data_1X8K # _model_server_result.job_id yYngsV4M2s9EfMRjSZU7hA _model_server_result.datetime_utc '2024-10-20 00:34:15' _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 1x8k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1101}' # _entry.id 1X8K # _exptl.entry_id 1X8K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 110.66 _cell.angle_gamma 90 _cell.entry_id 1X8K _cell.length_a 81.286 _cell.length_b 66.661 _cell.length_c 84.464 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1X8K _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I,J,K,L _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 ? 5 H N N ? 5 I 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 O GLU 118 A GLU 118 1_555 D CA CA . A CA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc2 A OD1 ASN 121 A ASN 121 1_555 D CA CA . A CA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc3 A OD1 ASP 122 A ASP 122 1_555 D CA CA . A CA 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc4 A SG CYS 318 A CYS 318 1_555 C HG EMC . A EMC 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc5 B O GLU 118 B GLU 118 1_555 G CA CA . B CA 2204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc6 B OD1 ASN 121 B ASN 121 1_555 G CA CA . B CA 2204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc7 B OD1 ASP 122 B ASP 122 1_555 G CA CA . B CA 2204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc8 B SG CYS 318 B CYS 318 1_555 F HG EMC . B EMC 2203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 1X8K _atom_sites.fract_transf_matrix[1][1] 0.012302 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004639 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015001 _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] 0.012653 _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 EMC A 1 1103 1103 EMC EMC . D 3 CA A 1 1104 1104 CA CA . E 4 ANR A 1 1102 1102 ANR ANR . F 2 EMC B 1 2203 2203 EMC EMC . G 3 CA B 1 2204 2204 CA CA . H 5 A3P B 1 1101 1101 A3P A3P . I 5 A3P B 1 2201 2201 A3P A3P . J 4 ANR B 1 2202 2202 ANR ANR . K 6 HOH A 1 1105 1 HOH HOH . K 6 HOH A 2 1106 3 HOH HOH . K 6 HOH A 3 1107 5 HOH HOH . K 6 HOH A 4 1108 7 HOH HOH . K 6 HOH A 5 1109 9 HOH HOH . K 6 HOH A 6 1110 12 HOH HOH . K 6 HOH A 7 1111 17 HOH HOH . K 6 HOH A 8 1112 19 HOH HOH . K 6 HOH A 9 1113 20 HOH HOH . K 6 HOH A 10 1114 21 HOH HOH . K 6 HOH A 11 1115 24 HOH HOH . K 6 HOH A 12 1116 26 HOH HOH . K 6 HOH A 13 1117 27 HOH HOH . K 6 HOH A 14 1118 29 HOH HOH . K 6 HOH A 15 1119 31 HOH HOH . K 6 HOH A 16 1120 35 HOH HOH . K 6 HOH A 17 1121 36 HOH HOH . K 6 HOH A 18 1122 37 HOH HOH . K 6 HOH A 19 1123 38 HOH HOH . K 6 HOH A 20 1124 39 HOH HOH . K 6 HOH A 21 1125 41 HOH HOH . K 6 HOH A 22 1126 42 HOH HOH . K 6 HOH A 23 1127 44 HOH HOH . K 6 HOH A 24 1128 45 HOH HOH . K 6 HOH A 25 1129 47 HOH HOH . K 6 HOH A 26 1130 48 HOH HOH . K 6 HOH A 27 1131 50 HOH HOH . K 6 HOH A 28 1132 52 HOH HOH . K 6 HOH A 29 1133 53 HOH HOH . K 6 HOH A 30 1134 54 HOH HOH . K 6 HOH A 31 1135 57 HOH HOH . K 6 HOH A 32 1136 58 HOH HOH . K 6 HOH A 33 1137 59 HOH HOH . K 6 HOH A 34 1138 60 HOH HOH . K 6 HOH A 35 1139 61 HOH HOH . K 6 HOH A 36 1140 64 HOH HOH . K 6 HOH A 37 1141 67 HOH HOH . K 6 HOH A 38 1142 68 HOH HOH . K 6 HOH A 39 1143 70 HOH HOH . K 6 HOH A 40 1144 71 HOH HOH . K 6 HOH A 41 1145 73 HOH HOH . L 6 HOH B 1 2205 2 HOH HOH . L 6 HOH B 2 2206 4 HOH HOH . L 6 HOH B 3 2207 6 HOH HOH . L 6 HOH B 4 2208 8 HOH HOH . L 6 HOH B 5 2209 10 HOH HOH . L 6 HOH B 6 2210 11 HOH HOH . L 6 HOH B 7 2211 13 HOH HOH . L 6 HOH B 8 2212 14 HOH HOH . L 6 HOH B 9 2213 15 HOH HOH . L 6 HOH B 10 2214 16 HOH HOH . L 6 HOH B 11 2215 18 HOH HOH . L 6 HOH B 12 2216 22 HOH HOH . L 6 HOH B 13 2217 23 HOH HOH . L 6 HOH B 14 2218 25 HOH HOH . L 6 HOH B 15 2219 28 HOH HOH . L 6 HOH B 16 2220 30 HOH HOH . L 6 HOH B 17 2221 32 HOH HOH . L 6 HOH B 18 2222 33 HOH HOH . L 6 HOH B 19 2223 34 HOH HOH . L 6 HOH B 20 2224 40 HOH HOH . L 6 HOH B 21 2225 43 HOH HOH . L 6 HOH B 22 2226 46 HOH HOH . L 6 HOH B 23 2227 49 HOH HOH . L 6 HOH B 24 2228 51 HOH HOH . L 6 HOH B 25 2229 55 HOH HOH . L 6 HOH B 26 2230 56 HOH HOH . L 6 HOH B 27 2231 62 HOH HOH . L 6 HOH B 28 2232 63 HOH HOH . L 6 HOH B 29 2233 65 HOH HOH . L 6 HOH B 30 2234 66 HOH HOH . L 6 HOH B 31 2235 69 HOH HOH . L 6 HOH B 32 2236 72 HOH HOH . L 6 HOH B 33 2237 74 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 P P1 A3P . . . H 5 12.692 8.489 38.432 1 20.48 ? P1 A3P 1101 B 1 HETATM 2 O O1P A3P . . . H 5 12.291 9.107 37.11 1 21.44 ? O1P A3P 1101 B 1 HETATM 3 O O2P A3P . . . H 5 12.567 9.44 39.602 1 17.34 ? O2P A3P 1101 B 1 HETATM 4 O O3P A3P . . . H 5 14.005 7.755 38.339 1 18.86 ? O3P A3P 1101 B 1 HETATM 5 P P2 A3P . . . H 5 9.679 1.627 38.707 1 20.42 ? P2 A3P 1101 B 1 HETATM 6 O O4P A3P . . . H 5 11.165 1.354 38.615 1 21 ? O4P A3P 1101 B 1 HETATM 7 O O5P A3P . . . H 5 9.067 1.289 40.046 1 17.95 ? O5P A3P 1101 B 1 HETATM 8 O O6P A3P . . . H 5 8.87 1.111 37.532 1 18.44 ? O6P A3P 1101 B 1 HETATM 9 O O5' A3P . . . H 5 9.598 3.245 38.626 1 21.66 ? O5' A3P 1101 B 1 HETATM 10 C C5' A3P . . . H 5 10.636 4.034 39.185 1 20.12 ? C5' A3P 1101 B 1 HETATM 11 C C4' A3P . . . H 5 10.403 5.512 38.924 1 20.2 ? C4' A3P 1101 B 1 HETATM 12 O O4' A3P . . . H 5 9.203 5.893 39.589 1 20.48 ? O4' A3P 1101 B 1 HETATM 13 C C3' A3P . . . H 5 11.55 6.27 39.555 1 20.57 ? C3' A3P 1101 B 1 HETATM 14 O O3' A3P . . . H 5 11.571 7.356 38.623 1 18.84 ? O3' A3P 1101 B 1 HETATM 15 C C2' A3P . . . H 5 11.013 6.903 40.811 1 20.51 ? C2' A3P 1101 B 1 HETATM 16 O O2' A3P . . . H 5 11.643 8.086 41.291 1 22.08 ? O2' A3P 1101 B 1 HETATM 17 C C1' A3P . . . H 5 9.499 6.832 40.643 1 20.38 ? C1' A3P 1101 B 1 HETATM 18 N N9 A3P . . . H 5 8.669 6.751 41.848 1 20.02 ? N9 A3P 1101 B 1 HETATM 19 C C8 A3P . . . H 5 8.734 5.833 42.83 1 21.59 ? C8 A3P 1101 B 1 HETATM 20 N N7 A3P . . . H 5 7.785 6.069 43.779 1 22.1 ? N7 A3P 1101 B 1 HETATM 21 C C5 A3P . . . H 5 7.111 7.164 43.364 1 21.01 ? C5 A3P 1101 B 1 HETATM 22 C C6 A3P . . . H 5 6.039 7.923 43.843 1 19.13 ? C6 A3P 1101 B 1 HETATM 23 N N6 A3P . . . H 5 5.472 7.561 45.018 1 16.16 ? N6 A3P 1101 B 1 HETATM 24 N N1 A3P . . . H 5 5.589 8.998 43.131 1 19.37 ? N1 A3P 1101 B 1 HETATM 25 C C2 A3P . . . H 5 6.159 9.367 41.95 1 20.49 ? C2 A3P 1101 B 1 HETATM 26 N N3 A3P . . . H 5 7.204 8.682 41.419 1 20.41 ? N3 A3P 1101 B 1 HETATM 27 C C4 A3P . . . H 5 7.676 7.546 42.17 1 20.28 ? C4 A3P 1101 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #