ? C07 A1A0E 805 A 1 HETATM 7 C C12 A1A0E . . . F 6 -21.388 0.436 23.496 1 76.63 ? C12 A1A0E 805 A 1 HETATM 8 C C13 A1A0E . . . F 6 -22.023 -0.798 23.43 1 66.1 ? C13 A1A0E 805 A 1 HETATM 9 C C14 A1A0E . . . F 6 -21.312 -1.956 23.735 1 62.37 ? C14 A1A0E 805 A 1 HETATM 10 C C15 A1A0E . . . F 6 -19.404 -0.54 24.172 1 79.92 ? C15 A1A0E 805 A 1 HETATM 11 C C16 A1A0E . . . F 6 -19.975 -1.804 24.102 1 69.83 ? C16 A1A0E 805 A 1 HETATM 12 C C17 A1A0E . . . F 6 -19.09 -2.974 24.452 1 68.55 ? C17 A1A0E 805 A 1 HETATM 13 C C19 A1A0E . . . F 6 -18.539 -4.545 26.143 1 62.48 ? C19 A1A0E 805 A 1 HETATM 14 N N01 A1A0E . . . F 6 -24.271 0.144 23.496 1 49.74 ? N01 A1A0E 805 A 1 HETATM 15 N N02 A1A0E . . . F 6 -26.352 1.165 23.698 1 54.7 ? N02 A1A0E 805 A 1 HETATM 16 N N11 A1A0E . . . F 6 -20.113 0.548 23.871 1 84.79 ? N11 A1A0E 805 A 1 HETATM 17 N N18 A1A0E . . . F 6 -19.652 -3.809 25.51 1 65.65 ? N18 A1A0E 805 A 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 541 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #