data_3CND # _model_server_result.job_id Ej4qc7CiewnVRDqEKIXxDg _model_server_result.datetime_utc '2025-01-10 07:54:16' _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 3cnd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":803}' # _entry.id 3CND # _exptl.entry_id 3CND _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.377 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide _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 3CND _cell.length_a 102.579 _cell.length_b 215.853 _cell.length_c 118.904 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CND _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 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 _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 3 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 221 B CYS 221 1_555 A SG CYS 238 B CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 B SG CYS 221 A CYS 221 1_555 B SG CYS 238 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? # _chem_comp.formula 'C12 H28 N4 O' _chem_comp.formula_weight 244.377 _chem_comp.id SP5 _chem_comp.mon_nstd_flag . _chem_comp.name N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N1-AcSpermine # 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 CAB CAC SP5 sing 381 n n CAC OAA SP5 doub 382 n n CAC NAD SP5 sing 383 n n NAD CAE SP5 sing 384 n n CAE CAF SP5 sing 385 n n CAF CAG SP5 sing 386 n n CAG NAH SP5 sing 387 n n NAH CAI SP5 sing 388 n n CAI CAJ SP5 sing 389 n n CAJ CAK SP5 sing 390 n n CAK CAL SP5 sing 391 n n CAL NAM SP5 sing 392 n n NAM CAN SP5 sing 393 n n CAN CAO SP5 sing 394 n n CAO CAP SP5 sing 395 n n CAP NAQ SP5 sing 396 n n CAB HAB SP5 sing 397 n n CAB HABA SP5 sing 398 n n CAB HABB SP5 sing 399 n n NAD HNAD SP5 sing 400 n n CAE HAE SP5 sing 401 n n CAE HAEA SP5 sing 402 n n CAF HAF SP5 sing 403 n n CAF HAFA SP5 sing 404 n n CAG HAG SP5 sing 405 n n CAG HAGA SP5 sing 406 n n NAH HNAH SP5 sing 407 n n CAI HAI SP5 sing 408 n n CAI HAIA SP5 sing 409 n n CAJ HAJ SP5 sing 410 n n CAJ HAJA SP5 sing 411 n n CAK HAK SP5 sing 412 n n CAK HAKA SP5 sing 413 n n CAL HAL SP5 sing 414 n n CAL HALA SP5 sing 415 n n NAM HNAM SP5 sing 416 n n CAN HAN SP5 sing 417 n n CAN HANA SP5 sing 418 n n CAO HAO SP5 sing 419 n n CAO HAOA SP5 sing 420 n n CAP HAP SP5 sing 421 n n CAP HAPA SP5 sing 422 n n NAQ HNAQ SP5 sing 423 n n NAQ HNAA SP5 sing 424 n n # _atom_sites.entry_id 3CND _atom_sites.fract_transf_matrix[1][1] 0.009749 _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] 0.004633 _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] 0.00841 _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 FAD B 1 802 802 FAD FAD . D 3 SP5 B 1 803 2 SP5 SP5 . E 2 FAD A 1 801 801 FAD FAD . F 4 HOH B 1 804 2 HOH TIP . F 4 HOH B 2 805 3 HOH TIP . F 4 HOH B 3 806 10 HOH TIP . F 4 HOH B 4 807 15 HOH TIP . F 4 HOH B 5 808 16 HOH TIP . F 4 HOH B 6 809 17 HOH TIP . F 4 HOH B 7 810 21 HOH TIP . F 4 HOH B 8 811 23 HOH TIP . F 4 HOH B 9 812 24 HOH TIP . F 4 HOH B 10 813 25 HOH TIP . F 4 HOH B 11 814 26 HOH TIP . F 4 HOH B 12 815 30 HOH TIP . F 4 HOH B 13 816 31 HOH TIP . F 4 HOH B 14 817 34 HOH TIP . F 4 HOH B 15 818 36 HOH TIP . F 4 HOH B 16 819 37 HOH TIP . F 4 HOH B 17 820 38 HOH TIP . F 4 HOH B 18 821 39 HOH TIP . F 4 HOH B 19 822 42 HOH TIP . F 4 HOH B 20 823 43 HOH TIP . F 4 HOH B 21 824 45 HOH TIP . F 4 HOH B 22 825 54 HOH TIP . F 4 HOH B 23 826 57 HOH TIP . F 4 HOH B 24 827 58 HOH TIP . F 4 HOH B 25 828 59 HOH TIP . G 4 HOH A 1 802 1 HOH TIP . G 4 HOH A 2 803 4 HOH TIP . G 4 HOH A 3 804 5 HOH TIP . G 4 HOH A 4 805 6 HOH TIP . G 4 HOH A 5 806 7 HOH TIP . G 4 HOH A 6 807 8 HOH TIP . G 4 HOH A 7 808 9 HOH TIP . G 4 HOH A 8 809 11 HOH TIP . G 4 HOH A 9 810 12 HOH TIP . G 4 HOH A 10 811 13 HOH TIP . G 4 HOH A 11 812 14 HOH TIP . G 4 HOH A 12 813 18 HOH TIP . G 4 HOH A 13 814 19 HOH TIP . G 4 HOH A 14 815 20 HOH TIP . G 4 HOH A 15 816 22 HOH TIP . G 4 HOH A 16 817 27 HOH TIP . G 4 HOH A 17 818 28 HOH TIP . G 4 HOH A 18 819 29 HOH TIP . G 4 HOH A 19 820 32 HOH TIP . G 4 HOH A 20 821 33 HOH TIP . G 4 HOH A 21 822 35 HOH TIP . G 4 HOH A 22 823 40 HOH TIP . G 4 HOH A 23 824 41 HOH TIP . G 4 HOH A 24 825 44 HOH TIP . G 4 HOH A 25 826 46 HOH TIP . G 4 HOH A 26 827 47 HOH TIP . G 4 HOH A 27 828 48 HOH TIP . G 4 HOH A 28 829 49 HOH TIP . G 4 HOH A 29 830 50 HOH TIP . G 4 HOH A 30 831 51 HOH TIP . G 4 HOH A 31 832 52 HOH TIP . G 4 HOH A 32 833 53 HOH TIP . G 4 HOH A 33 834 55 HOH TIP . G 4 HOH A 34 835 56 HOH TIP . # 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 CAB SP5 . . . D 3 56.391 -58.553 59.258 1 69.64 ? CAB SP5 803 B 1 HETATM 2 C CAC SP5 . . . D 3 57.169 -57.46 58.523 1 70.45 ? CAC SP5 803 B 1 HETATM 3 O OAA SP5 . . . D 3 58.061 -56.832 59.092 1 70.21 ? OAA SP5 803 B 1 HETATM 4 N NAD SP5 . . . D 3 56.827 -57.279 57.248 1 67.43 ? NAD SP5 803 B 1 HETATM 5 C CAE SP5 . . . D 3 55.781 -58.083 56.6 1 64.15 ? CAE SP5 803 B 1 HETATM 6 C CAF SP5 . . . D 3 55.705 -57.768 55.105 1 62.3 ? CAF SP5 803 B 1 HETATM 7 C CAG SP5 . . . D 3 54.68 -58.68 54.43 1 61.32 ? CAG SP5 803 B 1 HETATM 8 N NAH SP5 . . . D 3 53.854 -57.922 53.48 1 61.04 ? NAH SP5 803 B 1 HETATM 9 C CAI SP5 . . . D 3 52.464 -57.829 53.95 1 58.75 ? CAI SP5 803 B 1 HETATM 10 C CAJ SP5 . . . D 3 51.913 -56.449 53.583 1 57.62 ? CAJ SP5 803 B 1 HETATM 11 C CAK SP5 . . . D 3 51.068 -56.498 52.309 1 57.69 ? CAK SP5 803 B 1 HETATM 12 C CAL SP5 . . . D 3 50.16 -55.274 52.172 1 56.65 ? CAL SP5 803 B 1 HETATM 13 N NAM SP5 . . . D 3 50.487 -54.312 53.234 1 57.7 ? NAM SP5 803 B 1 HETATM 14 C CAN SP5 . . . D 3 49.947 -52.996 52.864 1 59.11 ? CAN SP5 803 B 1 HETATM 15 C CAO SP5 . . . D 3 50.556 -52.549 51.533 1 61.38 ? CAO SP5 803 B 1 HETATM 16 C CAP SP5 . . . D 3 50.05 -51.158 51.146 1 62.07 ? CAP SP5 803 B 1 HETATM 17 N NAQ SP5 . . . D 3 51.174 -50.211 51.098 1 62.94 ? NAQ SP5 803 B 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #