data_7P8Q # _model_server_result.job_id XFjQrGkZcnMjPxG-b8FQcw _model_server_result.datetime_utc '2025-01-11 03:45:52' _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 7p8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 7P8Q # _exptl.entry_id 7P8Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 424.455 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine" _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 105.36 _cell.angle_gamma 90 _cell.entry_id 7P8Q _cell.length_a 80.32 _cell.length_b 38.3 _cell.length_c 90.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7P8Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 3 _struct_asym.id C _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 covale ? covale1 B O3' GMP 1 B GMP 2 1_555 B P A 2 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.664 ? covale ? covale2 B N6 A 2 B A 3 1_555 C C1 6D6 . B 6D6 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? # _chem_comp.formula 'C17 H28 N8 O5' _chem_comp.formula_weight 424.455 _chem_comp.id 6D6 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine" _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 N6 C15 6D6 sing 1 n n C15 N7 6D6 doub 2 n y C15 C9 6D6 sing 3 n y N5 C9 6D6 sing 4 n y N5 C8 6D6 doub 5 n y N7 C16 6D6 sing 6 n y C9 C17 6D6 doub 7 n y C8 N4 6D6 sing 8 n y C16 N8 6D6 doub 9 n y C17 N4 6D6 sing 10 n y C17 N8 6D6 sing 11 n y N4 C13 6D6 sing 12 n n N1 C1 6D6 sing 13 n n C13 C14 6D6 sing 14 n n C13 O3 6D6 sing 15 n n C14 O4 6D6 sing 16 n n C14 C7 6D6 sing 17 n n O3 C12 6D6 sing 18 n n C1 C2 6D6 sing 19 n n C2 C3 6D6 sing 20 n n C6 C12 6D6 sing 21 n n C6 N2 6D6 sing 22 n n C7 C12 6D6 sing 23 n n C7 O5 6D6 sing 24 n n C3 N2 6D6 sing 25 n n N2 C4 6D6 sing 26 n n C4 C10 6D6 sing 27 n n C10 C5 6D6 sing 28 n n N3 C5 6D6 sing 29 n n C5 C11 6D6 sing 30 n n O1 C11 6D6 doub 31 n n C11 O2 6D6 sing 32 n n C1 H1 6D6 sing 33 n n C1 H2 6D6 sing 34 n n C2 H3 6D6 sing 35 n n C2 H4 6D6 sing 36 n n C3 H5 6D6 sing 37 n n C3 H6 6D6 sing 38 n n C4 H7 6D6 sing 39 n n C4 H8 6D6 sing 40 n n C5 H9 6D6 sing 41 n n C6 H10 6D6 sing 42 n n C6 H11 6D6 sing 43 n n C7 H12 6D6 sing 44 n n C8 H13 6D6 sing 45 n n N1 H14 6D6 sing 46 n n N1 H15 6D6 sing 47 n n C10 H18 6D6 sing 48 n n C10 H19 6D6 sing 49 n n N3 H20 6D6 sing 50 n n N3 H21 6D6 sing 51 n n O2 H23 6D6 sing 52 n n C12 H24 6D6 sing 53 n n C13 H25 6D6 sing 54 n n C14 H26 6D6 sing 55 n n O4 H27 6D6 sing 56 n n O5 H28 6D6 sing 57 n n N6 H29 6D6 sing 58 n n N6 H30 6D6 sing 59 n n C16 H31 6D6 sing 60 n n # _atom_sites.entry_id 7P8Q _atom_sites.fract_transf_matrix[1][1] 0.01245 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00342 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02611 _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] 0.011421 _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 6D6 B 1 101 301 6D6 LIG . D 4 HOH A 1 401 44 HOH HOH . D 4 HOH A 2 402 27 HOH HOH . D 4 HOH A 3 403 8 HOH HOH . D 4 HOH A 4 404 9 HOH HOH . D 4 HOH A 5 405 36 HOH HOH . D 4 HOH A 6 406 17 HOH HOH . D 4 HOH A 7 407 54 HOH HOH . D 4 HOH A 8 408 28 HOH HOH . D 4 HOH A 9 409 3 HOH HOH . D 4 HOH A 10 410 42 HOH HOH . D 4 HOH A 11 411 2 HOH HOH . D 4 HOH A 12 412 10 HOH HOH . D 4 HOH A 13 413 5 HOH HOH . D 4 HOH A 14 414 39 HOH HOH . D 4 HOH A 15 415 1 HOH HOH . D 4 HOH A 16 416 49 HOH HOH . D 4 HOH A 17 417 23 HOH HOH . D 4 HOH A 18 418 50 HOH HOH . D 4 HOH A 19 419 35 HOH HOH . D 4 HOH A 20 420 19 HOH HOH . D 4 HOH A 21 421 58 HOH HOH . D 4 HOH A 22 422 60 HOH HOH . D 4 HOH A 23 423 43 HOH HOH . D 4 HOH A 24 424 7 HOH HOH . D 4 HOH A 25 425 6 HOH HOH . D 4 HOH A 26 426 14 HOH HOH . D 4 HOH A 27 427 47 HOH HOH . D 4 HOH A 28 428 21 HOH HOH . D 4 HOH A 29 429 46 HOH HOH . D 4 HOH A 30 430 20 HOH HOH . D 4 HOH A 31 431 22 HOH HOH . D 4 HOH A 32 432 38 HOH HOH . D 4 HOH A 33 433 24 HOH HOH . D 4 HOH A 34 434 48 HOH HOH . D 4 HOH A 35 435 55 HOH HOH . D 4 HOH A 36 436 31 HOH HOH . D 4 HOH A 37 437 52 HOH HOH . D 4 HOH A 38 438 57 HOH HOH . D 4 HOH A 39 439 26 HOH HOH . D 4 HOH A 40 440 41 HOH HOH . D 4 HOH A 41 441 4 HOH HOH . D 4 HOH A 42 442 30 HOH HOH . D 4 HOH A 43 443 34 HOH HOH . D 4 HOH A 44 444 53 HOH HOH . D 4 HOH A 45 445 59 HOH HOH . D 4 HOH A 46 446 51 HOH HOH . D 4 HOH A 47 447 56 HOH HOH . D 4 HOH A 48 448 25 HOH HOH . E 4 HOH B 1 201 16 HOH HOH . E 4 HOH B 2 202 33 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 C1 6D6 . . . C 3 13.13 -11.687 22.466 1 50.62 ? C1 6D6 101 B 1 HETATM 2 C C2 6D6 . . . C 3 14.666 -11.555 22.231 1 56 ? C2 6D6 101 B 1 HETATM 3 C C3 6D6 . . . C 3 15.21 -12.377 20.99 1 58.28 ? C3 6D6 101 B 1 HETATM 4 C C4 6D6 . . . C 3 16.813 -10.604 20.166 1 49.68 ? C4 6D6 101 B 1 HETATM 5 C C5 6D6 . . . C 3 16.31 -8.949 18.203 1 50.78 ? C5 6D6 101 B 1 HETATM 6 C C6 6D6 . . . C 3 17.561 -12.31 21.826 1 49.28 ? C6 6D6 101 B 1 HETATM 7 C C7 6D6 . . . C 3 19.504 -13.794 20.832 1 56.35 ? C7 6D6 101 B 1 HETATM 8 C C8 6D6 . . . C 3 21.251 -13.805 24.78 1 58.77 ? C8 6D6 101 B 1 HETATM 9 C C9 6D6 . . . C 3 22.575 -12.267 25.504 1 64.71 ? C9 6D6 101 B 1 HETATM 10 N N2 6D6 . . . C 3 16.634 -12.012 20.675 1 54.53 ? N2 6D6 101 B 1 HETATM 11 C C10 6D6 . . . C 3 15.814 -10.204 19.046 1 53.41 ? C10 6D6 101 B 1 HETATM 12 N N3 6D6 . . . C 3 16.859 -7.936 19.109 1 49.27 ? N3 6D6 101 B 1 HETATM 13 C C11 6D6 . . . C 3 15.141 -8.34 17.428 1 49.76 ? C11 6D6 101 B 1 HETATM 14 O O1 6D6 . . . C 3 14.598 -8.928 16.462 1 45.72 -1 O1 6D6 101 B 1 HETATM 15 O O2 6D6 . . . C 3 14.725 -7.245 17.824 1 48.89 ? O2 6D6 101 B 1 HETATM 16 C C12 6D6 . . . C 3 19.066 -12.346 21.346 1 56.4 ? C12 6D6 101 B 1 HETATM 17 O O3 6D6 . . . C 3 19.842 -12.064 22.331 1 51.13 ? O3 6D6 101 B 1 HETATM 18 C C13 6D6 . . . C 3 21.059 -13.105 22.362 1 58.73 ? C13 6D6 101 B 1 HETATM 19 C C14 6D6 . . . C 3 20.537 -14.27 21.881 1 56.84 ? C14 6D6 101 B 1 HETATM 20 O O4 6D6 . . . C 3 21.498 -15.15 21.294 1 61.09 ? O4 6D6 101 B 1 HETATM 21 O O5 6D6 . . . C 3 20.056 -13.797 19.534 1 44.07 ? O5 6D6 101 B 1 HETATM 22 N N4 6D6 . . . C 3 21.548 -13.039 23.757 1 58.96 ? N4 6D6 101 B 1 HETATM 23 N N5 6D6 . . . C 3 21.882 -13.35 25.849 1 61.44 ? N5 6D6 101 B 1 HETATM 24 C C15 6D6 . . . C 3 23.412 -11.364 26.156 1 54.72 ? C15 6D6 101 B 1 HETATM 25 N N6 6D6 . . . C 3 23.685 -11.537 27.584 1 52.36 ? N6 6D6 101 B 1 HETATM 26 N N7 6D6 . . . C 3 23.949 -10.369 25.469 1 54.18 ? N7 6D6 101 B 1 HETATM 27 C C16 6D6 . . . C 3 23.712 -10.195 24.189 1 56.11 ? C16 6D6 101 B 1 HETATM 28 N N8 6D6 . . . C 3 22.925 -11.022 23.543 1 55 ? N8 6D6 101 B 1 HETATM 29 C C17 6D6 . . . C 3 22.354 -12.052 24.172 1 60.15 ? C17 6D6 101 B 1 HETATM 30 H H1 6D6 . . . C 3 12.892 -11.528 23.398 1 60.81 ? H1 6D6 101 B 1 HETATM 31 H H2 6D6 . . . C 3 12.663 -11.008 21.944 1 60.81 ? H2 6D6 101 B 1 HETATM 32 H H3 6D6 . . . C 3 15.147 -11.844 23.033 1 67.27 ? H3 6D6 101 B 1 HETATM 33 H H4 6D6 . . . C 3 14.902 -10.618 22.101 1 67.27 ? H4 6D6 101 B 1 HETATM 34 H H5 6D6 . . . C 3 14.635 -12.241 20.217 1 70.01 ? H5 6D6 101 B 1 HETATM 35 H H6 6D6 . . . C 3 15.18 -13.335 21.176 1 70.01 ? H6 6D6 101 B 1 HETATM 36 H H7 6D6 . . . C 3 17.708 -10.524 19.793 1 59.69 ? H7 6D6 101 B 1 HETATM 37 H H8 6D6 . . . C 3 16.763 -9.98 20.916 1 59.69 ? H8 6D6 101 B 1 HETATM 38 H H9 6D6 . . . C 3 17.002 -9.244 17.568 1 61.01 ? H9 6D6 101 B 1 HETATM 39 H H10 6D6 . . . C 3 17.336 -13.177 22.211 1 59.21 ? H10 6D6 101 B 1 HETATM 40 H H11 6D6 . . . C 3 17.422 -11.641 22.526 1 59.21 ? H11 6D6 101 B 1 HETATM 41 H H12 6D6 . . . C 3 18.719 -14.379 20.794 1 67.69 ? H12 6D6 101 B 1 HETATM 42 H H13 6D6 . . . C 3 20.699 -14.555 24.764 1 70.59 ? H13 6D6 101 B 1 HETATM 43 H H18 6D6 . . . C 3 14.942 -9.994 19.436 1 64.16 ? H18 6D6 101 B 1 HETATM 44 H H19 6D6 . . . C 3 15.663 -10.964 18.447 1 64.16 ? H19 6D6 101 B 1 HETATM 45 H H20 6D6 . . . C 3 16.238 -7.605 19.661 1 59.2 ? H20 6D6 101 B 1 HETATM 46 H H21 6D6 . . . C 3 17.263 -7.251 18.692 1 59.2 ? H21 6D6 101 B 1 HETATM 47 H H24 6D6 . . . C 3 19.248 -11.673 20.666 1 67.76 ? H24 6D6 101 B 1 HETATM 48 H H25 6D6 . . . C 3 21.753 -12.749 21.781 1 70.55 ? H25 6D6 101 B 1 HETATM 49 H H26 6D6 . . . C 3 20.089 -14.777 22.59 1 68.28 ? H26 6D6 101 B 1 HETATM 50 H H27 6D6 . . . C 3 21.877 -14.82 20.601 1 73.38 ? H27 6D6 101 B 1 HETATM 51 H H28 6D6 . . . C 3 20.572 -13.133 19.394 1 52.95 ? H28 6D6 101 B 1 HETATM 52 H H29 6D6 . . . C 3 24.186 -10.977 27.999 1 62.9 ? H29 6D6 101 B 1 HETATM 53 H H30 6D6 . . . C 3 23.347 -12.196 28.022 1 62.9 ? H30 6D6 101 B 1 HETATM 54 H H31 6D6 . . . C 3 24.104 -9.484 23.736 1 67.4 ? H31 6D6 101 B 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 54 #