data_8B77 # _model_server_result.job_id pcoyYl7AxPgsNldTDU2iIQ _model_server_result.datetime_utc '2024-10-11 05:20:36' _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 8b77 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1301}' # _entry.id 8B77 # _exptl.entry_id 8B77 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _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 112.99 _cell.angle_gamma 90 _cell.entry_id 8B77 _cell.length_a 158.994 _cell.length_b 71.03 _cell.length_c 155.255 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B77 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 covale ? covale1 B O3' DT 10 P DT 10 1_555 B P DOC 11 P DOC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A OD1 ASP 645 A ASP 640 1_555 E CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc2 A O VAL 646 A VAL 641 1_555 E CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc3 A OD2 ASP 882 A ASP 877 1_555 E CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc4 D O3G DTP . A DTP 1301 1_555 E CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc5 D O2B DTP . A DTP 1301 1_555 E CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc6 D O2A DTP . A DTP 1301 1_555 E CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? hydrog WATSON-CRICK hydrog1 B N3 DT 1 P DT 1 1_555 C N1 DA 16 T DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 DT 1 P DT 1 1_555 C N6 DA 16 T DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DA 2 P DA 2 1_555 C N3 DT 15 T DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N6 DA 2 P DA 2 1_555 C O4 DT 15 T DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DA 3 P DA 3 1_555 C N3 DT 14 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N6 DA 3 P DA 3 1_555 C O4 DT 14 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DC 4 P DC 4 1_555 C N1 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N4 DC 4 P DC 4 1_555 C O6 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O2 DC 4 P DC 4 1_555 C N2 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DC 5 P DC 5 1_555 C N1 DG 12 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 DC 5 P DC 5 1_555 C O6 DG 12 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 DC 5 P DC 5 1_555 C N2 DG 12 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 6 P DG 6 1_555 C N3 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 6 P DG 6 1_555 C O2 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 6 P DG 6 1_555 C N4 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 7 P DC 7 1_555 C N1 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 7 P DC 7 1_555 C O6 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 7 P DC 7 1_555 C N2 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 8 P DG 8 1_555 C N3 DC 9 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 8 P DG 8 1_555 C O2 DC 9 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 8 P DG 8 1_555 C N4 DC 9 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DT 9 P DT 9 1_555 C N1 DA 8 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O4 DT 9 P DT 9 1_555 C N6 DA 8 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DT 10 P DT 10 1_555 C N1 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O4 DT 10 P DT 10 1_555 C N6 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N3 DOC 11 P DOC 11 1_555 C N1 DG 6 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N4 DOC 11 P DOC 11 1_555 C O6 DG 6 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O2 DOC 11 P DOC 11 1_555 C N2 DG 6 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _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 PG O1G DTP doub 266 n n PG O2G DTP sing 267 n n PG O3G DTP sing 268 n n PG O3B DTP sing 269 n n O2G HOG2 DTP sing 270 n n O3G HOG3 DTP sing 271 n n PB O1B DTP doub 272 n n PB O2B DTP sing 273 n n PB O3B DTP sing 274 n n PB O3A DTP sing 275 n n O2B HOB2 DTP sing 276 n n PA O1A DTP doub 277 n n PA O2A DTP sing 278 n n PA O3A DTP sing 279 n n PA O5' DTP sing 280 n n O2A HOA2 DTP sing 281 n n O5' C5' DTP sing 282 n n C5' C4' DTP sing 283 n n C5' "H5'1" DTP sing 284 n n C5' "H5'2" DTP sing 285 n n C4' O4' DTP sing 286 n n C4' C3' DTP sing 287 n n C4' H4' DTP sing 288 n n O4' C1' DTP sing 289 n n C3' O3' DTP sing 290 n n C3' C2' DTP sing 291 n n C3' H3' DTP sing 292 n n O3' HO3' DTP sing 293 n n C2' C1' DTP sing 294 n n C2' "H2'1" DTP sing 295 n n C2' "H2'2" DTP sing 296 n n C1' N9 DTP sing 297 n n C1' H1' DTP sing 298 n n N9 C8 DTP sing 299 n y N9 C4 DTP sing 300 n y C8 N7 DTP doub 301 n y C8 H8 DTP sing 302 n n N7 C5 DTP sing 303 n y C5 C6 DTP sing 304 n y C5 C4 DTP doub 305 n y C6 N6 DTP sing 306 n n C6 N1 DTP doub 307 n y N6 HN61 DTP sing 308 n n N6 HN62 DTP sing 309 n n N1 C2 DTP sing 310 n y C2 N3 DTP doub 311 n y C2 H2 DTP sing 312 n n N3 C4 DTP sing 313 n y # _atom_sites.entry_id 8B77 _atom_sites.fract_transf_matrix[1][1] 0.00629 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002668 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014079 _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] 0.006997 _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 DTP A 1 1301 1301 DTP DTP . E 5 CA A 1 1302 1302 CA CA . # 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 PG DTP . . . D 4 10.124 20.226 30.905 1 47.7 ? PG DTP 1301 A 1 HETATM 2 O O1G DTP . . . D 4 9.058 21.041 31.567 1 51.76 ? O1G DTP 1301 A 1 HETATM 3 O O2G DTP . . . D 4 10.328 20.603 29.471 1 61.05 ? O2G DTP 1301 A 1 HETATM 4 O O3G DTP . . . D 4 11.402 20.215 31.682 1 56.1 ? O3G DTP 1301 A 1 HETATM 5 P PB DTP . . . D 4 10.168 17.281 31.177 1 45.25 ? PB DTP 1301 A 1 HETATM 6 O O1B DTP . . . D 4 9.421 16.279 30.377 1 55.18 ? O1B DTP 1301 A 1 HETATM 7 O O2B DTP . . . D 4 11.647 17.324 31.087 1 57.28 ? O2B DTP 1301 A 1 HETATM 8 O O3B DTP . . . D 4 9.563 18.726 30.877 1 36.86 ? O3B DTP 1301 A 1 HETATM 9 P PA DTP . . . D 4 10.554 17.298 34.074 1 56.89 ? PA DTP 1301 A 1 HETATM 10 O O1A DTP . . . D 4 9.65 17.901 35.092 1 51.17 ? O1A DTP 1301 A 1 HETATM 11 O O2A DTP . . . D 4 11.836 17.987 33.761 1 50.85 ? O2A DTP 1301 A 1 HETATM 12 O O3A DTP . . . D 4 9.747 17.106 32.708 1 63.84 ? O3A DTP 1301 A 1 HETATM 13 O O5' DTP . . . D 4 10.843 15.774 34.453 1 43.56 ? O5' DTP 1301 A 1 HETATM 14 C C5' DTP . . . D 4 11.884 15.099 33.715 1 47.64 ? C5' DTP 1301 A 1 HETATM 15 C C4' DTP . . . D 4 11.376 13.763 33.236 1 54.73 ? C4' DTP 1301 A 1 HETATM 16 O O4' DTP . . . D 4 10.707 13.082 34.316 1 49.99 ? O4' DTP 1301 A 1 HETATM 17 C C3' DTP . . . D 4 10.332 13.815 32.131 1 46.42 ? C3' DTP 1301 A 1 HETATM 18 O O3' DTP . . . D 4 10.928 14.022 30.857 1 51.59 ? O3' DTP 1301 A 1 HETATM 19 C C2' DTP . . . D 4 9.742 12.417 32.261 1 45.88 ? C2' DTP 1301 A 1 HETATM 20 C C1' DTP . . . D 4 9.699 12.233 33.771 1 43.47 ? C1' DTP 1301 A 1 HETATM 21 N N9 DTP . . . D 4 8.422 12.628 34.324 1 32.69 ? N9 DTP 1301 A 1 HETATM 22 C C8 DTP . . . D 4 8.097 13.808 34.934 1 33.56 ? C8 DTP 1301 A 1 HETATM 23 N N7 DTP . . . D 4 6.839 13.856 35.304 1 31.07 ? N7 DTP 1301 A 1 HETATM 24 C C5 DTP . . . D 4 6.31 12.637 34.903 1 28.25 ? C5 DTP 1301 A 1 HETATM 25 C C6 DTP . . . D 4 5.026 12.076 35.004 1 32.05 ? C6 DTP 1301 A 1 HETATM 26 N N6 DTP . . . D 4 3.989 12.694 35.557 1 28.25 ? N6 DTP 1301 A 1 HETATM 27 N N1 DTP . . . D 4 4.849 10.837 34.49 1 35.92 ? N1 DTP 1301 A 1 HETATM 28 C C2 DTP . . . D 4 5.894 10.219 33.928 1 30.81 ? C2 DTP 1301 A 1 HETATM 29 N N3 DTP . . . D 4 7.143 10.647 33.78 1 34.12 ? N3 DTP 1301 A 1 HETATM 30 C C4 DTP . . . D 4 7.282 11.877 34.295 1 32.83 ? C4 DTP 1301 A 1 # _model_server_stats.io_time_ms 165 _model_server_stats.parse_time_ms 152 _model_server_stats.create_model_time_ms 61 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #