data_1K39 # _model_server_result.job_id '_ZI_HjPAzIrF9CpX6BTRVQ' _model_server_result.datetime_utc '2025-08-31 20:23:21' _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 1k39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":302}' # _entry.id 1K39 # _exptl.entry_id 1K39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 893.73 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'OCTANOYL-COENZYME A' _entity.pdbx_number_of_molecules 3 _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 1K39 _cell.length_a 116.65 _cell.length_b 116.65 _cell.length_c 216.78 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1K39 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_556 -y,-x,-z+3/2 0 -1 0 -1 0 0 0 0 -1 0 0 325.17 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 G N N ? 3 I N N # _chem_comp.formula 'C29 H50 N7 O17 P3 S' _chem_comp.formula_weight 893.73 _chem_comp.id CO8 _chem_comp.mon_nstd_flag . _chem_comp.name 'OCTANOYL-COENZYME A' _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 N1A C2A CO8 sing 70 n y N1A C6A CO8 doub 71 n y C2A N3A CO8 doub 72 n y C2A H2A CO8 sing 73 n n N3A C4A CO8 sing 74 n y C4A C5A CO8 doub 75 n y C4A N9A CO8 sing 76 n y C5A C6A CO8 sing 77 n y C5A N7A CO8 sing 78 n y C6A N6A CO8 sing 79 n n N6A H61A CO8 sing 80 n n N6A H62A CO8 sing 81 n n N7A C8A CO8 doub 82 n y C8A N9A CO8 sing 83 n y C8A H8A CO8 sing 84 n n N9A C1B CO8 sing 85 n n C1B C2B CO8 sing 86 n n C1B O4B CO8 sing 87 n n C1B H1B CO8 sing 88 n n C2B O2B CO8 sing 89 n n C2B C3B CO8 sing 90 n n C2B H2B CO8 sing 91 n n O2B HO2A CO8 sing 92 n n C3B O3B CO8 sing 93 n n C3B C4B CO8 sing 94 n n C3B H3B CO8 sing 95 n n O3B P3B CO8 sing 96 n n P3B O7A CO8 doub 97 n n P3B O8A CO8 sing 98 n n P3B O9A CO8 sing 99 n n O8A HOA8 CO8 sing 100 n n O9A HOA9 CO8 sing 101 n n C4B O4B CO8 sing 102 n n C4B C5B CO8 sing 103 n n C4B H4B CO8 sing 104 n n C5B O5B CO8 sing 105 n n C5B H51A CO8 sing 106 n n C5B H52A CO8 sing 107 n n O5B P1A CO8 sing 108 n n P1A O1A CO8 doub 109 n n P1A O2A CO8 sing 110 n n P1A O3A CO8 sing 111 n n O2A HOA2 CO8 sing 112 n n O3A P2A CO8 sing 113 n n P2A O4A CO8 doub 114 n n P2A O5A CO8 sing 115 n n P2A O6A CO8 sing 116 n n O5A HOA5 CO8 sing 117 n n O6A CCP CO8 sing 118 n n CBP CCP CO8 sing 119 n n CBP CDP CO8 sing 120 n n CBP CEP CO8 sing 121 n n CBP CAP CO8 sing 122 n n CCP H121 CO8 sing 123 n n CCP H122 CO8 sing 124 n n CDP H131 CO8 sing 125 n n CDP H132 CO8 sing 126 n n CDP H133 CO8 sing 127 n n CEP H141 CO8 sing 128 n n CEP H142 CO8 sing 129 n n CEP H143 CO8 sing 130 n n CAP OAP CO8 sing 131 n n CAP C9P CO8 sing 132 n n CAP H10 CO8 sing 133 n n OAP HO1 CO8 sing 134 n n C9P O9P CO8 doub 135 n n C9P N8P CO8 sing 136 n n N8P C7P CO8 sing 137 n n N8P HN8 CO8 sing 138 n n C7P C6P CO8 sing 139 n n C7P H71 CO8 sing 140 n n C7P H72 CO8 sing 141 n n C6P C5P CO8 sing 142 n n C6P H61 CO8 sing 143 n n C6P H62 CO8 sing 144 n n C5P O5P CO8 doub 145 n n C5P N4P CO8 sing 146 n n N4P C3P CO8 sing 147 n n N4P HN4 CO8 sing 148 n n C3P C2P CO8 sing 149 n n C3P H31 CO8 sing 150 n n C3P H32 CO8 sing 151 n n C2P S1P CO8 sing 152 n n C2P H21 CO8 sing 153 n n C2P H22 CO8 sing 154 n n S1P C1' CO8 sing 155 n n C1' O1' CO8 doub 156 n n C1' C2' CO8 sing 157 n n C2' C3' CO8 sing 158 n n C2' "H2'1" CO8 sing 159 n n C2' "H2'2" CO8 sing 160 n n C3' C4' CO8 sing 161 n n C3' "H3'1" CO8 sing 162 n n C3' "H3'2" CO8 sing 163 n n C4' C5' CO8 sing 164 n n C4' "H4'1" CO8 sing 165 n n C4' "H4'2" CO8 sing 166 n n C5' C6' CO8 sing 167 n n C5' "H5'1" CO8 sing 168 n n C5' "H5'2" CO8 sing 169 n n C6' C7' CO8 sing 170 n n C6' "H6'1" CO8 sing 171 n n C6' "H6'2" CO8 sing 172 n n C7' C8' CO8 sing 173 n n C7' "H7'1" CO8 sing 174 n n C7' "H7'2" CO8 sing 175 n n C8' "H8'1" CO8 sing 176 n n C8' "H8'2" CO8 sing 177 n n C8' "H8'3" CO8 sing 178 n n # _atom_sites.entry_id 1K39 _atom_sites.fract_transf_matrix[1][1] 0.008573 _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] 0.008573 _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] 0.004613 _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 D 2 PO4 A 1 281 1 PO4 PO4 . E 2 PO4 A 1 282 3 PO4 PO4 . F 3 CO8 A 1 300 300 CO8 CO8 . G 3 CO8 B 1 301 301 CO8 CO8 . H 2 PO4 C 1 281 2 PO4 PO4 . I 3 CO8 C 1 302 302 CO8 CO8 . J 4 HOH B 1 302 4 HOH HOH . J 4 HOH B 2 303 5 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 N1A CO8 . . . I 3 9.861 -15.159 142.453 0.7 56.21 ? N1A CO8 302 C 1 HETATM 2 C C2A CO8 . . . I 3 10.876 -15.978 141.989 0.7 56.4 ? C2A CO8 302 C 1 HETATM 3 N N3A CO8 . . . I 3 11.152 -16.051 140.635 0.7 56.47 ? N3A CO8 302 C 1 HETATM 4 C C4A CO8 . . . I 3 10.423 -15.319 139.756 0.7 56.68 ? C4A CO8 302 C 1 HETATM 5 C C5A CO8 . . . I 3 9.399 -14.492 140.205 0.7 56.53 ? C5A CO8 302 C 1 HETATM 6 C C6A CO8 . . . I 3 9.114 -14.417 141.56 0.7 56.27 ? C6A CO8 302 C 1 HETATM 7 N N6A CO8 . . . I 3 8.131 -13.631 141.989 0.7 56.39 ? N6A CO8 302 C 1 HETATM 8 N N7A CO8 . . . I 3 8.85 -13.891 139.13 0.7 56.67 ? N7A CO8 302 C 1 HETATM 9 C C8A CO8 . . . I 3 9.494 -14.309 138.018 0.7 56.83 ? C8A CO8 302 C 1 HETATM 10 N N9A CO8 . . . I 3 10.474 -15.194 138.389 0.7 56.96 ? N9A CO8 302 C 1 HETATM 11 C C1B CO8 . . . I 3 11.411 -15.899 137.489 0.7 56.75 ? C1B CO8 302 C 1 HETATM 12 C C2B CO8 . . . I 3 10.748 -17.129 136.896 0.7 56.69 ? C2B CO8 302 C 1 HETATM 13 O O2B CO8 . . . I 3 10.795 -18.227 137.779 0.7 56.98 ? O2B CO8 302 C 1 HETATM 14 C C3B CO8 . . . I 3 11.597 -17.344 135.673 0.7 56.87 ? C3B CO8 302 C 1 HETATM 15 O O3B CO8 . . . I 3 12.783 -17.991 136.062 0.7 57.45 ? O3B CO8 302 C 1 HETATM 16 P P3B CO8 . . . I 3 13.272 -19.356 135.364 0.7 57.93 ? P3B CO8 302 C 1 HETATM 17 O O7A CO8 . . . I 3 12.943 -20.482 136.277 0.7 56.88 ? O7A CO8 302 C 1 HETATM 18 O O8A CO8 . . . I 3 12.541 -19.525 134.006 0.7 57.08 ? O8A CO8 302 C 1 HETATM 19 O O9A CO8 . . . I 3 14.802 -19.256 135.133 0.7 57.11 ? O9A CO8 302 C 1 HETATM 20 C C4B CO8 . . . I 3 11.981 -15.938 135.234 0.7 56.49 ? C4B CO8 302 C 1 HETATM 21 O O4B CO8 . . . I 3 11.818 -15.115 136.375 0.7 56.47 ? O4B CO8 302 C 1 HETATM 22 C C5B CO8 . . . I 3 11.136 -15.445 134.07 0.7 56.5 ? C5B CO8 302 C 1 HETATM 23 O O5B CO8 . . . I 3 9.787 -15.34 134.472 0.7 56.62 ? O5B CO8 302 C 1 HETATM 24 P P1A CO8 . . . I 3 8.616 -16.01 133.591 0.7 57.09 ? P1A CO8 302 C 1 HETATM 25 O O1A CO8 . . . I 3 9.21 -17.096 132.588 0.7 57.19 ? O1A CO8 302 C 1 HETATM 26 O O2A CO8 . . . I 3 7.528 -16.68 134.543 0.7 56.49 ? O2A CO8 302 C 1 HETATM 27 O O3A CO8 . . . I 3 7.996 -14.763 132.772 0.7 57.29 ? O3A CO8 302 C 1 HETATM 28 P P2A CO8 . . . I 3 6.401 -14.645 132.516 0.7 58.16 ? P2A CO8 302 C 1 HETATM 29 O O4A CO8 . . . I 3 6.056 -13.354 131.64 0.7 57.24 ? O4A CO8 302 C 1 HETATM 30 O O5A CO8 . . . I 3 5.859 -15.97 131.808 0.7 57.6 ? O5A CO8 302 C 1 HETATM 31 O O6A CO8 . . . I 3 5.754 -14.537 134 0.7 57.55 ? O6A CO8 302 C 1 HETATM 32 C CBP CO8 . . . I 3 4.093 -13.605 135.554 0.7 56.87 ? CBP CO8 302 C 1 HETATM 33 C CCP CO8 . . . I 3 5.183 -13.326 134.517 0.7 57.04 ? CCP CO8 302 C 1 HETATM 34 C CDP CO8 . . . I 3 2.904 -14.273 134.879 0.7 57 ? CDP CO8 302 C 1 HETATM 35 C CEP CO8 . . . I 3 3.634 -12.276 136.13 0.7 56.85 ? CEP CO8 302 C 1 HETATM 36 C CAP CO8 . . . I 3 4.64 -14.546 136.647 0.7 56.57 ? CAP CO8 302 C 1 HETATM 37 O OAP CO8 . . . I 3 6.378 -14.211 136.986 0.7 56.19 ? OAP CO8 302 C 1 HETATM 38 C C9P CO8 . . . I 3 3.913 -14.504 137.966 0.7 56.61 ? C9P CO8 302 C 1 HETATM 39 O O9P CO8 . . . I 3 2.116 -14.454 138.106 0.7 57.13 ? O9P CO8 302 C 1 HETATM 40 N N8P CO8 . . . I 3 4.671 -14.511 139.058 0.7 56.74 ? N8P CO8 302 C 1 HETATM 41 C C7P CO8 . . . I 3 4.095 -14.496 140.393 0.7 57.15 ? C7P CO8 302 C 1 HETATM 42 C C6P CO8 . . . I 3 3.719 -13.118 140.938 0.7 57.28 ? C6P CO8 302 C 1 HETATM 43 C C5P CO8 . . . I 3 3.516 -13.214 142.441 0.7 57.32 ? C5P CO8 302 C 1 HETATM 44 O O5P CO8 . . . I 3 2.748 -14.029 142.893 0.7 57.49 ? O5P CO8 302 C 1 HETATM 45 N N4P CO8 . . . I 3 4.215 -12.373 143.225 0.7 56.78 ? N4P CO8 302 C 1 HETATM 46 C C3P CO8 . . . I 3 4.121 -12.36 144.677 0.7 56.52 ? C3P CO8 302 C 1 HETATM 47 C C2P CO8 . . . I 3 3.845 -10.974 145.252 0.7 56.44 ? C2P CO8 302 C 1 HETATM 48 S S1P CO8 . . . I 3 2.408 -11.048 146.34 0.7 56.56 ? S1P CO8 302 C 1 HETATM 49 C C1' CO8 . . . I 3 2.98 -10.601 147.972 0.7 56.11 ? C1' CO8 302 C 1 HETATM 50 O O1' CO8 . . . I 3 3.74 -9.662 148.085 0.7 56.24 ? O1' CO8 302 C 1 HETATM 51 C C2' CO8 . . . I 3 2.497 -11.389 149.164 0.7 56.02 ? C2' CO8 302 C 1 HETATM 52 C C3' CO8 . . . I 3 3.664 -12.041 149.894 0.7 56.35 ? C3' CO8 302 C 1 HETATM 53 C C4' CO8 . . . I 3 4.258 -11.114 150.95 0.7 56.39 ? C4' CO8 302 C 1 HETATM 54 C C5' CO8 . . . I 3 5.643 -11.588 151.38 0.7 56.3 ? C5' CO8 302 C 1 HETATM 55 C C6' CO8 . . . I 3 6.563 -10.415 151.694 0.7 55.9 ? C6' CO8 302 C 1 HETATM 56 C C7' CO8 . . . I 3 7.809 -10.888 152.428 0.7 55.69 ? C7' CO8 302 C 1 HETATM 57 C C8' CO8 . . . I 3 8.333 -9.796 153.324 0.7 55.07 ? C8' CO8 302 C 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 57 #