data_3N5P # _model_server_result.job_id izTf_amaobvf0QYDaz_IoA _model_server_result.datetime_utc '2024-11-04 23:03:10' _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 3n5p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":800}' # _entry.id 3N5P # _exptl.entry_id 3N5P _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-(2-{6-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-2-yl}ethyl)-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 3N5P _cell.length_a 60.044 _cell.length_b 106.099 _cell.length_c 158.602 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N5P _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,R,S,T,U _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 G N N ? 5 Q 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 OE1 GLU 39 A GLU 77 1_555 S ZN ZN . B ZN 1 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc2 A OE2 GLU 39 A GLU 77 1_555 S ZN ZN . B ZN 1 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc3 A SG CYS 58 A CYS 96 1_555 J ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc4 A SG CYS 63 A CYS 101 1_555 J ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc5 A SG CYS 148 A CYS 186 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc6 J ZN ZN . A ZN 900 1_555 B SG CYS 58 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc7 J ZN ZN . A ZN 900 1_555 B SG CYS 63 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc8 S ZN ZN . B ZN 1 1_555 B OD2 ASP 333 B ASP 371 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.078 ? metalc ? metalc9 S ZN ZN . B ZN 1 1_555 U O HOH . B HOH 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc10 B SG CYS 148 B CYS 186 1_555 K FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? # _chem_comp.formula 'C21 H25 N5' _chem_comp.formula_weight 347.457 _chem_comp.id XFM _chem_comp.mon_nstd_flag . _chem_comp.name 6-(2-{6-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-2-yl}ethyl)-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 C6 N1 XFM doub 521 n y C2 N1 XFM sing 522 n y C3 C2 XFM doub 523 n y C2 C7 XFM sing 524 n n C4 C3 XFM sing 525 n y C3 H3 XFM sing 526 n n C25 C4 XFM sing 527 n n C4 C5 XFM doub 528 n y C5 C6 XFM sing 529 n y C5 H5 XFM sing 530 n n C6 N26 XFM sing 531 n n C7 C8 XFM sing 532 n n C7 H7 XFM sing 533 n n C7 H7A XFM sing 534 n n C9 C8 XFM sing 535 n n C8 H8 XFM sing 536 n n C8 H8A XFM sing 537 n n C14 C9 XFM doub 538 n y C9 N10 XFM sing 539 n y C11 N10 XFM doub 540 n y C12 C11 XFM sing 541 n y C11 C15 XFM sing 542 n n C13 C12 XFM doub 543 n y C12 H12 XFM sing 544 n n C13 C14 XFM sing 545 n y C13 H13 XFM sing 546 n n C14 H14 XFM sing 547 n n C15 C16 XFM sing 548 n n C15 H15 XFM sing 549 n n C15 H15A XFM sing 550 n n C16 C17 XFM sing 551 n n C16 H16 XFM sing 552 n n C16 H16A XFM sing 553 n n C18 C17 XFM doub 554 n y C17 C22 XFM sing 555 n y C18 C19 XFM sing 556 n y C18 H18 XFM sing 557 n n C24 C19 XFM sing 558 n n C19 N20 XFM doub 559 n y N20 C21 XFM sing 560 n y C22 C21 XFM doub 561 n y C21 N23 XFM sing 562 n n C22 H22 XFM sing 563 n n N23 HN23 XFM sing 564 n n N23 HN2A XFM sing 565 n n C24 H24 XFM sing 566 n n C24 H24A XFM sing 567 n n C24 H24B XFM sing 568 n n C25 H25 XFM sing 569 n n C25 H25A XFM sing 570 n n C25 H25B XFM sing 571 n n N26 HN26 XFM sing 572 n n N26 HN2B XFM sing 573 n n # _atom_sites.entry_id 3N5P _atom_sites.fract_transf_matrix[1][1] 0.016654 _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] 0.009425 _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] 0.006305 _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 1 850 850 ACT ACT . E 3 ACT A 1 860 860 ACT ACT . F 4 GOL A 1 880 880 GOL GOL . G 5 XFM A 1 800 800 XFM XFM . H 6 CAD A 1 950 950 CAD CAD . I 7 H4B A 1 600 600 H4B H4B . J 8 ZN A 1 900 900 ZN ZN . K 2 HEM B 1 500 500 HEM HEM . L 3 ACT B 1 850 850 ACT ACT . M 3 ACT B 1 860 860 ACT ACT . N 4 GOL B 1 880 880 GOL GOL . O 6 CAD B 1 950 950 CAD CAD . P 7 H4B B 1 600 600 H4B H4B . Q 5 XFM B 1 800 800 XFM XFM . R 4 GOL B 1 890 890 GOL GOL . S 8 ZN B 1 1 1 ZN ZN . T 9 HOH A 1 1001 1001 HOH HOH . T 9 HOH A 2 1002 1002 HOH HOH . T 9 HOH A 3 1003 1003 HOH HOH . T 9 HOH A 4 1004 1004 HOH HOH . T 9 HOH A 5 1005 1005 HOH HOH . T 9 HOH A 6 1006 1006 HOH HOH . T 9 HOH A 7 1007 1007 HOH HOH . T 9 HOH A 8 1008 1008 HOH HOH . T 9 HOH A 9 1009 1009 HOH HOH . T 9 HOH A 10 1010 1010 HOH HOH . T 9 HOH A 11 1011 1011 HOH HOH . T 9 HOH A 12 1012 1012 HOH HOH . T 9 HOH A 13 1013 1013 HOH HOH . T 9 HOH A 14 1014 1014 HOH HOH . T 9 HOH A 15 1015 1015 HOH HOH . T 9 HOH A 16 1016 1016 HOH HOH . T 9 HOH A 17 1017 1017 HOH HOH . T 9 HOH A 18 1018 1018 HOH HOH . T 9 HOH A 19 1019 1019 HOH HOH . T 9 HOH A 20 1020 1020 HOH HOH . T 9 HOH A 21 1021 1021 HOH HOH . T 9 HOH A 22 1022 1022 HOH HOH . T 9 HOH A 23 1023 1023 HOH HOH . T 9 HOH A 24 1024 1024 HOH HOH . T 9 HOH A 25 1025 1025 HOH HOH . T 9 HOH A 26 1026 1026 HOH HOH . T 9 HOH A 27 1027 1027 HOH HOH . T 9 HOH A 28 1028 1028 HOH HOH . T 9 HOH A 29 1029 1029 HOH HOH . T 9 HOH A 30 1030 1030 HOH HOH . T 9 HOH A 31 1031 1031 HOH HOH . T 9 HOH A 32 1032 1032 HOH HOH . T 9 HOH A 33 1033 1033 HOH HOH . T 9 HOH A 34 1034 1034 HOH HOH . T 9 HOH A 35 1035 1035 HOH HOH . T 9 HOH A 36 1036 1036 HOH HOH . T 9 HOH A 37 1037 1037 HOH HOH . T 9 HOH A 38 1038 1038 HOH HOH . T 9 HOH A 39 