data_3N5T # _model_server_result.job_id WG8mi9fZsthmWV5PE_VgLQ _model_server_result.datetime_utc '2024-11-23 12:54:49' _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 3n5t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":800}' # _entry.id 3N5T # _exptl.entry_id 3N5T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.457 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine)" _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 90 _cell.entry_id 3N5T _cell.length_a 58.12 _cell.length_b 106.744 _cell.length_c 157.382 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N5T _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,G,H,I,J,K,L,M,N,O,P,Q _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 ? 5 F N N ? 5 M 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 metalc ? metalc1 A SG CYS 58 A CYS 96 1_555 I ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc2 A SG CYS 63 A CYS 101 1_555 I ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc3 A SG CYS 148 A CYS 186 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc4 I ZN ZN . A ZN 900 1_555 B SG CYS 58 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc5 I ZN ZN . A ZN 900 1_555 B SG CYS 63 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc6 B SG CYS 148 B CYS 186 1_555 J FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? # _chem_comp.formula 'C21 H25 N5' _chem_comp.formula_weight 347.457 _chem_comp.id XFJ _chem_comp.mon_nstd_flag . _chem_comp.name "6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-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 N01 C06 XFJ doub 521 n y N01 C02 XFJ sing 522 n y N02 C02 XFJ sing 523 n n C02 C03 XFJ doub 524 n y N02 HN02 XFJ sing 525 n n N02 HN0A XFJ sing 526 n n C03 C04 XFJ sing 527 n y C03 H03 XFJ sing 528 n n C05 C04 XFJ doub 529 n y C04 C07 XFJ sing 530 n n C06 C05 XFJ sing 531 n y C05 H05 XFJ sing 532 n n C08 C06 XFJ sing 533 n n C07 H07 XFJ sing 534 n n C07 H07A XFJ sing 535 n n C07 H07B XFJ sing 536 n n C08 C09 XFJ sing 537 n n C08 H08 XFJ sing 538 n n C08 H08A XFJ sing 539 n n C13 C09 XFJ sing 540 n n C09 H09 XFJ sing 541 n n C09 H09A XFJ sing 542 n n C16 N11 XFJ doub 543 n y N11 C12 XFJ sing 544 n y C12 C13 XFJ doub 545 n y C12 H12 XFJ sing 546 n n C14 C13 XFJ sing 547 n y C15 C14 XFJ doub 548 n y C14 H14 XFJ sing 549 n n C17 C15 XFJ sing 550 n n C16 C15 XFJ sing 551 n y C16 H16 XFJ sing 552 n n C17 C18 XFJ sing 553 n n C17 H17 XFJ sing 554 n n C17 H17A XFJ sing 555 n n C26 C18 XFJ sing 556 n n C18 H18 XFJ sing 557 n n C18 H18A XFJ sing 558 n n C22 N21 XFJ doub 559 n y C26 N21 XFJ sing 560 n y C23 C22 XFJ sing 561 n y C22 N22 XFJ sing 562 n n N22 HN22 XFJ sing 563 n n N22 HN2A XFJ sing 564 n n C24 C23 XFJ doub 565 n y C23 H23 XFJ sing 566 n n C27 C24 XFJ sing 567 n n C24 C25 XFJ sing 568 n y C25 C26 XFJ doub 569 n y C25 H25 XFJ sing 570 n n C27 H27 XFJ sing 571 n n C27 H27A XFJ sing 572 n n C27 H27B XFJ sing 573 n n # _atom_sites.entry_id 3N5T _atom_sites.fract_transf_matrix[1][1] 0.017206 _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] 0.009368 _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] 0.006354 _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 2 HEM A 1 500 500 HEM HEM . D 3 ACT A 1 860 860 ACT ACT . E 4 GOL A 1 880 880 GOL GOL . F 5 XFJ A 1 800 800 XFJ XFJ . G 6 H4B A 1 600 600 H4B H4B . H 7 CAD A 1 950 950 CAD CAD . I 8 ZN A 1 900 900 ZN ZN . J 2 HEM B 1 500 500 HEM HEM . K 3 ACT B 1 860 860 ACT ACT . L 4 GOL B 1 880 880 GOL GOL . M 5 XFJ B 1 800 800 XFJ XFJ . N 6 H4B B 1 600 600 H4B H4B . O 7 CAD B 1 950 950 CAD CAD . P 9 HOH A 1 1001 1001 HOH HOH . P 9 HOH A 2 1002 1002 HOH HOH . P 9 HOH A 3 1003 1003 HOH HOH . P 9 HOH A 4 1004 1004 HOH HOH . P 9 HOH A 5 1005 1005 HOH HOH . P 9 HOH A 6 1006 1006 HOH HOH . P 9 HOH A 7 1007 1007 HOH HOH . P 9 HOH A 8 1008 1008 HOH HOH . P 9 HOH A 9 1009 1009 HOH HOH . P 9 HOH A 10 1010 1010 HOH HOH . P 9 HOH A 11 1011 1011 HOH HOH . P 9 HOH A 12 1012 1012 HOH HOH . P 9 HOH A 13 1013 1013 HOH HOH . P 9 HOH A 14 1014 1014 HOH HOH . P 9 HOH A 15 1015 1015 HOH HOH . P 9 HOH A 16 1016 1016 HOH HOH . P 9 HOH A 17 1017 1017 HOH HOH . P 9 HOH A 18 1018 1018 HOH HOH . P 9 HOH A 19 1019 1019 HOH HOH . P 9 HOH A 20 1020 1020 HOH HOH . P 9 HOH A 21 1021 1021 HOH HOH . P 9 HOH A 22 1022 1022 HOH HOH . P 9 HOH A 23 1023 1023 HOH HOH . P 9 HOH A 24 1024 1024 HOH HOH . P 9 HOH A 25 1025 1025 HOH HOH . P 9 HOH A 26 1026 1026 HOH HOH . P 9 HOH A 27 1027 1027 HOH HOH . P 9 HOH A 28 1028 1028 HOH HOH . P 9 HOH A 29 1029 1029 HOH HOH . P 9 HOH A 30 1030 1030 HOH HOH . P 9 HOH A 31 1031 1031 HOH HOH . P 9 HOH A 32 1032 1032 HOH HOH . P 9 HOH A 33 1033 1033 HOH HOH . P 9 HOH A 34 1034 1034 HOH HOH . P 9 HOH A 35 1035 1035 HOH HOH . P 9 HOH A 36 1036 1036 HOH HOH . P 9 HOH A 37 1037 1037 HOH HOH . P 9 HOH A 38 1038 1038 HOH HOH . P 9 HOH A 39 1039 1039 HOH HOH . P 9 HOH A 40 1040 1040 HOH HOH . P 9 HOH A 41 1041 1041 HOH HOH . P 9 HOH A 42 1042 1042 HOH HOH . P 9 HOH A 43 1043 1043 HOH HOH . P 9 HOH A 44 1044 1044 HOH HOH . P 9 HOH A 45 1045 1045 HOH HOH . P 9 HOH A 46 1046 1046 HOH HOH . P 9 HOH