data_5OOD # _model_server_result.job_id hT8vvZNQ-FoXm8etXN-KXA _model_server_result.datetime_utc '2025-07-17 05:39:40' _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 5ood # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":405}' # _entry.id 5OOD # _exptl.entry_id 5OOD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 673.841 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-10-(4-azanylbutyl)-4-(4-hydroxyphenyl)-7-(1~{H}-indol-3-ylmethyl)-8,13,15,19-tetramethyl-1-oxa-5,8,11-triazacyclononadec-15-ene-2,6,9,12-tetrone _entity.pdbx_number_of_molecules 5 _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 5OOD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OOD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,V,W,X,Y _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 ? _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 ? 4 H N N ? 4 J N N ? 4 N N N ? 4 R N N ? 4 V 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 covale ? covale1 A C GLU 72 A GLU 72 1_555 A N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C HIC 73 A HIC 73 1_555 A N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 B C GLU 72 B GLU 72 1_555 B N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 B C HIC 73 B HIC 73 1_555 B N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale9 E C GLU 72 E GLU 72 1_555 E N HIC 73 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 E C HIC 73 E HIC 73 1_555 E N GLY 74 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 F O3B ADP . A ADP 401 1_555 I MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc2 G O3 PO4 . A PO4 402 1_555 I MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc3 K O3B ADP . B ADP 401 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc4 L O3 PO4 . B PO4 402 1_555 M MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc5 O O3B ADP . C ADP 401 1_555 Q MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc6 P O3 PO4 . C PO4 402 1_555 Q MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc7 S O3B ADP . D ADP 401 1_555 U MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc8 T O3 PO4 . D PO4 402 1_555 U MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc9 W O3B ADP . E ADP 401 1_555 Y MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc10 X O3 PO4 . E PO4 402 1_555 Y MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? # _chem_comp.formula 'C38 H51 N5 O6' _chem_comp.formula_weight 673.841 _chem_comp.id 9ZK _chem_comp.mon_nstd_flag . _chem_comp.name (4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-10-(4-azanylbutyl)-4-(4-hydroxyphenyl)-7-(1~{H}-indol-3-ylmethyl)-8,13,15,19-tetramethyl-1-oxa-5,8,11-triazacyclononadec-15-ene-2,6,9,12-tetrone _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 O47 C36 9ZK doub 1 n n C40 C41 9ZK doub 2 n y C40 C39 9ZK sing 3 n y O05 C04 9ZK doub 4 n n C38 C46 9ZK sing 5 n n C38 C39 9ZK sing 6 n n C38 N37 9ZK sing 7 n n N21 C20 9ZK sing 8 n n C02 C01 9ZK sing 9 n n C02 O03 9ZK sing 10 n n C02 C06 9ZK sing 11 n n C46 C04 9ZK sing 12 n n C04 O03 9ZK sing 13 n n C26 C25 9ZK sing 14 n n C26 C27 9ZK sing 15 n n C41 C42 9ZK sing 16 n y C24 N23 9ZK sing 17 n n C17 C16 9ZK sing 18 n n C17 C18 9ZK sing 19 n n C16 C22 9ZK sing 20 n n C16 N15 9ZK sing 21 n n C36 N37 9ZK sing 22 n n C36 C25 9ZK sing 23 n n C39 C45 9ZK doub 24 n y C10 C09 9ZK sing 25 n n N23 C22 9ZK sing 26 n n N23 C25 9ZK sing 27 n n C22 O48 9ZK doub 28 n n C07 C06 9ZK sing 29 n n C07 C08 9ZK sing 30 n n C28 C27 9ZK doub 31 n y C28 N29 9ZK sing 32 n y C20 C19 9ZK sing 33 n n C27 C31 9ZK sing 34 n y N15 C14 9ZK sing 35 n n C42 O43 9ZK sing 36 n n C42 C44 9ZK doub 37 n y C45 C44 9ZK sing 38 n y C18 C19 9ZK sing 39 n n N29 C30 9ZK sing 40 n y C09 C08 9ZK doub 41 e n C09 C11 9ZK sing 42 n n C14 O49 9ZK doub 43 n n C14 C12 9ZK sing 44 n n C31 C30 9ZK doub 45 n y C31 C32 9ZK sing 46 n y C13 C12 9ZK sing 47 n n C30 C35 9ZK sing 48 n y C32 C33 9ZK doub 49 n y C12 C11 9ZK sing 50 n n C35 C34 9ZK doub 51 n y C33 C34 9ZK sing 52 n y C40 H1 9ZK sing 53 n n C41 H2 9ZK sing 54 n n C35 H3 9ZK sing 55 n n C34 H4 9ZK sing 56 n n C33 H5 9ZK sing 57 n n C32 H6 9ZK sing 58 n n C28 H7 9ZK sing 59 n n C38 H8 9ZK sing 60 n n C26 H9 9ZK sing 61 n n C26 H10 9ZK sing 62 n n C25 H11 9ZK sing 63 n n C24 H12 9ZK sing 64 n n C24 H13 9ZK sing 65 n n C24 H14 9ZK sing 66 n n C20 H15 9ZK sing 67 n n C20 H16 9ZK sing 68 n n C19 H17 9ZK sing 69 n n C19 H18 9ZK sing 70 n n C18 H19 9ZK sing 71 n n C18 H20 9ZK sing 72 n n C17 H21 9ZK sing 73 n n C17 H22 9ZK sing 74 n n C16 H23 9ZK sing 75 n n C13 H24 9ZK sing 76 n n C13 H25 9ZK sing 77 n n C13 H26 9ZK sing 78 n n C12 H27 9ZK sing 79 n n C11 H28 9ZK sing 80 n n C11 H29 9ZK sing 81 n n C10 H30 9ZK sing 82 n n C10 H31 9ZK sing 83 n n C10 H32 9ZK sing 84 n n C44 H33 9ZK sing 85 n n N15 H34 9ZK sing 86 n n C08 H35 9ZK sing 87 n n C07 H36 9ZK sing 88 n n C07 H37 9ZK sing 89 n n C06 H38 9ZK sing 90 n n C06 H39 9ZK sing 91 n n C02 H40 9ZK sing 92 n n C01 H41 9ZK sing 93 n n C01 H42 9ZK sing 94 n n C01 H43 9ZK sing 95 n n C46 H44 9ZK sing 96 n n C46 H45 9ZK sing 97 n n N37 H46 9ZK sing 98 n n N29 H47 9ZK sing 99 n n C45 H48 9ZK sing 100 n n O43 H49 9ZK sing 101 n n N21 H50 9ZK sing 102 n n N21 H51 9ZK sing 103 n n # _atom_sites.entry_id 5OOD _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 2 ADP A 1 401 376 ADP ADP . G 3 PO4 A 1 402 377 PO4 PO4 . H 4 9ZK A 1 403 378 9ZK 9ZK . I 5 MG A 1 404 379 MG MG . J 4 9ZK A 1 405 378 9ZK 9ZK . K 2 ADP B 1 401 376 ADP ADP . L 3 PO4 B 1 402 377 PO4 PO4 . M 5 MG B 1 403 379 MG MG . N 4 9ZK B 1 404 378 9ZK 9ZK . O 2 ADP C 1 401 376 ADP ADP . P 3 PO4 C 1 402 377 PO4 PO4 . Q 5 MG C 1 403 379 MG MG . R 4 9ZK C 1 404 378 9ZK 9ZK . S 2 ADP D 1 401 376 ADP ADP . T 3 PO4 D 1 402 377 PO4 PO4 . U 5 MG D 1 403 379 MG MG . V 4 9ZK D 1 404 378 9ZK 9ZK . W 2 ADP E 1 401 376 ADP ADP . X 3 PO4 E 1 402 377 PO4 PO4 . Y 5 MG E 1 403 379 MG MG . # 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 C40 9ZK . . . J 4 156.268 172.195 168.885 1 33.33 ? C40 9ZK 405 A 1 HETATM 2 C C41 9ZK . . . J 4 155.124 172.875 169.123 1 33.83 ? C41 9ZK 405 A 1 HETATM 3 C C35 9ZK . . . J 4 155.016 165.471 172.343 1 31.5 ? C35 9ZK 405 A 1 HETATM 4 C C34 9ZK . . . J 4 155.146 166.5 173.19 1 27.74 ? C34 9ZK 405 A 1 HETATM 5 C C33 9ZK . . . J 4 155.66 167.662 172.747 1 29.56 ? C33 9ZK 405 A 1 HETATM 6 C C32 9ZK . . . J 4 156.039 167.797 171.461 1 29.37 ? C32 9ZK 405 A 1 HETATM 7 C C42 9ZK . . . J 4 155.178 174.188 169.469 1 40.25 ? C42 9ZK 405 A 1 HETATM 8 C C31 9ZK . . . J 4 155.898 166.744 170.61 1 29.58 ? C31 9ZK 405 A 1 HETATM 9 C C39 9ZK . . . J 4 157.469 172.791 168.983 1 32.53 ? C39 9ZK 405 A 1 HETATM 10 C C30 9ZK . . . J 4 155.4 165.598 171.035 1 31.72 ? C30 9ZK 405 A 1 HETATM 11 C C28 9ZK . . . J 4 155.845 165.314 168.935 1 35.85 ? C28 9ZK 405 A 1 HETATM 12 C C27 9ZK . . . J 4 156.176 166.576 169.296 1 32.22 ? C27 9ZK 405 A 1 HETATM 13 C C38 9ZK . . . J 4 158.702 171.968 168.688 1 36.16 ? C38 9ZK 405 A 1 HETATM 14 C C26 9ZK . . . J 4 156.74 167.654 168.461 1 32.92 ? C26 9ZK 405 A 1 HETATM 15 C C25 9ZK . . . J 4 157.814 168.403 169.197 1 31.39 ? C25 9ZK 405 A 1 HETATM 16 C C24 9ZK . . . J 4 160.217 168.597 168.588 1 36.01 ? C24 9ZK 405 A 1 HETATM 17 C C22 9ZK . . . J 4 159.221 166.428 168.958 1 35.67 ? C22 9ZK 405 A 1 HETATM 18 C C20 9ZK . . . J 4 159.934 161.174 169.842 1 49.05 ? C20 9ZK 405 A 1 HETATM 19 C C19 9ZK . . . J 4 160.62 162.544 169.977 1 44.02 ? C19 9ZK 405 A 1 HETATM 20 C C18 9ZK . . . J 4 159.705 163.688 169.605 1 37.92 ? C18 9ZK 405 A 1 HETATM 21 C C17 9ZK . . . J 4 160.164 164.36 168.33 1 34.87 ? C17 9ZK 405 A 1 HETATM 22 C C16 9ZK . . . J 4 160.543 165.764 168.667 1 36.67 ? C16 9ZK 405 A 1 HETATM 23 C C14 9ZK . . . J 4 162.614 164.85 169.778 1 38.79 ? C14 9ZK 405 A 1 HETATM 24 C C13 9ZK . . . J 4 164.975 164.991 170.351 1 34.42 ? C13 9ZK 405 A 1 HETATM 25 C C12 9ZK . . . J 4 163.591 164.943 170.911 1 33.58 ? C12 9ZK 405 A 1 HETATM 26 C C11 9ZK . . . J 4 163.317 166.193 171.646 1 35.24 ? C11 9ZK 405 A 1 HETATM 27 C C10 9ZK . . . J 4 163.475 167.19 169.248 1 37.92 ? C10 9ZK 405 A 1 HETATM 28 C C44 9ZK . . . J 4 156.411 174.781 169.571 1 42.56 ? C44 9ZK 405 A 1 HETATM 29 C C36 9ZK . . . J 4 157.92 169.75 168.664 1 31.9 ? C36 9ZK 405 A 1 HETATM 30 N N23 9ZK . . . J 4 159.068 167.824 168.92 1 33.28 ? N23 9ZK 405 A 1 HETATM 31 N N15 9ZK . . . J 4 161.523 165.781 169.731 1 35.11 ? N15 9ZK 405 A 1 HETATM 32 C C09 9ZK . . . J 4 163.57 167.371 170.742 1 32.65 ? C09 9ZK 405 A 1 HETATM 33 C C08 9ZK . . . J 4 163.874 168.56 171.161 1 33.34 ? C08 9ZK 405 A 1 HETATM 34 C C07 9ZK . . . J 4 164.111 169.693 170.199 1 34.71 ? C07 9ZK 405 A 1 HETATM 35 C C06 9ZK . . . J 4 162.849 170.095 169.511 1 37.38 ? C06 9ZK 405 A 1 HETATM 36 C C02 9ZK . . . J 4 163.125 171.067 168.386 1 40.37 ? C02 9ZK 405 A 1 HETATM 37 C C01 9ZK . . . J 4 164.642 171.273 168.289 1 41 ? C01 9ZK 405 A 1 HETATM 38 O O03 9ZK . . . J 4 162.448 172.298 168.592 1 36.7 ? O03 9ZK 405 A 1 HETATM 39 C C04 9ZK . . . J 4 161.141 172.368 168.122 1 41.51 ? C04 9ZK 405 A 1 HETATM 40 C C46 9ZK . . . J 4 159.992 172.739 169.012 1 37.07 ? C46 9ZK 405 A 1 HETATM 41 N N37 9ZK . . . J 4 158.696 170.695 169.365 1 33.56 ? N37 9ZK 405 A 1 HETATM 42 N N29 9ZK . . . J 4 155.372 164.724 170.007 1 33.94 ? N29 9ZK 405 A 1 HETATM 43 O O47 9ZK . . . J 4 157.394 170.059 167.69 1 35.25 ? O47 9ZK 405 A 1 HETATM 44 C C45 9ZK . . . J 4 157.547 174.082 169.327 1 34.42 ? C45 9ZK 405 A 1 HETATM 45 O O43 9ZK . . . J 4 153.999 174.9 169.707 1 38.8 ? O43 9ZK 405 A 1 HETATM 46 O O05 9ZK . . . J 4 160.932 172.124 167.002 1 43.9 ? O05 9ZK 405 A 1 HETATM 47 O O49 9ZK . . . J 4 162.765 164.029 168.961 1 44.09 ? O49 9ZK 405 A 1 HETATM 48 N N21 9ZK . . . J 4 159.017 161.069 168.72 1 55.13 ? N21 9ZK 405 A 1 HETATM 49 O O48 9ZK . . . J 4 158.286 165.786 169.222 1 38.21 ? O48 9ZK 405 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 49 #