data_8DHB # _model_server_result.job_id 4j5RD-psjfaJ2_w_AUem-Q _model_server_result.datetime_utc '2024-12-23 04:26:30' _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 8dhb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 8DHB # _exptl.entry_id 8DHB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 444.185 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate' _entity.pdbx_number_of_molecules 1 _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 8DHB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DHB _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 _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,M _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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 11 _struct_asym.id K _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 J SG CYS 51 J CYS 8 1_555 J SG CYS 168 J CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 K O12 CZC . A CZC 501 1_555 L BE BEF . A BEF 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.779 ? # _chem_comp.formula 'C10 H14 N4 O12 P2' _chem_comp.formula_weight 444.185 _chem_comp.id CZC _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'xanthosine diphosphate' # 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 O12 P2 CZC doub 86 n n O11 P2 CZC sing 87 n n P2 O10 CZC sing 88 n n P2 O7 CZC sing 89 n n O7 P1 CZC sing 90 n n C6 O3 CZC sing 91 n n C6 C5 CZC sing 92 n n C6 C7 CZC sing 93 n n O2 C5 CZC sing 94 n n C8 C7 CZC sing 95 n n C8 O5 CZC sing 96 n n O9 P1 CZC doub 97 n n P1 O5 CZC sing 98 n n P1 O8 CZC sing 99 n n C5 C4 CZC sing 100 n n C7 O4 CZC sing 101 n n C4 O4 CZC sing 102 n n C4 N4 CZC sing 103 n n N4 C10 CZC sing 104 n y N4 C2 CZC sing 105 n y C10 N3 CZC doub 106 n y C2 N2 CZC sing 107 n n C2 C3 CZC doub 108 n y N2 C1 CZC sing 109 n n N3 C3 CZC sing 110 n y C3 C9 CZC sing 111 n n C1 O1 CZC doub 112 n n C1 N1 CZC sing 113 n n C9 N1 CZC sing 114 n n C9 O6 CZC doub 115 n n C4 H1 CZC sing 116 n n C5 H2 CZC sing 117 n n C6 H3 CZC sing 118 n n C7 H4 CZC sing 119 n n C8 H5 CZC sing 120 n n C8 H6 CZC sing 121 n n C10 H7 CZC sing 122 n n N1 H8 CZC sing 123 n n N2 H9 CZC sing 124 n n O2 H10 CZC sing 125 n n O3 H11 CZC sing 126 n n O8 H12 CZC sing 127 n n O10 H13 CZC sing 128 n n O11 H14 CZC sing 129 n n # _atom_sites.entry_id 8DHB _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 K 11 CZC A 1 501 502 CZC XDP . L 12 BEF A 1 502 503 BEF BEF . M 13 GDP B 1 500 500 GDP GDP . # 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 C C1 CZC . . . K 11 218.126 254.34 227.779 1 54.69 ? C1 CZC 501 A 1 HETATM 2 C C2 CZC . . . K 11 218.482 252.728 226.127 1 55.69 ? C2 CZC 501 A 1 HETATM 3 C C3 CZC . . . K 11 218.134 251.736 226.959 1 55.72 ? C3 CZC 501 A 1 HETATM 4 C C4 CZC . . . K 11 219.214 252.95 223.738 1 58.72 ? C4 CZC 501 A 1 HETATM 5 C C5 CZC . . . K 11 220.692 253.292 223.665 1 59.88 ? C5 CZC 501 A 1 HETATM 6 C C6 CZC . . . K 11 221.206 252.368 222.59 1 60.93 ? C6 CZC 501 A 1 HETATM 7 C C7 CZC . . . K 11 219.994 252.216 221.687 1 60.88 ? C7 CZC 501 A 1 HETATM 8 C C8 CZC . . . K 11 220.081 250.893 220.932 1 61.53 ? C8 CZC 501 A 1 HETATM 9 C C9 CZC . . . K 11 217.768 252.001 228.225 1 55.7 ? C9 CZC 501 A 1 HETATM 10 C C10 CZC . . . K 11 218.643 250.872 225.052 1 56.31 ? C10 CZC 501 A 1 HETATM 11 N N1 CZC . . . K 11 217.758 253.332 228.673 1 55.31 ? N1 CZC 501 A 1 HETATM 12 N N2 CZC . . . K 11 218.478 254.01 226.529 1 54.93 ? N2 CZC 501 A 1 HETATM 13 N N3 CZC . . . K 11 218.236 250.592 226.286 1 55.78 ? N3 CZC 501 A 1 HETATM 14 N N4 CZC . . . K 11 218.804 252.189 224.957 1 56.83 ? N4 CZC 501 A 1 HETATM 15 O O1 CZC . . . K 11 218.128 255.579 228.156 1 54.06 ? O1 CZC 501 A 1 HETATM 16 O O2 CZC . . . K 11 220.803 254.648 223.205 1 59.95 ? O2 CZC 501 A 1 HETATM 17 O O3 CZC . . . K 11 222.289 253 221.857 1 61.45 ? O3 CZC 501 A 1 HETATM 18 O O4 CZC . . . K 11 218.887 252.143 222.581 1 59.7 ? O4 CZC 501 A 1 HETATM 19 O O5 CZC . . . K 11 219.316 249.892 221.603 1 62.15 ? O5 CZC 501 A 1 HETATM 20 O O6 CZC . . . K 11 217.441 251.103 229.007 1 55.44 ? O6 CZC 501 A 1 HETATM 21 O O7 CZC . . . K 11 218.519 248.196 219.935 1 63.69 ? O7 CZC 501 A 1 HETATM 22 O O8 CZC . . . K 11 219.086 247.505 222.307 1 62.8 -1 O8 CZC 501 A 1 HETATM 23 O O9 CZC . . . K 11 220.894 248.216 220.632 1 63.63 ? O9 CZC 501 A 1 HETATM 24 O O10 CZC . . . K 11 218.66 245.796 219.887 1 64.22 ? O10 CZC 501 A 1 HETATM 25 O O11 CZC . . . K 11 216.597 246.934 220.698 1 64.16 -1 O11 CZC 501 A 1 HETATM 26 O O12 CZC . . . K 11 217.224 247.058 218.304 1 64.27 ? O12 CZC 501 A 1 HETATM 27 P P1 CZC . . . K 11 219.528 248.363 221.185 1 63.3 ? P1 CZC 501 A 1 HETATM 28 P P2 CZC . . . K 11 217.675 246.867 219.701 1 64.14 ? P2 CZC 501 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #