data_5JA1 # _model_server_result.job_id MSYWGgMJ2JU3-I5f9yhAfw _model_server_result.datetime_utc '2024-11-04 23:08:41' _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 5ja1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1301}' # _entry.id 5JA1 # _exptl.entry_id 5JA1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 773.773 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}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 97.93 _cell.angle_gamma 90 _cell.entry_id 5JA1 _cell.length_a 161.185 _cell.length_b 57.679 _cell.length_c 183.945 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JA1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 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,F _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OG _struct_conn.ptnr1_label_comp_id SER _struct_conn.ptnr1_label_seq_id 1008 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id SER _struct_conn.ptnr1_auth_seq_id 1006 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id P1 _struct_conn.ptnr2_label_comp_id 75C _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 75C _struct_conn.ptnr2_auth_seq_id 1301 _struct_conn.ptnr2_symmetry 1_555 _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 1.61 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C25 H44 N9 O13 P S2' _chem_comp.formula_weight 773.773 _chem_comp.id 75C _chem_comp.mon_nstd_flag . _chem_comp.name "5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}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 C20 C18 75C sing 1 n n O6 P1 75C sing 2 n n O9 C16 75C doub 3 n n O8 P1 75C sing 4 n n O8 C19 75C sing 5 n n C18 C17 75C sing 6 n n C18 C19 75C sing 7 n n C18 C21 75C sing 8 n n P1 O1 75C doub 9 n n C16 C17 75C sing 10 n n C16 N9 75C sing 11 n n C17 O10 75C sing 12 n n N9 C15 75C sing 13 n n C15 C14 75C sing 14 n n O7 C13 75C doub 15 n n C14 C13 75C sing 16 n n C13 N8 75C sing 17 n n N8 C12 75C sing 18 n n C12 C11 75C sing 19 n n C11 S2 75C sing 20 n n C4 S2 75C sing 21 n n C4 C9 75C sing 22 n n C4 C5 75C sing 23 n n C9 C10 75C sing 24 n n C9 N3 75C sing 25 n n O11 C10 75C sing 26 n n O4 S1 75C doub 27 n n C5 S1 75C sing 28 n n S1 N1 75C sing 29 n n S1 O5 75C doub 30 n n N1 C7 75C sing 31 n n C7 C25 75C sing 32 n n N6 C3 75C doub 33 n y N6 C8 75C sing 34 n y C3 N7 75C sing 35 n y O12 C25 75C sing 36 n n O12 C22 75C sing 37 n n N5 C2 75C sing 38 n n C25 C24 75C sing 39 n n C8 C2 75C doub 40 n y C8 C1 75C sing 41 n y N7 C22 75C sing 42 n n N7 C1 75C sing 43 n y C2 N2 75C sing 44 n y C22 C23 75C sing 45 n n C1 N4 75C doub 46 n y N2 C6 75C doub 47 n y C24 C23 75C sing 48 n n C24 O2 75C sing 49 n n N4 C6 75C sing 50 n y C23 O3 75C sing 51 n n C3 H2 75C sing 52 n n O2 H3 75C sing 53 n n C4 H4 75C sing 54 n n N1 H5 75C sing 55 n n C5 H6 75C sing 56 n n C5 H7 75C sing 57 n n C6 H8 75C sing 58 n n N3 H9 75C sing 59 n n N3 H10 75C sing 60 n n O3 H12 75C sing 61 n n C7 H13 75C sing 62 n n C7 H14 75C sing 63 n n N5 H15 75C sing 64 n n N5 H16 75C sing 65 n n C9 H17 75C sing 66 n n C10 H18 75C sing 67 n n C10 H19 75C sing 68 n n C11 H20 75C sing 69 n n C11 H21 75C sing 70 n n C12 H22 75C sing 71 n n C12 H23 75C sing 72 n n O6 H24 75C sing 73 n n N8 H25 75C sing 74 n n C14 H26 75C sing 75 n n C14 H27 75C sing 76 n n C15 H28 75C sing 77 n n C15 H29 75C sing 78 n n N9 H30 75C sing 79 n n C17 H31 75C sing 80 n n O10 H32 75C sing 81 n n C19 H33 75C sing 82 n n C19 H34 75C sing 83 n n C20 H35 75C sing 84 n n C20 H36 75C sing 85 n n C20 H37 75C sing 86 n n C21 H38 75C sing 87 n n C21 H39 75C sing 88 n n C21 H40 75C sing 89 n n O11 H41 75C sing 90 n n C22 H42 75C sing 91 n n C23 H43 75C sing 92 n n C24 H44 75C sing 93 n n C25 H45 75C sing 94 n n P1 O13 75C sing 95 n n O13 H1 75C sing 96 n n # _atom_sites.entry_id 5JA1 _atom_sites.fract_transf_matrix[1][1] 0.006204 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000864 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017337 _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] 0.005489 _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 75C A 1 1301 701 75C 4T8 . D 4 CL A 1 1302 1 CL CL . E 5 HOH A 1 1401 20 HOH HOH . E 5 HOH A 2 1402 3 HOH HOH . E 5 HOH A 3 1403 29 HOH HOH . E 5 HOH A 4 1404 19 HOH HOH . E 5 HOH A 5 1405 10 HOH HOH . E 5 HOH A 6 1406 40 HOH HOH . E 5 HOH A 7 1407 11 HOH HOH . E 5 HOH A 8 1408 56 HOH HOH . E 5 HOH A 9 1409 8 HOH HOH . E 5 HOH A 10 1410 5 HOH HOH . E 5 HOH A 11 1411 7 HOH HOH . E 5 HOH A 12 1412 25 HOH HOH . E 5 HOH A 13 1413 21 HOH HOH . E 5 HOH A 14 1414 54 HOH HOH . E 5 HOH A 15 1415 12 HOH HOH . E 5 HOH A 16 1416 2 HOH HOH . E 5 HOH A 17 1417 4 HOH HOH . E 5 HOH A 18 1418 6 HOH HOH . E 5 HOH A 19 1419 50 HOH HOH . E 5 HOH A 20 1420 15 HOH HOH . E 5 HOH A 21 1421 30 HOH HOH . E 5 HOH A 22 1422 58 HOH HOH . E 5 HOH A 23 1423 39 HOH HOH . E 5 HOH A 24 1424 51 HOH HOH . E 5 HOH A 25 1425 52 HOH HOH . E 5 HOH A 26 1426 45 HOH HOH . E 5 HOH A 27 1427 17 HOH HOH . E 5 HOH A 28 1428 28 HOH HOH . E 5 HOH A 29 1429 44 HOH HOH . E 5 HOH A 30 1430 14 HOH HOH . E 5 HOH A 31 1431 16 HOH HOH . E 5 HOH A 32 1432 41 HOH HOH . E 5 HOH A 33 1433 36 HOH HOH . E 5 HOH A 34 1434 31 HOH HOH . E 5 HOH A 35 1435 13 HOH HOH . E 5 HOH A 36 1436 55 HOH HOH . E 5 HOH A 37 1437 22 HOH HOH . E 5 HOH A 38 1438 23 HOH HOH . E 5 HOH A 39 1439 18 HOH HOH . E 5 HOH A 40 1440 27 HOH HOH . E 5 HOH A 41 1441 46 HOH HOH . E 5 HOH A 42 1442 26 HOH HOH . E 5 HOH A 43 1443 53 HOH HOH . E 5 HOH A 44 1444 57 HOH HOH . E 5 HOH A 45 1445 43 HOH HOH . F 5 HOH B 1 101 9 HOH HOH . F 5 HOH B 2 102 1 HOH HOH . F 5 HOH B 3 103 24 HOH HOH . F 5 HOH B 4 104 42 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 O O1 75C . . . C 3 -47.689 8.435 -25.78 1 22.64 ? O1 75C 1301 A 1 HETATM 2 C C1 75C . . . C 3 -58.873 8.923 -14.763 1 17.74 ? C1 75C 1301 A 1 HETATM 3 C C2 75C . . . C 3 -60.438 10.702 -15.068 1 19.03 ? C2 75C 1301 A 1 HETATM 4 C C3 75C . . . C 3 -59.689 7.369 -16.042 1 23.39 ? C3 75C 1301 A 1 HETATM 5 O O2 75C . . . C 3 -58.014 3.74 -12.95 1 27.87 ? O2 75C 1301 A 1 HETATM 6 C C4 75C . . . C 3 -59.776 3.346 -20.141 1 45.25 ? C4 75C 1301 A 1 HETATM 7 N N1 75C . . . C 3 -57.849 3.662 -17.493 1 24.7 ? N1 75C 1301 A 1 HETATM 8 S S1 75C . . . C 3 -58.138 2.287 -18.265 1 26.12 ? S1 75C 1301 A 1 HETATM 9 C C5 75C . . . C 3 -59.652 2.383 -18.95 1 43.2 ? C5 75C 1301 A 1 HETATM 10 N N2 75C . . . C 3 -59.708 11.452 -14.212 1 19.19 ? N2 75C 1301 A 1 HETATM 11 C C6 75C . . . C 3 -58.597 10.957 -13.647 1 20.71 ? C6 75C 1301 A 1 HETATM 12 N N3 75C . . . C 3 -62.05 3.123 -19.295 1 27.28 ? N3 75C 1301 A 1 HETATM 13 O O3 75C . . . C 3 -56.733 5.967 -12.706 1 11.75 ? O3 75C 1301 A 1 HETATM 14 C C7 75C . . . C 3 -58.586 3.691 -16.223 1 16.29 ? C7 75C 1301 A 1 HETATM 15 N N4 75C . . . C 3 -58.176 9.713 -13.912 1 15.12 ? N4 75C 1301 A 1 HETATM 16 C C8 75C . . . C 3 -60.024 9.41 -15.359 1 22.91 ? C8 75C 1301 A 1 HETATM 17 N N5 75C . . . C 3 -61.56 11.206 -15.638 1 5.56 ? N5 75C 1301 A 1 HETATM 18 N N6 75C . . . C 3 -60.516 8.433 -16.149 1 21.37 ? N6 75C 1301 A 1 HETATM 19 N N7 75C . . . C 3 -58.689 7.675 -15.2 1 21.06 ? N7 75C 1301 A 1 HETATM 20 C C9 75C . . . C 3 -61.176 3.961 -20.138 1 32.09 ? C9 75C 1301 A 1 HETATM 21 C C10 75C . . . C 3 -61.223 5.381 -19.587 1 30.77 ? C10 75C 1301 A 1 HETATM 22 S S2 75C . . . C 3 -58.546 4.619 -20.156 1 58.44 ? S2 75C 1301 A 1 HETATM 23 P P1 75C . . . C 3 -47.681 8.703 -27.595 1 21.84 ? P1 75C 1301 A 1 HETATM 24 C C11 75C . . . C 3 -58.547 5.494 -21.694 1 45.56 ? C11 75C 1301 A 1 HETATM 25 O O4 75C . . . C 3 -57.122 2.069 -19.258 1 27.86 ? O4 75C 1301 A 1 HETATM 26 C C12 75C . . . C 3 -58.11 4.608 -22.856 1 37.95 ? C12 75C 1301 A 1 HETATM 27 O O5 75C . . . C 3 -58.111 1.21 -17.315 1 35.38 ? O5 75C 1301 A 1 HETATM 28 O O6 75C . . . C 3 -46.849 7.483 -28.684 1 30.35 ? O6 75C 1301 A 1 HETATM 29 N N8 75C . . . C 3 -56.865 5.196 -23.336 1 36.14 ? N8 75C 1301 A 1 HETATM 30 C C13 75C . . . C 3 -56.656 5.814 -24.418 1 36.99 ? C13 75C 1301 A 1 HETATM 31 O O7 75C . . . C 3 -57.527 6.008 -25.25 1 53.45 ? O7 75C 1301 A 1 HETATM 32 O O8 75C . . . C 3 -49.316 8.869 -28.146 1 15.86 ? O8 75C 1301 A 1 HETATM 33 C C14 75C . . . C 3 -55.251 6.319 -24.66 1 26.1 ? C14 75C 1301 A 1 HETATM 34 C C15 75C . . . C 3 -55.172 6.937 -26.052 1 26.95 ? C15 75C 1301 A 1 HETATM 35 N N9 75C . . . C 3 -53.806 7.417 -26.203 1 24.84 ? N9 75C 1301 A 1 HETATM 36 C C16 75C . . . C 3 -53.136 7.402 -27.272 1 27.78 ? C16 75C 1301 A 1 HETATM 37 O O9 75C . . . C 3 -53.584 6.945 -28.312 1 30.24 ? O9 75C 1301 A 1 HETATM 38 C C17 75C . . . C 3 -51.734 7.946 -27.218 1 25.88 ? C17 75C 1301 A 1 HETATM 39 O O10 75C . . . C 3 -51.276 7.939 -25.86 1 26.01 ? O10 75C 1301 A 1 HETATM 40 C C18 75C . . . C 3 -51.621 9.368 -27.765 1 24.38 ? C18 75C 1301 A 1 HETATM 41 C C19 75C . . . C 3 -50.187 9.836 -27.564 1 20.96 ? C19 75C 1301 A 1 HETATM 42 C C20 75C . . . C 3 -51.965 9.427 -29.247 1 24.91 ? C20 75C 1301 A 1 HETATM 43 C C21 75C . . . C 3 -52.551 10.3 -26.998 1 24.04 ? C21 75C 1301 A 1 HETATM 44 O O11 75C . . . C 3 -62.471 5.962 -19.984 1 31.75 ? O11 75C 1301 A 1 HETATM 45 C C22 75C . . . C 3 -57.573 6.783 -14.807 1 8.22 ? C22 75C 1301 A 1 HETATM 46 C C23 75C . . . C 3 -57.915 6.092 -13.5 1 10.83 ? C23 75C 1301 A 1 HETATM 47 C C24 75C . . . C 3 -58.411 4.723 -13.91 1 16.36 ? C24 75C 1301 A 1 HETATM 48 C C25 75C . . . C 3 -57.731 4.481 -15.245 1 14.37 ? C25 75C 1301 A 1 HETATM 49 O O12 75C . . . C 3 -57.413 5.763 -15.795 1 1.01 ? O12 75C 1301 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 49 #