data_8T3X # _model_server_result.job_id tMeCQqqYch6xQcafevTkUg _model_server_result.datetime_utc '2024-10-18 05:24:49' _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 8t3x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":801}' # _entry.id 8T3X # _exptl.entry_id 8T3X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.155 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] 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 8T3X _cell.length_a 76.869 _cell.length_b 99.525 _cell.length_c 110.727 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8T3X _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 A SG CYS 429 A CYS 429 1_555 A SG CYS 443 A CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 507 A CYS 507 1_555 A SG CYS 510 A CYS 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 C O3' DG 11 P DG 11 1_555 C P YTI 12 P YTI 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? metalc ? metalc1 A OD2 ASP 405 A ASP 405 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc2 A O PHE 406 A PHE 406 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc3 A OD2 ASP 543 A ASP 543 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc4 D O2B 9O7 . A 9O7 801 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc5 D O2G 9O7 . A 9O7 801 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc6 D O3A 9O7 . A 9O7 801 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? hydrog WATSON-CRICK hydrog1 B N3 DC 5 T DC 11 1_555 C N1 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 5 T DC 11 1_555 C O6 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 5 T DC 11 1_555 C N2 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 6 T DG 12 1_555 C N3 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 6 T DG 12 1_555 C O2 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 6 T DG 12 1_555 C N4 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DC 7 T DC 13 1_555 C N1 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N4 DC 7 T DC 13 1_555 C O6 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O2 DC 7 T DC 13 1_555 C N2 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 8 T DA 14 1_555 C N3 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 8 T DA 14 1_555 C O4 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DG 9 T DG 15 1_555 C N3 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 DG 9 T DG 15 1_555 C O2 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 9 T DG 15 1_555 C N4 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DT 10 T DT 16 1_555 C N1 DA 6 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O4 DT 10 T DT 16 1_555 C N6 DA 6 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 11 T DT 17 1_555 C N1 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 11 T DT 17 1_555 C N6 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DC 12 T DC 18 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N4 DC 12 T DC 18 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O2 DC 12 T DC 18 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DG 13 T DG 19 1_555 C N3 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 DG 13 T DG 19 1_555 C O2 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 DG 13 T DG 19 1_555 C N4 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 DC 14 T DC 20 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N4 DC 14 T DC 20 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O2 DC 14 T DC 20 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N1 DG 15 T DG 21 1_555 C N3 DC 1 P DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N2 DG 15 T DG 21 1_555 C O2 DC 1 P DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B O6 DG 15 T DG 21 1_555 C N4 DC 1 P DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H14 N5 O12 P3' _chem_comp.formula_weight 477.155 _chem_comp.id 9O7 _chem_comp.mon_nstd_flag . _chem_comp.name '[(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate' _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 O4' C4' 9O7 sing 1 n n O4' C1' 9O7 sing 2 n n C4' C3' 9O7 sing 3 n n C2 N3 9O7 doub 4 n y C2 N1 9O7 sing 5 n y N3 C4 9O7 sing 6 n y N1 C6 9O7 doub 7 n y O1A PA 9O7 doub 8 n n C4 C5 9O7 doub 9 n y C4 N9 9O7 sing 10 n y C6 N6 9O7 sing 11 n n C6 C5 9O7 sing 12 n y O2A PA 9O7 sing 13 n n C1' N9 9O7 sing 14 n n C1' C2' 9O7 sing 15 n n C5 N7 9O7 sing 16 n y N9 C8 9O7 sing 17 n y C3' O3' 9O7 sing 18 n n C3' C2' 9O7 sing 19 n n C8 N7 9O7 doub 20 n y PA O3' 9O7 sing 21 n n PA O3A 9O7 sing 22 n n C2' O2' 9O7 sing 23 n n O3A PB 9O7 sing 24 n n O2B PB 9O7 doub 25 n n O2G PG 9O7 doub 26 n n PB O1B 9O7 sing 27 n n PB O3B 9O7 sing 28 n n PG O3B 9O7 sing 29 n n PG O3G 9O7 sing 30 n n PG O1G 9O7 sing 31 n n C2 H1 9O7 sing 32 n n N6 H2 9O7 sing 33 n n N6 H3 9O7 sing 34 n n C8 H4 9O7 sing 35 n n C1' H5 9O7 sing 36 n n O1B H6 9O7 sing 37 n n C2' H7 9O7 sing 38 n n O2' H8 9O7 sing 39 n n O2A H9 9O7 sing 40 n n C3' H10 9O7 sing 41 n n O3G H11 9O7 sing 42 n n C4' H12 9O7 sing 43 n n C4' H13 9O7 sing 44 n n O1G H14 9O7 sing 45 n n # _atom_sites.entry_id 8T3X _atom_sites.fract_transf_matrix[1][1] 0.013009 _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] 0.010048 _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] 0.009031 _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 4 9O7 A 1 801 13 9O7 9O7 . E 5 MG A 1 802 14 MG MG . F 6 EPE A 1 803 1 EPE EPE . G 7 HOH A 1 901 60 HOH HOH . G 7 HOH A 2 902 10 HOH HOH . G 7 HOH A 3 903 42 HOH HOH . G 7 HOH A 4 904 12 HOH HOH . G 7 HOH A 5 905 26 HOH HOH . G 7 HOH A 6 906 29 HOH HOH . G 7 HOH A 7 907 13 HOH HOH . G 7 HOH A 8 908 9 HOH HOH . G 7 HOH A 9 909 5 HOH HOH . G 7 HOH A 10 910 11 HOH HOH . G 7 HOH A 11 911 23 HOH HOH . G 7 HOH A 12 912 19 HOH HOH . G 7 HOH A 13 913 20 HOH HOH . G 7 HOH A 14 914 45 HOH HOH . G 7 HOH A 15 915 7 HOH HOH . G 7 HOH A 16 916 21 HOH HOH . G 7 HOH A 17 917 43 HOH HOH . G 7 HOH A 18 918 16 HOH HOH . G 7 HOH A 19 919 40 HOH HOH . G 7 HOH A 20 920 36 HOH HOH . G 7 HOH A 21 921 32 HOH HOH . G 7 HOH A 22 922 27 HOH HOH . G 7 HOH A 23 923 3 HOH HOH . G 7 HOH A 24 924 41 HOH HOH . G 7 HOH A 25 925 4 HOH HOH . G 7 HOH A 26 926 18 HOH HOH . G 7 HOH A 27 927 14 HOH HOH . G 7 HOH A 28 928 22 HOH HOH . G 7 HOH A 29 929 50 HOH HOH . G 7 HOH A 30 930 28 HOH HOH . G 7 HOH A 31 931 15 HOH HOH . G 7 HOH A 32 932 31 HOH HOH . G 7 HOH A 33 933 54 HOH HOH . G 7 HOH A 34 934 17 HOH HOH . G 7 HOH A 35 935 59 HOH HOH . G 7 HOH A 36 936 48 HOH HOH . G 7 HOH A 37 937 61 HOH HOH . G 7 HOH A 38 938 55 HOH HOH . G 7 HOH A 39 939 57 HOH HOH . G 7 HOH A 40 940 53 HOH HOH . G 7 HOH A 41 941 49 HOH HOH . H 7 HOH T 1 101 46 HOH HOH . H 7 HOH T 2 102 39 HOH HOH . I 7 HOH P 1 101 47 HOH HOH . I 7 HOH P 2 102 35 HOH HOH . I 7 HOH P 3 103 33 HOH HOH . I 7 HOH P 4 104 24 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 N1 9O7 . . . D 4 3.295 4.885 9.311 1 40.78 ? N1 9O7 801 A 1 HETATM 2 C C2 9O7 . . . D 4 2.776 4.503 8.073 1 41.17 ? C2 9O7 801 A 1 HETATM 3 N N3 9O7 . . . D 4 2.956 5.138 6.883 1 41.52 ? N3 9O7 801 A 1 HETATM 4 C C4 9O7 . . . D 4 3.754 6.299 6.956 1 41.46 ? C4 9O7 801 A 1 HETATM 5 C C5 9O7 . . . D 4 4.334 6.781 8.174 1 41.07 ? C5 9O7 801 A 1 HETATM 6 C C6 9O7 . . . D 4 4.08 6.033 9.381 1 40.72 ? C6 9O7 801 A 1 HETATM 7 N N6 9O7 . . . D 4 4.605 6.424 10.628 1 40.33 ? N6 9O7 801 A 1 HETATM 8 N N7 9O7 . . . D 4 5.071 7.954 7.919 1 41.12 ? N7 9O7 801 A 1 HETATM 9 C C8 9O7 . . . D 4 4.957 8.197 6.589 1 41.53 ? C8 9O7 801 A 1 HETATM 10 N N9 9O7 . . . D 4 4.163 7.204 5.969 1 41.75 ? N9 9O7 801 A 1 HETATM 11 P PA 9O7 . . . D 4 5.798 11.469 4.536 1 41.65 ? PA 9O7 801 A 1 HETATM 12 P PB 9O7 . . . D 4 3.05 12.471 3.879 1 40.29 ? PB 9O7 801 A 1 HETATM 13 P PG 9O7 . . . D 4 3.594 15.46 3.503 1 39.7 ? PG 9O7 801 A 1 HETATM 14 C C1' 9O7 . . . D 4 3.898 7.282 4.51 1 42.19 ? C1' 9O7 801 A 1 HETATM 15 O O1A 9O7 . . . D 4 7.266 11.664 4.269 1 42.39 ? O1A 9O7 801 A 1 HETATM 16 O O1B 9O7 . . . D 4 2.887 11.815 5.23 1 39.87 -1 O1B 9O7 801 A 1 HETATM 17 C C2' 9O7 . . . D 4 3.591 8.73 3.998 1 41.76 ? C2' 9O7 801 A 1 HETATM 18 O O2' 9O7 . . . D 4 2.52 8.686 3.069 1 41.65 ? O2' 9O7 801 A 1 HETATM 19 O O2A 9O7 . . . D 4 5.393 11.172 5.954 1 40.97 -1 O2A 9O7 801 A 1 HETATM 20 O O2B 9O7 . . . D 4 2.73 11.596 2.692 1 40.92 ? O2B 9O7 801 A 1 HETATM 21 O O2G 9O7 . . . D 4 4.648 15.046 2.489 1 40.75 -1 O2G 9O7 801 A 1 HETATM 22 C C3' 9O7 . . . D 4 4.91 9.116 3.242 1 42.56 ? C3' 9O7 801 A 1 HETATM 23 O O3' 9O7 . . . D 4 5.752 9.653 4.121 1 42.41 ? O3' 9O7 801 A 1 HETATM 24 O O3A 9O7 . . . D 4 4.821 12.245 3.631 1 41.3 ? O3A 9O7 801 A 1 HETATM 25 O O3B 9O7 . . . D 4 2.612 13.952 3.813 1 39.61 ? O3B 9O7 801 A 1 HETATM 26 O O3G 9O7 . . . D 4 2.735 16.61 2.984 1 39.64 -1 O3G 9O7 801 A 1 HETATM 27 C C4' 9O7 . . . D 4 5.307 7.663 2.772 1 43.44 ? C4' 9O7 801 A 1 HETATM 28 O O4' 9O7 . . . D 4 5.057 6.82 3.871 1 43.16 ? O4' 9O7 801 A 1 HETATM 29 O O1G 9O7 . . . D 4 4.134 15.719 4.891 1 39.36 ? O1G 9O7 801 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #