data_4XC8 # _model_server_result.job_id 0ACpOB_aX-X-LYvXAl0MSQ _model_server_result.datetime_utc '2024-11-24 14:08:09' _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 4xc8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1101}' # _entry.id 4XC8 # _exptl.entry_id 4XC8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 837.624 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Butyryl Coenzyme A' _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 4XC8 _cell.length_a 316.51 _cell.length_b 316.51 _cell.length_c 342.27 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XC8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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,G,H,I,J _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 C N N ? 2 G 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 metalc ? metalc1 A OG SER 243 A SER 223 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc2 A O ILE 268 A ILE 248 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc5 A OD1 ASP 282 A ASP 262 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc6 A OD2 ASP 282 A ASP 262 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc7 A OE1 GLU 330 A GLU 310 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc8 D O2B GDP . A GDP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc9 B OG SER 243 B SER 223 1_555 I MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc10 B O ILE 268 B ILE 248 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc11 B OD1 ASP 269 B ASP 249 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc12 B OD1 ASP 282 B ASP 262 1_555 I MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc13 B OD1 ASP 282 B ASP 262 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc14 B OD2 ASP 282 B ASP 262 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc15 B OE1 GLU 330 B GLU 310 1_555 J MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? # _chem_comp.formula 'C25 H42 N7 O17 P3 S' _chem_comp.formula_weight 837.624 _chem_comp.id BCO _chem_comp.mon_nstd_flag . _chem_comp.name 'Butyryl Coenzyme A' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)' # 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 C15 N4 BCO doub 70 n y C15 N3 BCO sing 71 n y N4 C12 BCO sing 72 n y N3 C6 BCO doub 73 n y O9 P1 BCO doub 74 n n C12 N5 BCO sing 75 n n C12 C8 BCO doub 76 n y O3 C2 BCO sing 77 n n C6 C8 BCO sing 78 n y C6 N1 BCO sing 79 n y C2 C4 BCO sing 80 n n C2 C1 BCO sing 81 n n C8 N2 BCO sing 82 n y P1 O6 BCO sing 83 n n P1 O5 BCO sing 84 n n P1 O2 BCO sing 85 n n C4 N1 BCO sing 86 n n C4 O1 BCO sing 87 n n N1 C7 BCO sing 88 n y O2 C1 BCO sing 89 n n C1 C3 BCO sing 90 n n N2 C7 BCO doub 91 n y O1 C3 BCO sing 92 n n C3 C5 BCO sing 93 n n C5 O4 BCO sing 94 n n O4 P2 BCO sing 95 n n O10 P2 BCO doub 96 n n P2 O7 BCO sing 97 n n P2 O12 BCO sing 98 n n O7 P3 BCO sing 99 n n P3 O13 BCO doub 100 n n P3 O14 BCO sing 101 n n P3 O8 BCO sing 102 n n O8 C11 BCO sing 103 n n C14 C9 BCO sing 104 n n C11 C9 BCO sing 105 n n C9 C13 BCO sing 106 n n C9 C10 BCO sing 107 n n C10 O11 BCO sing 108 n n C10 C16 BCO sing 109 n n C16 O15 BCO doub 110 n n C16 N6 BCO sing 111 n n N6 C17 BCO sing 112 n n C17 C18 BCO sing 113 n n C18 C19 BCO sing 114 n n C19 O16 BCO doub 115 n n C19 N7 BCO sing 116 n n N7 C20 BCO sing 117 n n C20 C21 BCO sing 118 n n C21 S1 BCO sing 119 n n S1 C22 BCO sing 120 n n C22 O17 BCO doub 121 n n C22 C23 BCO sing 122 n n C23 C24 BCO sing 123 n n C24 C25 BCO sing 124 n n O5 H1 BCO sing 125 n n O6 H2 BCO sing 126 n n C1 H3 BCO sing 127 n n C2 H4 BCO sing 128 n n O3 H5 BCO sing 129 n n C4 H6 BCO sing 130 n n C7 H7 BCO sing 131 n n C15 H8 BCO sing 132 n n N5 H9 BCO sing 133 n n N5 H10 BCO sing 134 n n C3 H11 BCO sing 135 n n C5 H12 BCO sing 136 n n C5 H13 BCO sing 137 n n O12 H14 BCO sing 138 n n O14 H15 BCO sing 139 n n C11 H16 BCO sing 140 n n C11 H17 BCO sing 141 n n C13 H18 BCO sing 142 n n C13 H19 BCO sing 143 n n C13 H20 BCO sing 144 n n C14 H21 BCO sing 145 n n C14 H22 BCO sing 146 n n C14 H23 BCO sing 147 n n C10 H24 BCO sing 148 n n O11 H25 BCO sing 149 n n N6 H26 BCO sing 150 n n C17 H27 BCO sing 151 n n C18 H28 BCO sing 152 n n N7 H29 BCO sing 153 n n C20 H30 BCO sing 154 n n C20 H31 BCO sing 155 n n C21 H32 BCO sing 156 n n C21 H33 BCO sing 157 n n C23 H34 BCO sing 158 n n C24 H35 BCO sing 159 n n C25 H36 BCO sing 160 n n C25 H37 BCO sing 161 n n C25 H38 BCO sing 162 n n C17 H39 BCO sing 163 n n C18 H40 BCO sing 164 n n C23 H41 BCO sing 165 n n C24 H42 BCO sing 166 n n # _atom_sites.entry_id 4XC8 _atom_sites.fract_transf_matrix[1][1] 0.003159 _atom_sites.fract_transf_matrix[1][2] 0.001824 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003648 _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] 0.002922 _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 2 BCO A 1 1101 1211 BCO BCO . D 3 GDP A 1 1102 1200 GDP GDP . E 4 MG A 1 1103 1 MG MG . F 4 MG A 1 1104 3 MG MG . G 2 BCO B 1 1101 1212 BCO BCO . H 3 GDP B 1 1102 1201 GDP GDP . I 4 MG B 1 1103 2 MG MG . J 4 MG B 1 1104 4 MG MG . # 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 O9 BCO . . . C 2 -205.89 -101.701 -34.64 1 131.47 ? O9 BCO 1101 A 1 HETATM 2 P P1 BCO . . . C 2 -205.7 -101.646 -33.135 1 132.17 ? P1 BCO 1101 A 1 HETATM 3 O O5 BCO . . . C 2 -204.223 -101.707 -32.809 1 135.05 ? O5 BCO 1101 A 1 HETATM 4 O O6 BCO . . . C 2 -206.271 -100.367 -32.598 1 130.18 ? O6 BCO 1101 A 1 HETATM 5 O O2 BCO . . . C 2 -206.41 -102.857 -32.464 1 108.23 ? O2 BCO 1101 A 1 HETATM 6 C C1 BCO . . . C 2 -207.785 -102.814 -32.209 1 107.46 ? C1 BCO 1101 A 1 HETATM 7 C C2 BCO . . . C 2 -208.516 -103.029 -33.399 1 110.61 ? C2 BCO 1101 A 1 HETATM 8 O O3 BCO . . . C 2 -207.754 -103.856 -34.292 1 112.93 ? O3 BCO 1101 A 1 HETATM 9 C C4 BCO . . . C 2 -209.706 -103.729 -32.988 1 109.29 ? C4 BCO 1101 A 1 HETATM 10 N N1 BCO . . . C 2 -210.901 -102.92 -32.871 1 107.61 ? N1 BCO 1101 A 1 HETATM 11 C C7 BCO . . . C 2 -211.549 -102.63 -31.733 1 106.44 ? C7 BCO 1101 A 1 HETATM 12 N N2 BCO . . . C 2 -212.613 -101.857 -32.015 1 104.45 ? N2 BCO 1101 A 1 HETATM 13 C C8 BCO . . . C 2 -212.634 -101.658 -33.352 1 103.84 ? C8 BCO 1101 A 1 HETATM 14 C C6 BCO . . . C 2 -211.546 -102.331 -33.906 1 105.7 ? C6 BCO 1101 A 1 HETATM 15 N N3 BCO . . . C 2 -211.355 -102.277 -35.243 1 104.13 ? N3 BCO 1101 A 1 HETATM 16 C C15 BCO . . . C 2 -212.193 -101.589 -36.031 1 101.57 ? C15 BCO 1101 A 1 HETATM 17 N N4 BCO . . . C 2 -213.24 -100.938 -35.51 1 98.97 ? N4 BCO 1101 A 1 HETATM 18 C C12 BCO . . . C 2 -213.499 -100.945 -34.19 1 100.56 ? C12 BCO 1101 A 1 HETATM 19 N N5 BCO . . . C 2 -214.657 -100.221 -33.637 1 100.13 ? N5 BCO 1101 A 1 HETATM 20 O O1 BCO . . . C 2 -209.452 -104.286 -31.729 1 108.05 ? O1 BCO 1101 A 1 HETATM 21 C C3 BCO . . . C 2 -208.148 -103.956 -31.367 1 106.18 ? C3 BCO 1101 A 1 HETATM 22 C C5 BCO . . . C 2 -208.098 -103.554 -29.942 1 102.58 ? C5 BCO 1101 A 1 HETATM 23 O O4 BCO . . . C 2 -209.221 -102.876 -29.425 1 100.8 ? O4 BCO 1101 A 1 HETATM 24 P P2 BCO . . . C 2 -209.063 -101.914 -28.161 1 102.24 ? P2 BCO 1101 A 1 HETATM 25 O O12 BCO . . . C 2 -207.993 -102.494 -27.212 1 105.15 ? O12 BCO 1101 A 1 HETATM 26 O O10 BCO . . . C 2 -208.629 -100.51 -28.619 1 98.66 ? O10 BCO 1101 A 1 HETATM 27 O O7 BCO . . . C 2 -210.504 -101.824 -27.415 1 126.8 ? O7 BCO 1101 A 1 HETATM 28 P P3 BCO . . . C 2 -210.625 -102.015 -25.868 1 116.67 ? P3 BCO 1101 A 1 HETATM 29 O O14 BCO . . . C 2 -210.099 -103.354 -25.473 1 117.88 ? O14 BCO 1101 A 1 HETATM 30 O O13 BCO . . . C 2 -212.076 -101.9 -25.469 1 115.09 ? O13 BCO 1101 A 1 HETATM 31 O O8 BCO . . . C 2 -209.781 -100.888 -25.137 1 95.52 ? O8 BCO 1101 A 1 HETATM 32 C C11 BCO . . . C 2 -210.455 -99.866 -24.431 1 98.52 ? C11 BCO 1101 A 1 HETATM 33 C C9 BCO . . . C 2 -209.598 -98.846 -23.688 1 102.01 ? C9 BCO 1101 A 1 HETATM 34 C C13 BCO . . . C 2 -210.464 -97.798 -23.026 1 105.36 ? C13 BCO 1101 A 1 HETATM 35 C C14 BCO . . . C 2 -208.669 -98.137 -24.731 1 65.28 ? C14 BCO 1101 A 1 HETATM 36 C C10 BCO . . . C 2 -208.742 -99.525 -22.678 1 100.02 ? C10 BCO 1101 A 1 HETATM 37 O O11 BCO . . . C 2 -207.747 -98.596 -22.306 1 100.77 ? O11 BCO 1101 A 1 HETATM 38 C C16 BCO . . . C 2 -209.468 -100.013 -21.438 1 95.48 ? C16 BCO 1101 A 1 HETATM 39 O O15 BCO . . . C 2 -210.175 -101.029 -21.474 1 91.46 ? O15 BCO 1101 A 1 HETATM 40 N N6 BCO . . . C 2 -209.315 -99.278 -20.186 1 96.18 ? N6 BCO 1101 A 1 HETATM 41 C C17 BCO . . . C 2 -209.989 -99.754 -19.005 1 97.52 ? C17 BCO 1101 A 1 HETATM 42 C C18 BCO . . . C 2 -211.18 -98.999 -18.46 1 99.1 ? C18 BCO 1101 A 1 HETATM 43 C C19 BCO . . . C 2 -211.283 -98.882 -16.974 1 102.5 ? C19 BCO 1101 A 1 HETATM 44 O O16 BCO . . . C 2 -212.381 -98.863 -16.436 1 101.97 ? O16 BCO 1101 A 1 HETATM 45 N N7 BCO . . . C 2 -210.05 -98.798 -16.186 1 105.38 ? N7 BCO 1101 A 1 HETATM 46 C C20 BCO . . . C 2 -210.078 -98.692 -14.753 1 105.13 ? C20 BCO 1101 A 1 HETATM 47 C C21 BCO . . . C 2 -210.575 -97.39 -14.119 1 104.13 ? C21 BCO 1101 A 1 HETATM 48 S S1 BCO . . . C 2 -211.991 -97.491 -13.005 1 128.06 ? S1 BCO 1101 A 1 HETATM 49 C C22 BCO . . . C 2 -211.699 -96.429 -11.547 1 132.47 ? C22 BCO 1101 A 1 HETATM 50 O O17 BCO . . . C 2 -210.529 -96.081 -11.254 1 133.41 ? O17 BCO 1101 A 1 HETATM 51 C C23 BCO . . . C 2 -212.891 -95.877 -10.733 1 131.34 ? C23 BCO 1101 A 1 HETATM 52 C C24 BCO . . . C 2 -212.711 -95.707 -9.249 1 129.98 ? C24 BCO 1101 A 1 HETATM 53 C C25 BCO . . . C 2 -211.945 -94.494 -8.765 1 128.74 ? C25 BCO 1101 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 213 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 53 #