A 47 1047 1047 HOH HOH . P 9 HOH A 48 1048 1048 HOH HOH . P 9 HOH A 49 1049 1049 HOH HOH . P 9 HOH A 50 1050 1050 HOH HOH . P 9 HOH A 51 1051 1051 HOH HOH . P 9 HOH A 52 1052 1052 HOH HOH . P 9 HOH A 53 1053 1053 HOH HOH . P 9 HOH A 54 1054 1054 HOH HOH . P 9 HOH A 55 1055 1055 HOH HOH . P 9 HOH A 56 1056 1056 HOH HOH . P 9 HOH A 57 1057 1057 HOH HOH . P 9 HOH A 58 1058 1058 HOH HOH . P 9 HOH A 59 1059 1059 HOH HOH . P 9 HOH A 60 1060 1060 HOH HOH . P 9 HOH A 61 1061 1061 HOH HOH . P 9 HOH A 62 1062 1062 HOH HOH . P 9 HOH A 63 1063 1063 HOH HOH . P 9 HOH A 64 1064 1064 HOH HOH . Q 9 HOH B 1 1065 1065 HOH HOH . Q 9 HOH B 2 1066 1066 HOH HOH . Q 9 HOH B 3 1067 1067 HOH HOH . Q 9 HOH B 4 1068 1068 HOH HOH . Q 9 HOH B 5 1069 1069 HOH HOH . Q 9 HOH B 6 1070 1070 HOH HOH . Q 9 HOH B 7 1071 1071 HOH HOH . Q 9 HOH B 8 1072 1072 HOH HOH . Q 9 HOH B 9 1073 1073 HOH HOH . Q 9 HOH B 10 1074 1074 HOH HOH . Q 9 HOH B 11 1075 1075 HOH HOH . Q 9 HOH B 12 1076 1076 HOH HOH . Q 9 HOH B 13 1077 1077 HOH HOH . Q 9 HOH B 14 1078 1078 HOH HOH . Q 9 HOH B 15 1079 1079 HOH HOH . Q 9 HOH B 16 1080 1080 HOH HOH . Q 9 HOH B 17 1081 1081 HOH HOH . Q 9 HOH B 18 1082 1082 HOH HOH . Q 9 HOH B 19 1083 1083 HOH HOH . Q 9 HOH B 20 1084 1084 HOH HOH . Q 9 HOH B 21 1085 1085 HOH HOH . Q 9 HOH B 22 1086 1086 HOH HOH . Q 9 HOH B 23 1087 1087 HOH HOH . Q 9 HOH B 24 1088 1088 HOH HOH . Q 9 HOH B 25 1089 1089 HOH HOH . Q 9 HOH B 26 1090 1090 HOH HOH . Q 9 HOH B 27 1091 1091 HOH HOH . Q 9 HOH B 28 1092 1092 HOH HOH . Q 9 HOH B 29 1093 1093 HOH HOH . Q 9 HOH B 30 1094 1094 HOH HOH . Q 9 HOH B 31 1095 1095 HOH HOH . Q 9 HOH B 32 1096 1096 HOH HOH . Q 9 HOH B 33 1097 1097 HOH HOH . Q 9 HOH B 34 1098 1098 HOH HOH . Q 9 HOH B 35 1099 1099 HOH HOH . Q 9 HOH B 36 1100 1100 HOH HOH . Q 9 HOH B 37 1101 1101 HOH HOH . Q 9 HOH B 38 1102 1102 HOH HOH . Q 9 HOH B 39 1103 1103 HOH HOH . Q 9 HOH B 40 1104 1104 HOH HOH . Q 9 HOH B 41 1105 1105 HOH HOH . Q 9 HOH B 42 1106 1106 HOH HOH . Q 9 HOH B 43 1107 1107 HOH HOH . Q 9 HOH B 44 1108 1108 HOH HOH . Q 9 HOH B 45 1109 1109 HOH HOH . Q 9 HOH B 46 1110 1110 HOH HOH . Q 9 HOH B 47 1111 1111 HOH HOH . Q 9 HOH B 48 1112 1112 HOH HOH . Q 9 HOH B 49 1113 1113 HOH HOH . Q 9 HOH B 50 1114 1114 HOH HOH . Q 9 HOH B 51 1115 1115 HOH HOH . Q 9 HOH B 52 1116 1116 HOH HOH . Q 9 HOH B 53 1117 1117 HOH HOH . Q 9 HOH B 54 1118 1118 HOH HOH . Q 9 HOH B 55 1119 1119 HOH HOH . Q 9 HOH B 56 1120 1120 HOH HOH . Q 9 HOH B 57 1121 1121 HOH HOH . Q 9 HOH B 58 1122 1122 HOH HOH . Q 9 HOH B 59 1123 1123 HOH HOH . Q 9 HOH B 60 1124 1124 HOH HOH . Q 9 HOH B 61 1125 1125 HOH HOH . Q 9 HOH B 62 1126 1126 HOH HOH . Q 9 HOH B 63 1127 1127 HOH HOH . Q 9 HOH B 64 1128 1128 HOH HOH . Q 9 HOH B 65 1129 1129 HOH HOH . Q 9 HOH B 66 1130 1130 HOH HOH . Q 9 HOH B 67 1131 1131 HOH HOH . Q 9 HOH B 68 1132 1132 HOH HOH . Q 9 HOH B 69 1133 1133 HOH HOH . Q 9 HOH B 70 1134 1134 HOH HOH . Q 9 HOH B 71 1135 1135 HOH HOH . Q 9 HOH B 72 1136 1136 HOH HOH . Q 9 HOH B 73 1137 1137 HOH HOH . Q 9 HOH B 74 1138 1138 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 N N01 XFJ . . . F 5 6.596 12.517 32.491 1 38.11 ? N01 XFJ 800 A 1 HETATM 2 C C02 XFJ . . . F 5 5.833 11.773 31.668 1 37.59 ? C02 XFJ 800 A 1 HETATM 3 N N02 XFJ . . . F 5 4.49 11.76 31.929 1 36.58 ? N02 XFJ 800 A 1 HETATM 4 C C03 XFJ . . . F 5 6.438 11.074 30.607 1 36.14 ? C03 XFJ 800 A 1 HETATM 5 C C04 XFJ . . . F 5 7.835 11.167 30.441 1 36.33 ? C04 XFJ 800 A 1 HETATM 6 C C05 XFJ . . . F 5 8.581 11.94 31.334 1 36.61 ? C05 XFJ 800 A 1 HETATM 7 C C06 XFJ . . . F 5 7.928 12.622 32.367 1 38.76 ? C06 XFJ 800 A 1 HETATM 8 C C07 XFJ . . . F 5 8.542 10.44 29.319 1 31.31 ? C07 XFJ 800 A 1 HETATM 9 C C08 XFJ . . . F 5 8.61 13.5 33.401 1 41.08 ? C08 XFJ 800 A 1 HETATM 10 C C09 XFJ . . . F 5 10.113 13.663 33.197 1 44.48 ? C09 XFJ 800 A 1 HETATM 11 N N11 XFJ . . . F 5 10.878 16.752 35.254 1 50.36 ? N11 XFJ 800 A 1 HETATM 12 C C12 XFJ . . . F 5 10.324 15.925 34.342 1 49 ? C12 XFJ 800 A 1 HETATM 13 C C13 XFJ . . . F 5 10.744 14.595 34.214 1 46.2 ? C13 XFJ 800 A 1 HETATM 14 C C14 XFJ . . . F 5 11.765 14.132 35.032 1 48.1 ? C14 XFJ 800 A 1 HETATM 15 C C15 XFJ . . . F 5 12.336 15.001 35.968 1 50.03 ? C15 XFJ 800 A 1 HETATM 16 C C16 XFJ . . . F 5 11.874 16.319 36.055 1 50.46 ? C16 XFJ 800 A 1 HETATM 17 C C17 XFJ . . . F 5 13.422 14.501 36.89 1 50.16 ? C17 XFJ 800 A 1 HETATM 18 C C18 XFJ . . . F 5 14.734 15.179 36.548 1 52.75 ? C18 XFJ 800 A 1 HETATM 19 N N21 XFJ . . . F 5 15.914 13.122 37.291 1 53.32 ? N21 XFJ 800 A 1 HETATM 20 C C22 XFJ . . . F 5 16.873 12.438 37.961 1 51.49 ? C22 XFJ 800 A 1 HETATM 21 N N22 XFJ . . . F 5 16.934 11.078 37.871 1 50.34 ? N22 XFJ 800 A 1 HETATM 22 C C23 XFJ . . . F 5 17.765 13.164 38.76 1 51.07 ? C23 XFJ 800 A 1 HETATM 23 C C24 XFJ . . . F 5 17.665 14.564 38.84 1 51.66 ? C24 XFJ 800 A 1 HETATM 24 C C25 XFJ . . . F 5 16.68 15.239 38.12 1 51.95 ? C25 XFJ 800 A 1 HETATM 25 C C26 XFJ . . . F 5 15.807 14.483 37.344 1 53.08 ? C26 XFJ 800 A 1 HETATM 26 C C27 XFJ . . . F 5 18.624 15.358 39.693 1 50.8 ? C27 XFJ 800 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 26 #