1039 1039 HOH HOH . T 9 HOH A 40 1040 1040 HOH HOH . T 9 HOH A 41 1041 1041 HOH HOH . T 9 HOH A 42 1042 1042 HOH HOH . T 9 HOH A 43 1043 1043 HOH HOH . T 9 HOH A 44 1044 1044 HOH HOH . T 9 HOH A 45 1045 1045 HOH HOH . T 9 HOH A 46 1046 1046 HOH HOH . T 9 HOH A 47 1047 1047 HOH HOH . T 9 HOH A 48 1048 1048 HOH HOH . T 9 HOH A 49 1049 1049 HOH HOH . T 9 HOH A 50 1050 1050 HOH HOH . T 9 HOH A 51 1051 1051 HOH HOH . T 9 HOH A 52 1052 1052 HOH HOH . T 9 HOH A 53 1053 1053 HOH HOH . T 9 HOH A 54 1054 1054 HOH HOH . T 9 HOH A 55 1055 1055 HOH HOH . T 9 HOH A 56 1056 1056 HOH HOH . T 9 HOH A 57 1057 1057 HOH HOH . T 9 HOH A 58 1058 1058 HOH HOH . T 9 HOH A 59 1059 1059 HOH HOH . T 9 HOH A 60 1060 1060 HOH HOH . T 9 HOH A 61 1061 1061 HOH HOH . T 9 HOH A 62 1062 1062 HOH HOH . T 9 HOH A 63 1063 1063 HOH HOH . T 9 HOH A 64 1064 1064 HOH HOH . T 9 HOH A 65 1065 1065 HOH HOH . U 9 HOH B 1 1066 1066 HOH HOH . U 9 HOH B 2 1067 1067 HOH HOH . U 9 HOH B 3 1068 1068 HOH HOH . U 9 HOH B 4 1069 1069 HOH HOH . U 9 HOH B 5 1070 1070 HOH HOH . U 9 HOH B 6 1071 1071 HOH HOH . U 9 HOH B 7 1072 1072 HOH HOH . U 9 HOH B 8 1073 1073 HOH HOH . U 9 HOH B 9 1074 1074 HOH HOH . U 9 HOH B 10 1075 1075 HOH HOH . U 9 HOH B 11 1076 1076 HOH HOH . U 9 HOH B 12 1077 1077 HOH HOH . U 9 HOH B 13 1078 1078 HOH HOH . U 9 HOH B 14 1079 1079 HOH HOH . U 9 HOH B 15 1080 1080 HOH HOH . U 9 HOH B 16 1081 1081 HOH HOH . U 9 HOH B 17 1082 1082 HOH HOH . U 9 HOH B 18 1083 1083 HOH HOH . U 9 HOH B 19 1084 1084 HOH HOH . U 9 HOH B 20 1085 1085 HOH HOH . U 9 HOH B 21 1086 1086 HOH HOH . U 9 HOH B 22 1087 1087 HOH HOH . U 9 HOH B 23 1088 1088 HOH HOH . U 9 HOH B 24 1089 1089 HOH HOH . U 9 HOH B 25 1090 1090 HOH HOH . U 9 HOH B 26 1091 1091 HOH HOH . U 9 HOH B 27 1092 1092 HOH HOH . U 9 HOH B 28 1093 1093 HOH HOH . U 9 HOH B 29 1094 1094 HOH HOH . U 9 HOH B 30 1095 1095 HOH HOH . U 9 HOH B 31 1096 1096 HOH HOH . U 9 HOH B 32 1097 1097 HOH HOH . U 9 HOH B 33 1098 1098 HOH HOH . U 9 HOH B 34 1099 1099 HOH HOH . U 9 HOH B 35 1100 1100 HOH HOH . U 9 HOH B 36 1101 1101 HOH HOH . U 9 HOH B 37 1102 1102 HOH HOH . U 9 HOH B 38 1103 1103 HOH HOH . U 9 HOH B 39 1104 1104 HOH HOH . U 9 HOH B 40 1105 1105 HOH HOH . U 9 HOH B 41 1106 1106 HOH HOH . U 9 HOH B 42 1107 1107 HOH HOH . U 9 HOH B 43 1108 1108 HOH HOH . U 9 HOH B 44 1109 1109 HOH HOH . U 9 HOH B 45 1110 1110 HOH HOH . U 9 HOH B 46 1111 1111 HOH HOH . U 9 HOH B 47 1112 1112 HOH HOH . U 9 HOH B 48 1113 1113 HOH HOH . U 9 HOH B 49 1114 1114 HOH HOH . U 9 HOH B 50 1115 1115 HOH HOH . U 9 HOH B 51 1116 1116 HOH HOH . U 9 HOH B 52 1117 1117 HOH HOH . U 9 HOH B 53 1118 1118 HOH HOH . U 9 HOH B 54 1119 1119 HOH HOH . U 9 HOH B 55 1120 1120 HOH HOH . U 9 HOH B 56 1121 1121 HOH HOH . U 9 HOH B 57 1122 1122 HOH HOH . U 9 HOH B 58 1123 1123 HOH HOH . U 9 HOH B 59 1124 1124 HOH HOH . U 9 HOH B 60 1125 1125 HOH HOH . U 9 HOH B 61 1126 1126 HOH HOH . U 9 HOH B 62 1127 1127 HOH HOH . U 9 HOH B 63 1128 1128 HOH HOH . U 9 HOH B 64 1129 1129 HOH HOH . U 9 HOH B 65 1130 1130 HOH HOH . U 9 HOH B 66 1131 1131 HOH HOH . U 9 HOH B 67 1132 1132 HOH HOH . U 9 HOH B 68 1133 1133 HOH HOH . U 9 HOH B 69 1134 1134 HOH HOH . U 9 HOH B 70 1135 1135 HOH HOH . U 9 HOH B 71 1136 1136 HOH HOH . U 9 HOH B 72 1137 1137 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 N1 XFM . . . Q 5 -0.2 7.98 66.911 1 34.82 ? N1 XFM 800 B 1 HETATM 2 C C2 XFM . . . Q 5 -0.027 6.692 67.337 1 37.59 ? C2 XFM 800 B 1 HETATM 3 C C3 XFM . . . Q 5 0.724 6.422 68.489 1 37.58 ? C3 XFM 800 B 1 HETATM 4 C C4 XFM . . . Q 5 1.269 7.469 69.203 1 37.45 ? C4 XFM 800 B 1 HETATM 5 C C5 XFM . . . Q 5 1.05 8.778 68.768 1 37.79 ? C5 XFM 800 B 1 HETATM 6 C C6 XFM . . . Q 5 0.309 9.019 67.611 1 35.97 ? C6 XFM 800 B 1 HETATM 7 C C7 XFM . . . Q 5 -0.604 5.528 66.558 1 36.06 ? C7 XFM 800 B 1 HETATM 8 C C8 XFM . . . Q 5 0.392 5.134 65.467 1 40.03 ? C8 XFM 800 B 1 HETATM 9 C C9 XFM . . . Q 5 1.473 4.214 66.011 1 44.57 ? C9 XFM 800 B 1 HETATM 10 N N10 XFM . . . Q 5 1.265 2.871 65.978 1 46.16 ? N10 XFM 800 B 1 HETATM 11 C C11 XFM . . . Q 5 2.184 1.998 66.454 1 47.26 ? C11 XFM 800 B 1 HETATM 12 C C12 XFM . . . Q 5 3.394 2.454 67.011 1 46.29 ? C12 XFM 800 B 1 HETATM 13 C C13 XFM . . . Q 5 3.649 3.83 67.065 1 45.59 ? C13 XFM 800 B 1 HETATM 14 C C14 XFM . . . Q 5 2.676 4.713 66.552 1 45.95 ? C14 XFM 800 B 1 HETATM 15 C C15 XFM . . . Q 5 1.865 0.526 66.389 1 50.79 ? C15 XFM 800 B 1 HETATM 16 C C16 XFM . . . Q 5 2.175 0.037 64.982 1 57.25 ? C16 XFM 800 B 1 HETATM 17 C C17 XFM . . . Q 5 1.673 -1.368 64.742 1 61.11 ? C17 XFM 800 B 1 HETATM 18 C C18 XFM . . . Q 5 2.583 -2.396 64.498 1 62.44 ? C18 XFM 800 B 1 HETATM 19 C C19 XFM . . . Q 5 2.105 -3.689 64.265 1 64.33 ? C19 XFM 800 B 1 HETATM 20 N N20 XFM . . . Q 5 0.764 -3.946 64.288 1 64.83 ? N20 XFM 800 B 1 HETATM 21 C C21 XFM . . . Q 5 -0.137 -2.947 64.529 1 64.41 ? C21 XFM 800 B 1 HETATM 22 C C22 XFM . . . Q 5 0.3 -1.642 64.762 1 62.94 ? C22 XFM 800 B 1 HETATM 23 N N23 XFM . . . Q 5 -1.468 -3.201 64.542 1 65.33 ? N23 XFM 800 B 1 HETATM 24 C C24 XFM . . . Q 5 3.088 -4.798 63.994 1 64.27 ? C24 XFM 800 B 1 HETATM 25 C C25 XFM . . . Q 5 2.074 7.201 70.448 1 38.18 ? C25 XFM 800 B 1 HETATM 26 N N26 XFM . . . Q 5 0.124 10.295 67.196 1 33.56 ? N26 XFM 800 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #