data_4XQ8 # _model_server_result.job_id FePUZXMW7V4bMiRmkzn2fA _model_server_result.datetime_utc '2024-11-22 19:19:28' _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 4xq8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 4XQ8 # _exptl.entry_id 4XQ8 _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 90 _cell.angle_gamma 120 _cell.entry_id 4XQ8 _cell.length_a 83.743 _cell.length_b 83.743 _cell.length_c 398.746 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XQ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G,I,J 1 1 B,E,F,H 2 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 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 disulf ? disulf1 A SG CYS 302 B CYS 543 1_555 B SG CYS 302 A CYS 543 5_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc1 B OD1 ASP 186 A ASP 427 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.774 ? metalc ? metalc2 B OD2 ASP 188 A ASP 429 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.711 ? metalc ? metalc3 E O2G DTP . A DTP 601 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc4 E O2B DTP . A DTP 601 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc5 E O2A DTP . A DTP 601 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc6 F MG MG . A MG 602 1_555 H O HOH . A HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? hydrog WATSON-CRICK hydrog1 C N3 DC 1 P DC 1 1_555 D N1 DG 6 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N4 DC 1 P DC 1 1_555 D O6 DG 6 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C O2 DC 1 P DC 1 1_555 D N2 DG 6 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N1 DA 2 P DA 2 1_555 D N3 DT 5 T DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N6 DA 2 P DA 2 1_555 D O4 DT 5 T DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N1 DG 3 P DG 3 1_555 D N3 DC 4 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N2 DG 3 P DG 3 1_555 D O2 DC 4 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C O6 DG 3 P DG 3 1_555 D N4 DC 4 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N3 DT 4 P DT 4 1_555 D N1 DA 3 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C O4 DT 4 P DT 4 1_555 D N6 DA 3 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N1 DA 5 P DA 5 1_555 D N3 DT 2 T DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N6 DA 5 P DA 5 1_555 D O4 DT 2 T DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N3 DC 6 P DC 6 1_555 D N1 DG 1 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N4 DC 6 P DC 6 1_555 D O6 DG 1 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O2 DC 6 P DC 6 1_555 D N2 DG 1 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 232 n n PG O2G DTP sing 233 n n PG O3G DTP sing 234 n n PG O3B DTP sing 235 n n O2G HOG2 DTP sing 236 n n O3G HOG3 DTP sing 237 n n PB O1B DTP doub 238 n n PB O2B DTP sing 239 n n PB O3B DTP sing 240 n n PB O3A DTP sing 241 n n O2B HOB2 DTP sing 242 n n PA O1A DTP doub 243 n n PA O2A DTP sing 244 n n PA O3A DTP sing 245 n n PA O5' DTP sing 246 n n O2A HOA2 DTP sing 247 n n O5' C5' DTP sing 248 n n C5' C4' DTP sing 249 n n C5' "H5'1" DTP sing 250 n n C5' "H5'2" DTP sing 251 n n C4' O4' DTP sing 252 n n C4' C3' DTP sing 253 n n C4' H4' DTP sing 254 n n O4' C1' DTP sing 255 n n C3' O3' DTP sing 256 n n C3' C2' DTP sing 257 n n C3' H3' DTP sing 258 n n O3' HO3' DTP sing 259 n n C2' C1' DTP sing 260 n n C2' "H2'1" DTP sing 261 n n C2' "H2'2" DTP sing 262 n n C1' N9 DTP sing 263 n n C1' H1' DTP sing 264 n n N9 C8 DTP sing 265 n y N9 C4 DTP sing 266 n y C8 N7 DTP doub 267 n y C8 H8 DTP sing 268 n n N7 C5 DTP sing 269 n y C5 C6 DTP sing 270 n y C5 C4 DTP doub 271 n y C6 N6 DTP sing 272 n n C6 N1 DTP doub 273 n y N6 HN61 DTP sing 274 n n N6 HN62 DTP sing 275 n n N1 C2 DTP sing 276 n y C2 N3 DTP doub 277 n y C2 H2 DTP sing 278 n n N3 C4 DTP sing 279 n y # _atom_sites.entry_id 4XQ8 _atom_sites.fract_transf_matrix[1][1] 0.011941 _atom_sites.fract_transf_matrix[1][2] 0.006894 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013789 _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] 0.002508 _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 E 4 DTP A 1 601 601 DTP DTP . F 5 MG A 1 602 602 MG MG . G 6 HOH B 1 601 10 HOH HOH . G 6 HOH B 2 602 32 HOH HOH . G 6 HOH B 3 603 18 HOH HOH . G 6 HOH B 4 604 27 HOH HOH . G 6 HOH B 5 605 26 HOH HOH . G 6 HOH B 6 606 5 HOH HOH . G 6 HOH B 7 607 1 HOH HOH . G 6 HOH B 8 608 9 HOH HOH . G 6 HOH B 9 609 90 HOH HOH . G 6 HOH B 10 610 2 HOH HOH . G 6 HOH B 11 611 11 HOH HOH . G 6 HOH B 12 612 4 HOH HOH . G 6 HOH B 13 613 97 HOH HOH . G 6 HOH B 14 614 3 HOH HOH . G 6 HOH B 15 615 28 HOH HOH . G 6 HOH B 16 616 33 HOH HOH . G 6 HOH B 17 617 20 HOH HOH . G 6 HOH B 18 618 35 HOH HOH . G 6 HOH B 19 619 93 HOH HOH . G 6 HOH B 20 620 7 HOH HOH . G 6 HOH B 21 621 36 HOH HOH . G 6 HOH B 22 622 17 HOH HOH . G 6 HOH B 23 623 15 HOH HOH . G 6 HOH B 24 624 99 HOH HOH . G 6 HOH B 25 625 13 HOH HOH . G 6 HOH B 26 626 12 HOH HOH . G 6 HOH B 27 627 30 HOH HOH . G 6 HOH B 28 628 31 HOH HOH . G 6 HOH B 29 629 16 HOH HOH . G 6 HOH B 30 630 8 HOH HOH . G 6 HOH B 31 631 21 HOH HOH . G 6 HOH B 32 632 92 HOH HOH . G 6 HOH B 33 633 6 HOH HOH . G 6 HOH B 34 634 24 HOH HOH . G 6 HOH B 35 635 25 HOH HOH . G 6 HOH B 36 636 14 HOH HOH . G 6 HOH B 37 637 29 HOH HOH . G 6 HOH B 38 638 23 HOH HOH . G 6 HOH B 39 639 83 HOH HOH . G 6 HOH B 40 640 96 HOH HOH . G 6 HOH B 41 641 22 HOH HOH . G 6 HOH B 42 642 95 HOH HOH . G 6 HOH B 43 643 94 HOH HOH . G 6 HOH B 44 644 19 HOH HOH . G 6 HOH B 45 645 34 HOH HOH . H 6 HOH A 1 701 64 HOH HOH . H 6 HOH A 2 702 37 HOH HOH . H 6 HOH A 3 703 75 HOH HOH . H 6 HOH A 4 704 88 HOH HOH . H 6 HOH A 5 705 57 HOH HOH . H 6 HOH A 6 706 58 HOH HOH . H 6 HOH A 7 707 87 HOH HOH . H 6 HOH A 8 708 38 HOH HOH . H 6 HOH A 9 709 69 HOH HOH . H 6 HOH A 10 710 40 HOH HOH . H 6 HOH A 11 711 42 HOH HOH . H 6 HOH A 12 712 41 HOH HOH . H 6 HOH A 13 713 60 HOH HOH . H 6 HOH A 14 714 68 HOH HOH . H 6 HOH A 15 715 62 HOH HOH . H 6 HOH A 16 716 43 HOH HOH . H 6 HOH A 17 717 91 HOH HOH . H 6 HOH A 18 718 47 HOH HOH . H 6 HOH A 19 719 56 HOH HOH . H 6 HOH A 20 720 59 HOH HOH . H 6 HOH A 21 721 74 HOH HOH . H 6 HOH A 22 722 46 HOH HOH . H 6 HOH A 23 723 72 HOH HOH . H 6 HOH A 24 724 48 HOH HOH . H 6 HOH A 25 725 45 HOH HOH . H 6 HOH A 26 726 39 HOH HOH . H 6 HOH A 27 727 50 HOH HOH . H 6 HOH A 28 728 51 HOH HOH . H 6 HOH A 29 729 44 HOH HOH . H 6 HOH A 30 730 71 HOH HOH . H 6 HOH A 31 731 63 HOH HOH . H 6 HOH A 32 732 65 HOH HOH . H 6 HOH A 33 733 67 HOH HOH . H 6 HOH A 34 734 73 HOH HOH . H 6 HOH A 35 735 61 HOH HOH . H 6 HOH A 36 736 84 HOH HOH . H 6 HOH A 37 737 70 HOH HOH . H 6 HOH A 38 738 53 HOH HOH . H 6 HOH A 39 739 49 HOH HOH . H 6 HOH A 40 740 52 HOH HOH . H 6 HOH A 41 741 86 HOH HOH . H 6 HOH A 42 742 98 HOH HOH . H 6 HOH A 43 743 54 HOH HOH . H 6 HOH A 44 744 76 HOH HOH . H 6 HOH A 45 745 55 HOH HOH . H 6 HOH A 46 746 66 HOH HOH . H 6 HOH A 47 747 85 HOH HOH . I 6 HOH P 1 101 80 HOH HOH . I 6 HOH P 2 102 78 HOH HOH . I 6 HOH P 3 103 77 HOH HOH . I 6 HOH P 4 104 79 HOH HOH . J 6 HOH T 1 101 81 HOH HOH . J 6 HOH T 2 102 82 HOH HOH . J 6 HOH T 3 103 89 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 PG DTP . . . E 4 21.301 42.049 -48.441 1 28.98 ? PG DTP 601 A 1 HETATM 2 O O1G DTP . . . E 4 21.625 43.451 -48.44 1 27.27 ? O1G DTP 601 A 1 HETATM 3 O O2G DTP . . . E 4 21.881 41.399 -47.321 1 26.47 ? O2G DTP 601 A 1 HETATM 4 O O3G DTP . . . E 4 19.903 41.963 -48.411 1 29.42 ? O3G DTP 601 A 1 HETATM 5 P PB DTP . . . E 4 23.043 40.775 -49.904 1 26.28 ? PB DTP 601 A 1 HETATM 6 O O1B DTP . . . E 4 23.502 41.277 -51.125 1 27.63 ? O1B DTP 601 A 1 HETATM 7 O O2B DTP . . . E 4 23.928 41.041 -48.776 1 28.79 ? O2B DTP 601 A 1 HETATM 8 O O3B DTP . . . E 4 21.714 41.418 -49.728 1 37.52 ? O3B DTP 601 A 1 HETATM 9 P PA DTP . . . E 4 23.1 38.223 -49.051 1 26.88 ? PA DTP 601 A 1 HETATM 10 O O1A DTP . . . E 4 21.819 37.589 -49.048 1 28.63 ? O1A DTP 601 A 1 HETATM 11 O O2A DTP . . . E 4 23.357 38.778 -47.755 1 25.59 ? O2A DTP 601 A 1 HETATM 12 O O3A DTP . . . E 4 22.951 39.293 -50.085 1 31.94 ? O3A DTP 601 A 1 HETATM 13 O O5' DTP . . . E 4 24.193 37.319 -49.514 1 33.13 ? O5' DTP 601 A 1 HETATM 14 C C5' DTP . . . E 4 25.375 37.849 -49.94 1 31.76 ? C5' DTP 601 A 1 HETATM 15 C C4' DTP . . . E 4 25.912 37.299 -51.2 1 28.2 ? C4' DTP 601 A 1 HETATM 16 O O4' DTP . . . E 4 25.951 35.9 -51.155 1 30.96 ? O4' DTP 601 A 1 HETATM 17 C C3' DTP . . . E 4 25.021 37.527 -52.233 1 29.31 ? C3' DTP 601 A 1 HETATM 18 O O3' DTP . . . E 4 25.191 38.811 -52.66 1 30.6 ? O3' DTP 601 A 1 HETATM 19 C C2' DTP . . . E 4 25.468 36.652 -53.274 1 31.24 ? C2' DTP 601 A 1 HETATM 20 C C1' DTP . . . E 4 25.766 35.476 -52.494 1 33.12 ? C1' DTP 601 A 1 HETATM 21 N N9 DTP . . . E 4 24.691 34.615 -52.598 1 35.27 ? N9 DTP 601 A 1 HETATM 22 C C8 DTP . . . E 4 23.849 34.285 -51.651 1 35.95 ? C8 DTP 601 A 1 HETATM 23 N N7 DTP . . . E 4 23 33.444 -52.099 1 36.53 ? N7 DTP 601 A 1 HETATM 24 C C5 DTP . . . E 4 23.229 33.171 -53.332 1 32.91 ? C5 DTP 601 A 1 HETATM 25 C C6 DTP . . . E 4 22.635 32.363 -54.244 1 33.46 ? C6 DTP 601 A 1 HETATM 26 N N6 DTP . . . E 4 21.482 31.562 -53.937 1 41.05 ? N6 DTP 601 A 1 HETATM 27 N N1 DTP . . . E 4 23.12 32.301 -55.458 1 40.3 ? N1 DTP 601 A 1 HETATM 28 C C2 DTP . . . E 4 24.193 33.042 -55.756 1 34.08 ? C2 DTP 601 A 1 HETATM 29 N N3 DTP . . . E 4 24.802 33.84 -54.915 1 30.78 ? N3 DTP 601 A 1 HETATM 30 C C4 DTP . . . E 4 24.34 33.931 -53.671 1 33.21 ? C4 DTP 601 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #