data_1YVK # _model_server_result.job_id Jjk6OTob308MNZSyaBT7tg _model_server_result.datetime_utc '2025-07-03 03:02:57' _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 1yvk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":202}' # _entry.id 1YVK # _exptl.entry_id 1YVK _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 4 _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 1YVK _cell.length_a 59.596 _cell.length_b 124.425 _cell.length_c 216.942 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YVK _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 E N N ? 2 F N N ? 2 G N N ? 2 H 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 ASP 147 A ASP 147 1_555 A N MSE 148 A MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 A C MSE 148 A MSE 148 1_555 A N VAL 149 A VAL 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale3 B C ASP 147 B ASP 147 1_555 B N MSE 148 B MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 B C MSE 148 B MSE 148 1_555 B N VAL 149 B VAL 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 C C ASP 147 C ASP 147 1_555 C N MSE 148 C MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 C C MSE 148 C MSE 148 1_555 C N VAL 149 C VAL 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale7 D C ASP 147 D ASP 147 1_555 D N MSE 148 D MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 D C MSE 148 D MSE 148 1_555 D N VAL 149 D VAL 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? # _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 1YVK _atom_sites.fract_transf_matrix[1][1] 0.01678 _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] 0.008037 _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] 0.00461 _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 E 2 COA A 1 201 201 COA COA . F 2 COA B 1 202 202 COA COA . G 2 COA C 1 203 203 COA COA . H 2 COA D 1 204 204 COA COA . # 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 . . . F 2 68.324 131.766 158.525 1 83.73 ? N1A COA 202 B 1 HETATM 2 C C2A COA . . . F 2 68.22 131.455 159.948 1 83.09 ? C2A COA 202 B 1 HETATM 3 N N3A COA . . . F 2 66.866 131.528 160.452 1 83.5 ? N3A COA 202 B 1 HETATM 4 C C4A COA . . . F 2 65.743 131.889 159.576 1 84.84 ? C4A COA 202 B 1 HETATM 5 C C5A COA . . . F 2 65.865 132.182 158.189 1 84.31 ? C5A COA 202 B 1 HETATM 6 C C6A COA . . . F 2 67.184 132.126 157.663 1 84.18 ? C6A COA 202 B 1 HETATM 7 N N6A COA . . . F 2 67.371 132.419 156.283 1 84.46 ? N6A COA 202 B 1 HETATM 8 N N7A COA . . . F 2 64.647 132.481 157.629 1 84.67 ? N7A COA 202 B 1 HETATM 9 C C8A COA . . . F 2 63.747 132.367 158.689 1 85.7 ? C8A COA 202 B 1 HETATM 10 N N9A COA . . . F 2 64.408 132.004 159.891 1 86.36 ? N9A COA 202 B 1 HETATM 11 C C1B COA . . . F 2 63.865 131.794 161.202 1 87.88 ? C1B COA 202 B 1 HETATM 12 C C2B COA . . . F 2 63.902 130.358 161.833 1 88.72 ? C2B COA 202 B 1 HETATM 13 O O2B COA . . . F 2 62.609 129.765 161.877 1 88.93 ? O2B COA 202 B 1 HETATM 14 C C3B COA . . . F 2 64.557 130.537 163.216 1 87.61 ? C3B COA 202 B 1 HETATM 15 O O3B COA . . . F 2 63.603 130.082 164.192 1 90.67 ? O3B COA 202 B 1 HETATM 16 P P3B COA . . . F 2 64.007 129.362 165.475 1 93.85 ? P3B COA 202 B 1 HETATM 17 O O7A COA . . . F 2 64.794 128.14 165.232 1 94.22 ? O7A COA 202 B 1 HETATM 18 O O8A COA . . . F 2 64.804 130.269 166.327 1 94.27 ? O8A COA 202 B 1 HETATM 19 O O9A COA . . . F 2 62.749 129.055 166.184 1 94.73 ? O9A COA 202 B 1 HETATM 20 C C4B COA . . . F 2 64.892 131.968 163.379 1 85.03 ? C4B COA 202 B 1 HETATM 21 O O4B COA . . . F 2 64.482 132.689 162.204 1 86.56 ? O4B COA 202 B 1 HETATM 22 C C5B COA . . . F 2 66.441 131.939 163.728 1 80.27 ? C5B COA 202 B 1 HETATM 23 O O5B COA . . . F 2 66.797 133.248 164.227 1 73.52 ? O5B COA 202 B 1 HETATM 24 P P1A COA . . . F 2 67.986 134.322 163.74 1 68.55 ? P1A COA 202 B 1 HETATM 25 O O1A COA . . . F 2 69.319 133.819 163.869 1 65.58 ? O1A COA 202 B 1 HETATM 26 O O2A COA . . . F 2 67.764 134.823 162.344 1 69.1 ? O2A COA 202 B 1 HETATM 27 O O3A COA . . . F 2 67.614 135.49 164.728 1 64.07 ? O3A COA 202 B 1 HETATM 28 P P2A COA . . . F 2 68.215 136.904 164.799 1 60.08 ? P2A COA 202 B 1 HETATM 29 O O4A COA . . . F 2 69.247 137.088 163.782 1 59.05 ? O4A COA 202 B 1 HETATM 30 O O5A COA . . . F 2 67.146 137.832 164.551 1 58.91 ? O5A COA 202 B 1 HETATM 31 O O6A COA . . . F 2 68.673 137.336 166.118 1 56.14 ? O6A COA 202 B 1 HETATM 32 C CBP COA . . . F 2 68.063 137.826 168.494 1 50.07 ? CBP COA 202 B 1 HETATM 33 C CCP COA . . . F 2 68.743 136.818 167.43 1 52.53 ? CCP COA 202 B 1 HETATM 34 C CDP COA . . . F 2 69.499 138.108 169.04 1 51.47 ? CDP COA 202 B 1 HETATM 35 C CEP COA . . . F 2 67.182 137.102 169.581 1 52.34 ? CEP COA 202 B 1 HETATM 36 C CAP COA . . . F 2 67.389 139.177 167.826 1 48.22 ? CAP COA 202 B 1 HETATM 37 O OAP COA . . . F 2 66.08 138.692 167.453 1 45.79 ? OAP COA 202 B 1 HETATM 38 C C9P COA . . . F 2 67.216 140.313 168.804 1 48.14 ? C9P COA 202 B 1 HETATM 39 O O9P COA . . . F 2 68.216 140.857 169.246 1 51.14 ? O9P COA 202 B 1 HETATM 40 N N8P COA . . . F 2 65.909 140.702 169.165 1 48.37 ? N8P COA 202 B 1 HETATM 41 C C7P COA . . . F 2 65.514 141.766 170.078 1 46.51 ? C7P COA 202 B 1 HETATM 42 C C6P COA . . . F 2 66.405 141.97 171.396 1 44.59 ? C6P COA 202 B 1 HETATM 43 C C5P COA . . . F 2 66.638 140.757 172.267 1 43.83 ? C5P COA 202 B 1 HETATM 44 O O5P COA . . . F 2 65.717 139.955 172.475 1 45.7 ? O5P COA 202 B 1 HETATM 45 N N4P COA . . . F 2 67.954 140.593 172.811 1 42.79 ? N4P COA 202 B 1 HETATM 46 C C3P COA . . . F 2 68.433 139.514 173.665 1 44.6 ? C3P COA 202 B 1 HETATM 47 C C2P COA . . . F 2 68.219 139.765 175.229 1 46.05 ? C2P COA 202 B 1 HETATM 48 S S1P COA . . . F 2 69.665 139.183 176.246 1 50.39 ? S1P COA 202 B 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 48 #