data_1K39 # _model_server_result.job_id dsmz7PePKBUmYprzIKZcog _model_server_result.datetime_utc '2025-03-06 01:05:07' _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":"F","auth_seq_id":300}' # _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 . . . F 3 -0.356 41.67 140.849 0.7 56.08 ? N1A CO8 300 A 1 HETATM 2 C C2A CO8 . . . F 3 -0.232 42.944 140.33 0.7 56.33 ? C2A CO8 300 A 1 HETATM 3 N N3A CO8 . . . F 3 -0.432 43.179 138.983 0.7 56.47 ? N3A CO8 300 A 1 HETATM 4 C C4A CO8 . . . F 3 -0.755 42.152 138.155 0.7 56.71 ? C4A CO8 300 A 1 HETATM 5 C C5A CO8 . . . F 3 -0.884 40.861 138.656 0.7 56.55 ? C5A CO8 300 A 1 HETATM 6 C C6A CO8 . . . F 3 -0.678 40.623 140.013 0.7 56.26 ? C6A CO8 300 A 1 HETATM 7 N N6A CO8 . . . F 3 -0.8 39.394 140.505 0.7 56.41 ? N6A CO8 300 A 1 HETATM 8 N N7A CO8 . . . F 3 -1.204 40.052 137.624 0.7 56.61 ? N7A CO8 300 A 1 HETATM 9 C C8A CO8 . . . F 3 -1.281 40.788 136.495 0.7 56.75 ? C8A CO8 300 A 1 HETATM 10 N N9A CO8 . . . F 3 -1.009 42.095 136.806 0.7 56.9 ? N9A CO8 300 A 1 HETATM 11 C C1B CO8 . . . F 3 -0.968 43.24 135.877 0.7 56.66 ? C1B CO8 300 A 1 HETATM 12 C C2B CO8 . . . F 3 0.369 43.281 135.172 0.7 56.72 ? C2B CO8 300 A 1 HETATM 13 O O2B CO8 . . . F 3 1.343 43.922 135.961 0.7 57.05 ? O2B CO8 300 A 1 HETATM 14 C C3B CO8 . . . F 3 0.032 44.07 133.937 0.7 56.87 ? C3B CO8 300 A 1 HETATM 15 O O3B CO8 . . . F 3 -0.006 45.431 134.277 0.7 57.48 ? O3B CO8 300 A 1 HETATM 16 P P3B CO8 . . . F 3 0.873 46.506 133.463 0.7 57.97 ? P3B CO8 300 A 1 HETATM 17 O O7A CO8 . . . F 3 2.084 46.827 134.267 0.7 56.91 ? O7A CO8 300 A 1 HETATM 18 O O8A CO8 . . . F 3 1.285 45.897 132.1 0.7 57.04 ? O8A CO8 300 A 1 HETATM 19 O O9A CO8 . . . F 3 -0.015 47.758 133.256 0.7 57.09 ? O9A CO8 300 A 1 HETATM 20 C C4B CO8 . . . F 3 -1.388 43.653 133.623 0.7 56.47 ? C4B CO8 300 A 1 HETATM 21 O O4B CO8 . . . F 3 -1.913 43.134 134.831 0.7 56.42 ? O4B CO8 300 A 1 HETATM 22 C C5B CO8 . . . F 3 -1.474 42.641 132.489 0.7 56.48 ? C5B CO8 300 A 1 HETATM 23 O O5B CO8 . . . F 3 -0.857 41.436 132.872 0.7 56.62 ? O5B CO8 300 A 1 HETATM 24 P P1A CO8 . . . F 3 0.267 40.744 131.946 0.7 57.11 ? P1A CO8 300 A 1 HETATM 25 O O1A CO8 . . . F 3 0.812 41.767 130.853 0.7 57.27 ? O1A CO8 300 A 1 HETATM 26 O O2A CO8 . . . F 3 1.467 40.192 132.844 0.7 56.48 ? O2A CO8 300 A 1 HETATM 27 O O3A CO8 . . . F 3 -0.53 39.543 131.214 0.7 57.33 ? O3A CO8 300 A 1 HETATM 28 P P2A CO8 . . . F 3 0.16 38.103 130.941 0.7 58.11 ? P2A CO8 300 A 1 HETATM 29 O O4A CO8 . . . F 3 -0.854 37.134 130.178 0.7 57.24 ? O4A CO8 300 A 1 HETATM 30 O O5A CO8 . . . F 3 1.503 38.281 130.096 0.7 57.57 ? O5A CO8 300 A 1 HETATM 31 O O6A CO8 . . . F 3 0.513 37.55 132.421 0.7 57.51 ? O6A CO8 300 A 1 HETATM 32 C CBP CO8 . . . F 3 0.683 35.704 134.023 0.7 56.89 ? CBP CO8 300 A 1 HETATM 33 C CCP CO8 . . . F 3 -0.199 36.47 133.037 0.7 57.04 ? CCP CO8 300 A 1 HETATM 34 C CDP CO8 . . . F 3 1.816 35.013 133.273 0.7 57.02 ? CDP CO8 300 A 1 HETATM 35 C CEP CO8 . . . F 3 -0.16 34.627 134.686 0.7 56.89 ? CEP CO8 300 A 1 HETATM 36 C CAP CO8 . . . F 3 1.298 36.679 135.048 0.7 56.57 ? CAP CO8 300 A 1 HETATM 37 O OAP CO8 . . . F 3 0.177 38.038 135.423 0.7 56.14 ? OAP CO8 300 A 1 HETATM 38 C C9P CO8 . . . F 3 1.724 36.082 136.367 0.7 56.62 ? C9P CO8 300 A 1 HETATM 39 O O9P CO8 . . . F 3 2.609 34.514 136.496 0.7 57.08 ? O9P CO8 300 A 1 HETATM 40 N N8P CO8 . . . F 3 1.43 36.778 137.46 0.7 56.71 ? N8P CO8 300 A 1 HETATM 41 C C7P CO8 . . . F 3 1.815 36.315 138.78 0.7 57.11 ? C7P CO8 300 A 1 HETATM 42 C C6P CO8 . . . F 3 0.877 35.298 139.421 0.7 57.22 ? C6P CO8 300 A 1 HETATM 43 C C5P CO8 . . . F 3 1.179 35.215 140.907 0.7 57.25 ? C5P CO8 300 A 1 HETATM 44 O O5P CO8 . . . F 3 2.297 34.972 141.279 0.7 57.47 ? O5P CO8 300 A 1 HETATM 45 N N4P CO8 . . . F 3 0.176 35.422 141.772 0.7 56.78 ? N4P CO8 300 A 1 HETATM 46 C C3P CO8 . . . F 3 0.329 35.372 143.219 0.7 56.57 ? C3P CO8 300 A 1 HETATM 47 C C2P CO8 . . . F 3 -0.67 34.438 143.905 0.7 56.48 ? C2P CO8 300 A 1 HETATM 48 S S1P CO8 . . . F 3 0.173 33.246 144.967 0.7 56.66 ? S1P CO8 300 A 1 HETATM 49 C C1' CO8 . . . F 3 -0.34 33.584 146.648 0.7 56.09 ? C1' CO8 300 A 1 HETATM 50 O O1' CO8 . . . F 3 -1.519 33.772 146.859 0.7 56.17 ? O1' CO8 300 A 1 HETATM 51 C C2' CO8 . . . F 3 0.685 33.621 147.757 0.7 56.04 ? C2' CO8 300 A 1 HETATM 52 C C3' CO8 . . . F 3 0.712 34.985 148.443 0.7 56.36 ? C3' CO8 300 A 1 HETATM 53 C C4' CO8 . . . F 3 -0.286 35.061 149.594 0.7 56.36 ? C4' CO8 300 A 1 HETATM 54 C C5' CO8 . . . F 3 -0.537 36.505 150.008 0.7 56.28 ? C5' CO8 300 A 1 HETATM 55 C C6' CO8 . . . F 3 -1.987 36.719 150.418 0.7 55.93 ? C6' CO8 300 A 1 HETATM 56 C C7' CO8 . . . F 3 -2.149 38.051 151.139 0.7 55.7 ? C7' CO8 300 A 1 HETATM 57 C C8' CO8 . . . F 3 -3.268 37.969 152.146 0.7 55.09 ? C8' CO8 300 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 57 #