data_6QIB # _model_server_result.job_id jPpBAF2xUFPYPYuo3aECKw _model_server_result.datetime_utc '2024-10-19 22:32:23' _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 6qib # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1202}' # _entry.id 6QIB # _exptl.entry_id 6QIB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 5 _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 6QIB _cell.length_a 158.36 _cell.length_b 70.402 _cell.length_c 154.24 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QIB _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 software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 5 _struct_asym.id E _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.584 ? metalc ? metalc1 A OD1 ASP 645 A ASP 640 1_555 F CA CA . A CA 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.053 ? metalc ? metalc2 A OD2 ASP 645 A ASP 640 1_555 F CA CA . A CA 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc3 A O VAL 646 A VAL 641 1_555 F CA CA . A CA 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc4 A SG CYS 670 A CYS 665 1_555 D FE1 SF4 . A SF4 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc5 A SG CYS 673 A CYS 668 1_555 D FE2 SF4 . A SF4 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc6 A SG CYS 682 A CYS 677 1_555 D FE3 SF4 . A SF4 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc7 A SG CYS 768 A CYS 763 1_555 D FE4 SF4 . A SF4 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc8 A OD2 ASP 882 A ASP 877 1_555 F CA CA . A CA 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc9 E O3G DTP . A DTP 1202 1_555 F CA CA . A CA 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 E O1B DTP . A DTP 1202 1_555 F CA CA . A CA 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc11 E O1A DTP . A DTP 1202 1_555 F CA CA . A CA 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 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 6QIB _atom_sites.fract_transf_matrix[1][1] 0.006315 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002679 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014204 _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] 0.007043 _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 SF4 A 1 1201 1201 SF4 SF4 . E 5 DTP A 1 1202 1301 DTP DTP . F 6 CA A 1 1203 1401 CA 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 P PG DTP . . . E 5 10.428 18.71 30.761 1 48.86 ? PG DTP 1202 A 1 HETATM 2 O O1G DTP . . . E 5 10.518 18.321 29.351 1 44.23 ? O1G DTP 1202 A 1 HETATM 3 O O2G DTP . . . E 5 9.38 19.696 31.13 1 40.32 ? O2G DTP 1202 A 1 HETATM 4 O O3G DTP . . . E 5 11.698 18.776 31.57 1 45.52 ? O3G DTP 1202 A 1 HETATM 5 P PB DTP . . . E 5 10.385 15.892 31.053 1 48.78 ? PB DTP 1202 A 1 HETATM 6 O O1B DTP . . . E 5 11.857 16.054 31.006 1 49.8 ? O1B DTP 1202 A 1 HETATM 7 O O2B DTP . . . E 5 9.756 14.999 30.059 1 49.99 ? O2B DTP 1202 A 1 HETATM 8 O O3B DTP . . . E 5 9.67 17.345 31.184 1 42.22 ? O3B DTP 1202 A 1 HETATM 9 P PA DTP . . . E 5 10.724 15.915 33.794 1 45.1 ? PA DTP 1202 A 1 HETATM 10 O O1A DTP . . . E 5 11.853 16.805 33.334 1 45.54 ? O1A DTP 1202 A 1 HETATM 11 O O2A DTP . . . E 5 9.741 16.39 34.811 1 38.3 ? O2A DTP 1202 A 1 HETATM 12 O O3A DTP . . . E 5 9.945 15.377 32.496 1 46.3 ? O3A DTP 1202 A 1 HETATM 13 O O5' DTP . . . E 5 11.308 14.472 34.22 1 41.37 ? O5' DTP 1202 A 1 HETATM 14 C C5' DTP . . . E 5 12.105 13.751 33.297 1 40.57 ? C5' DTP 1202 A 1 HETATM 15 C C4' DTP . . . E 5 11.533 12.349 33.087 1 41.25 ? C4' DTP 1202 A 1 HETATM 16 O O4' DTP . . . E 5 10.73 11.923 34.214 1 36.25 ? O4' DTP 1202 A 1 HETATM 17 C C3' DTP . . . E 5 10.518 12.34 31.951 1 43.71 ? C3' DTP 1202 A 1 HETATM 18 O O3' DTP . . . E 5 11.145 12.544 30.659 1 47.35 ? O3' DTP 1202 A 1 HETATM 19 C C2' DTP . . . E 5 9.996 10.935 32.149 1 39.38 ? C2' DTP 1202 A 1 HETATM 20 C C1' DTP . . . E 5 9.861 10.892 33.695 1 36.01 ? C1' DTP 1202 A 1 HETATM 21 N N9 DTP . . . E 5 8.573 11.408 34.053 1 35.82 ? N9 DTP 1202 A 1 HETATM 22 C C8 DTP . . . E 5 8.328 12.642 34.517 1 37.38 ? C8 DTP 1202 A 1 HETATM 23 N N7 DTP . . . E 5 7.013 12.756 34.731 1 38.79 ? N7 DTP 1202 A 1 HETATM 24 C C5 DTP . . . E 5 6.463 11.586 34.394 1 38 ? C5 DTP 1202 A 1 HETATM 25 C C6 DTP . . . E 5 5.201 11.186 34.427 1 39.69 ? C6 DTP 1202 A 1 HETATM 26 N N6 DTP . . . E 5 4.328 12.089 34.85 1 40.65 ? N6 DTP 1202 A 1 HETATM 27 N N1 DTP . . . E 5 4.832 9.95 34.04 1 40.41 ? N1 DTP 1202 A 1 HETATM 28 C C2 DTP . . . E 5 5.827 9.047 33.597 1 39.51 ? C2 DTP 1202 A 1 HETATM 29 N N3 DTP . . . E 5 7.151 9.487 33.594 1 38.32 ? N3 DTP 1202 A 1 HETATM 30 C C4 DTP . . . E 5 7.426 10.749 33.976 1 37.39 ? C4 DTP 1202 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #