data_8KHL # _model_server_result.job_id SkUKWPuyx076005Vr-r20Q _model_server_result.datetime_utc '2024-12-26 11:33:53' _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 8khl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 8KHL # _exptl.entry_id 8KHL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 767.534 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '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 102.089 _cell.angle_gamma 90 _cell.entry_id 8KHL _cell.length_a 96.107 _cell.length_b 79.067 _cell.length_c 121.783 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KHL _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y (x,y,-x+z)' _symmetry.space_group_name_H-M 'I 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C21 H36 N7 O16 P3 S' _chem_comp.formula_weight 767.534 _chem_comp.id COA _chem_comp.mon_nstd_flag . _chem_comp.name '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 COA sing 70 n y N1A C6A COA doub 71 n y C2A N3A COA doub 72 n y C2A H2A COA sing 73 n n N3A C4A COA sing 74 n y C4A C5A COA doub 75 n y C4A N9A COA sing 76 n y C5A C6A COA sing 77 n y C5A N7A COA sing 78 n y C6A N6A COA sing 79 n n N6A H61A COA sing 80 n n N6A H62A COA sing 81 n n N7A C8A COA doub 82 n y C8A N9A COA sing 83 n y C8A H8A COA sing 84 n n N9A C1B COA sing 85 n n C1B C2B COA sing 86 n n C1B O4B COA sing 87 n n C1B H1B COA sing 88 n n C2B O2B COA sing 89 n n C2B C3B COA sing 90 n n C2B H2B COA sing 91 n n O2B HO2A COA sing 92 n n C3B O3B COA sing 93 n n C3B C4B COA sing 94 n n C3B H3B COA sing 95 n n O3B P3B COA sing 96 n n P3B O7A COA doub 97 n n P3B O8A COA sing 98 n n P3B O9A COA sing 99 n n O8A HOA8 COA sing 100 n n O9A HOA9 COA sing 101 n n C4B O4B COA sing 102 n n C4B C5B COA sing 103 n n C4B H4B COA sing 104 n n C5B O5B COA sing 105 n n C5B H51A COA sing 106 n n C5B H52A COA sing 107 n n O5B P1A COA sing 108 n n P1A O1A COA doub 109 n n P1A O2A COA sing 110 n n P1A O3A COA sing 111 n n O2A HOA2 COA sing 112 n n O3A P2A COA sing 113 n n P2A O4A COA doub 114 n n P2A O5A COA sing 115 n n P2A O6A COA sing 116 n n O5A HOA5 COA sing 117 n n O6A CCP COA sing 118 n n CBP CCP COA sing 119 n n CBP CDP COA sing 120 n n CBP CEP COA sing 121 n n CBP CAP COA sing 122 n n CCP H121 COA sing 123 n n CCP H122 COA sing 124 n n CDP H131 COA sing 125 n n CDP H132 COA sing 126 n n CDP H133 COA sing 127 n n CEP H141 COA sing 128 n n CEP H142 COA sing 129 n n CEP H143 COA sing 130 n n CAP OAP COA sing 131 n n CAP C9P COA sing 132 n n CAP H10 COA sing 133 n n OAP HO1 COA sing 134 n n C9P O9P COA doub 135 n n C9P N8P COA sing 136 n n N8P C7P COA sing 137 n n N8P HN8 COA sing 138 n n C7P C6P COA sing 139 n n C7P H71 COA sing 140 n n C7P H72 COA sing 141 n n C6P C5P COA sing 142 n n C6P H61 COA sing 143 n n C6P H62 COA sing 144 n n C5P O5P COA doub 145 n n C5P N4P COA sing 146 n n N4P C3P COA sing 147 n n N4P HN4 COA sing 148 n n C3P C2P COA sing 149 n n C3P H31 COA sing 150 n n C3P H32 COA sing 151 n n C2P S1P COA sing 152 n n C2P H21 COA sing 153 n n C2P H22 COA sing 154 n n S1P HS1 COA sing 155 n n # _atom_sites.entry_id 8KHL _atom_sites.fract_transf_matrix[1][1] 0.010405 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002229 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012648 _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] 0.008398 _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 COA A 1 301 301 COA COA . E 2 COA B 1 301 301 COA COA . F 2 COA C 1 301 302 COA COA . G 3 HOH A 1 401 5 HOH HOH . G 3 HOH A 2 402 21 HOH HOH . G 3 HOH A 3 403 31 HOH HOH . G 3 HOH A 4 404 26 HOH HOH . G 3 HOH A 5 405 15 HOH HOH . G 3 HOH A 6 406 29 HOH HOH . G 3 HOH A 7 407 23 HOH HOH . G 3 HOH A 8 408 14 HOH HOH . G 3 HOH A 9 409 27 HOH HOH . G 3 HOH A 10 410 8 HOH HOH . G 3 HOH A 11 411 9 HOH HOH . H 3 HOH B 1 401 18 HOH HOH . H 3 HOH B 2 402 11 HOH HOH . H 3 HOH B 3 403 12 HOH HOH . H 3 HOH B 4 404 24 HOH HOH . H 3 HOH B 5 405 22 HOH HOH . H 3 HOH B 6 406 28 HOH HOH . H 3 HOH B 7 407 16 HOH HOH . H 3 HOH B 8 408 10 HOH HOH . H 3 HOH B 9 409 30 HOH HOH . H 3 HOH B 10 410 32 HOH HOH . I 3 HOH C 1 401 7 HOH HOH . I 3 HOH C 2 402 6 HOH HOH . I 3 HOH C 3 403 2 HOH HOH . I 3 HOH C 4 404 1 HOH HOH . I 3 HOH C 5 405 3 HOH HOH . I 3 HOH C 6 406 13 HOH HOH . I 3 HOH C 7 407 20 HOH HOH . I 3 HOH C 8 408 19 HOH HOH . I 3 HOH C 9 409 17 HOH HOH . I 3 HOH C 10 410 4 HOH HOH . I 3 HOH C 11 411 25 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 COA . . . D 2 -1.188 22.747 -58.59 1 20.63 ? N1A COA 301 A 1 HETATM 2 C C2A COA . . . D 2 -0.897 23.654 -59.53 1 19.46 ? C2A COA 301 A 1 HETATM 3 N N3A COA . . . D 2 0.286 24.102 -59.933 1 19.33 ? N3A COA 301 A 1 HETATM 4 C C4A COA . . . D 2 1.271 23.513 -59.241 1 24.89 ? C4A COA 301 A 1 HETATM 5 C C5A COA . . . D 2 1.135 22.573 -58.245 1 21.46 ? C5A COA 301 A 1 HETATM 6 C C6A COA . . . D 2 -0.17 22.177 -57.905 1 24.73 ? C6A COA 301 A 1 HETATM 7 N N6A COA . . . D 2 -0.445 21.275 -56.969 1 20.81 ? N6A COA 301 A 1 HETATM 8 N N7A COA . . . D 2 2.381 22.2 -57.768 1 18.14 ? N7A COA 301 A 1 HETATM 9 C C8A COA . . . D 2 3.233 22.907 -58.47 1 24.49 ? C8A COA 301 A 1 HETATM 10 N N9A COA . . . D 2 2.616 23.724 -59.373 1 26.04 ? N9A COA 301 A 1 HETATM 11 C C1B COA . . . D 2 3.249 24.613 -60.322 1 22.79 ? C1B COA 301 A 1 HETATM 12 C C2B COA . . . D 2 4.029 25.773 -59.715 1 28.02 ? C2B COA 301 A 1 HETATM 13 O O2B COA . . . D 2 3.216 26.899 -59.48 1 29.85 ? O2B COA 301 A 1 HETATM 14 C C3B COA . . . D 2 5.04 26.044 -60.825 1 29.82 ? C3B COA 301 A 1 HETATM 15 O O3B COA . . . D 2 4.454 26.776 -61.893 1 42.94 ? O3B COA 301 A 1 HETATM 16 P P3B COA . . . D 2 5.026 28.269 -62.068 1 47.34 ? P3B COA 301 A 1 HETATM 17 O O7A COA . . . D 2 4.158 28.878 -63.138 1 34.45 ? O7A COA 301 A 1 HETATM 18 O O8A COA . . . D 2 6.463 28.16 -62.504 1 49.05 ? O8A COA 301 A 1 HETATM 19 O O9A COA . . . D 2 4.89 28.985 -60.747 1 40.62 ? O9A COA 301 A 1 HETATM 20 C C4B COA . . . D 2 5.369 24.643 -61.316 1 28.79 ? C4B COA 301 A 1 HETATM 21 O O4B COA . . . D 2 4.187 23.849 -61.041 1 24.44 ? O4B COA 301 A 1 HETATM 22 C C5B COA . . . D 2 6.572 23.994 -60.677 1 32.86 ? C5B COA 301 A 1 HETATM 23 O O5B COA . . . D 2 6.381 23.876 -59.25 1 24.93 ? O5B COA 301 A 1 HETATM 24 P P1A COA . . . D 2 7.543 23.169 -58.417 1 33.03 ? P1A COA 301 A 1 HETATM 25 O O1A COA . . . D 2 8.567 24.188 -58.055 1 31.65 ? O1A COA 301 A 1 HETATM 26 O O2A COA . . . D 2 7.996 21.949 -59.134 1 25.64 ? O2A COA 301 A 1 HETATM 27 O O3A COA . . . D 2 6.765 22.715 -57.102 1 25.36 ? O3A COA 301 A 1 HETATM 28 P P2A COA . . . D 2 6.767 23.272 -55.608 1 24.95 ? P2A COA 301 A 1 HETATM 29 O O4A COA . . . D 2 7.948 22.741 -54.878 1 30.13 ? O4A COA 301 A 1 HETATM 30 O O5A COA . . . D 2 6.556 24.74 -55.645 1 27.37 ? O5A COA 301 A 1 HETATM 31 O O6A COA . . . D 2 5.444 22.596 -55.033 1 26.61 ? O6A COA 301 A 1 HETATM 32 C CBP COA . . . D 2 4.175 20.853 -53.97 1 20.28 ? CBP COA 301 A 1 HETATM 33 C CCP COA . . . D 2 5.429 21.17 -54.771 1 22.72 ? CCP COA 301 A 1 HETATM 34 C CDP COA . . . D 2 4.218 19.393 -53.515 1 20.23 ? CDP COA 301 A 1 HETATM 35 C CEP COA . . . D 2 4.141 21.751 -52.736 1 19.45 ? CEP COA 301 A 1 HETATM 36 C CAP COA . . . D 2 2.927 21.104 -54.819 1 17.59 ? CAP COA 301 A 1 HETATM 37 O OAP COA . . . D 2 2.951 20.262 -55.953 1 20.41 ? OAP COA 301 A 1 HETATM 38 C C9P COA . . . D 2 1.64 20.891 -54.048 1 19.21 ? C9P COA 301 A 1 HETATM 39 O O9P COA . . . D 2 1.277 21.713 -53.215 1 26.73 ? O9P COA 301 A 1 HETATM 40 N N8P COA . . . D 2 0.949 19.797 -54.323 1 17.17 ? N8P COA 301 A 1 HETATM 41 C C7P COA . . . D 2 0.687 18.773 -53.328 1 25.49 ? C7P COA 301 A 1 HETATM 42 C C6P COA . . . D 2 -0.756 18.377 -53.307 1 27.26 ? C6P COA 301 A 1 HETATM 43 C C5P COA . . . D 2 -1.331 18.451 -51.912 1 19.5 ? C5P COA 301 A 1 HETATM 44 O O5P COA . . . D 2 -2.163 19.3 -51.619 1 21.06 ? O5P COA 301 A 1 HETATM 45 N N4P COA . . . D 2 -0.888 17.551 -51.034 1 18.9 ? N4P COA 301 A 1 HETATM 46 C C3P COA . . . D 2 -1.76 16.733 -50.208 1 15.42 ? C3P COA 301 A 1 HETATM 47 C C2P COA . . . D 2 -2.396 15.608 -50.985 1 18.17 ? C2P COA 301 A 1 HETATM 48 S S1P COA . . . D 2 -1.563 14.011 -50.806 1 18.96 ? S1P COA 301 A 1 HETATM 49 H H2A COA . . . D 2 -1.749 24.074 -60.044 1 23.46 ? H2A COA 301 A 1 HETATM 50 H H61A COA . . . D 2 -0.387 21.535 -55.988 1 25.08 ? H61A COA 301 A 1 HETATM 51 H H62A COA . . . D 2 -0.701 20.33 -57.238 1 25.08 ? H62A COA 301 A 1 HETATM 52 H H8A COA . . . D 2 4.304 22.843 -58.335 1 29.49 ? H8A COA 301 A 1 HETATM 53 H H1B COA . . . D 2 2.497 25.01 -61.002 1 27.45 ? H1B COA 301 A 1 HETATM 54 H H2B COA . . . D 2 4.532 25.465 -58.8 1 33.72 ? H2B COA 301 A 1 HETATM 55 H HO2A COA . . . D 2 3.765 27.696 -59.53 1 35.92 ? HO2A COA 301 A 1 HETATM 56 H H3B COA . . . D 2 5.925 26.548 -60.44 1 35.89 ? H3B COA 301 A 1 HETATM 57 H H4B COA . . . D 2 5.531 24.673 -62.392 1 34.65 ? H4B COA 301 A 1 HETATM 58 H H51A COA . . . D 2 7.457 24.595 -60.879 1 39.54 ? H51A COA 301 A 1 HETATM 59 H H52A COA . . . D 2 6.722 23.006 -61.109 1 39.54 ? H52A COA 301 A 1 HETATM 60 H H121 COA . . . D 2 6.311 20.881 -54.203 1 27.37 ? H121 COA 301 A 1 HETATM 61 H H122 COA . . . D 2 5.423 20.616 -55.708 1 27.37 ? H122 COA 301 A 1 HETATM 62 H H131 COA . . . D 2 4.158 18.737 -54.382 1 24.37 ? H131 COA 301 A 1 HETATM 63 H H132 COA . . . D 2 3.379 19.192 -52.85 1 24.37 ? H132 COA 301 A 1 HETATM 64 H H133 COA . . . D 2 5.152 19.207 -52.985 1 24.37 ? H133 COA 301 A 1 HETATM 65 H H141 COA . . . D 2 3.573 21.263 -51.945 1 23.44 ? H141 COA 301 A 1 HETATM 66 H H142 COA . . . D 2 3.671 22.7 -52.99 1 23.44 ? H142 COA 301 A 1 HETATM 67 H H143 COA . . . D 2 5.158 21.931 -52.392 1 23.44 ? H143 COA 301 A 1 HETATM 68 H H10 COA . . . D 2 2.957 22.139 -55.155 1 21.22 ? H10 COA 301 A 1 HETATM 69 H HO1 COA . . . D 2 2.25 20.545 -56.56 1 24.59 ? HO1 COA 301 A 1 HETATM 70 H HN8 COA . . . D 2 0.594 19.661 -55.265 1 20.71 ? HN8 COA 301 A 1 HETATM 71 H H71 COA . . . D 2 0.97 19.148 -52.346 1 30.69 ? H71 COA 301 A 1 HETATM 72 H H72 COA . . . D 2 1.297 17.898 -53.545 1 30.69 ? H72 COA 301 A 1 HETATM 73 H H61 COA . . . D 2 -0.86 17.359 -53.679 1 32.82 ? H61 COA 301 A 1 HETATM 74 H H62 COA . . . D 2 -1.323 19.038 -53.961 1 32.82 ? H62 COA 301 A 1 HETATM 75 H HN4 COA . . . D 2 0.117 17.434 -50.945 1 22.79 ? HN4 COA 301 A 1 HETATM 76 H H31 COA . . . D 2 -1.182 16.316 -49.385 1 18.6 ? H31 COA 301 A 1 HETATM 77 H H32 COA . . . D 2 -2.544 17.36 -49.788 1 18.6 ? H32 COA 301 A 1 HETATM 78 H H21 COA . . . D 2 -3.428 15.497 -50.656 1 21.9 ? H21 COA 301 A 1 HETATM 79 H H22 COA . . . D 2 -2.404 15.876 -52.04 1 21.9 ? H22 COA 301 A 1 HETATM 80 H HS1 COA . . . D 2 -1.053 14.221 -49.587 1 22.85 ? HS1 COA 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 80 #