data_4PAO # _model_server_result.job_id TpH6bUUV2fGaUk1QroAHtg _model_server_result.datetime_utc '2024-11-22 15:43:18' _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 4pao # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4PAO # _exptl.entry_id 4PAO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 4PAO _cell.length_a 79.177 _cell.length_b 79.177 _cell.length_c 104.885 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PAO _symmetry.cell_setting . _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 metalc ? metalc1 A OG SER 47 A SER 47 1_555 C MG MG . A MG 402 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc2 A OG1 THR 181 A THR 181 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc3 B O2G GSP . A GSP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc4 B O2B GSP . A GSP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc5 C MG MG . A MG 402 1_555 D O HOH . A HOH 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc6 C MG MG . A MG 402 1_555 D O HOH . A HOH 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 O3B GSP sing 129 n n PG S1G GSP doub 130 n n PG O2G GSP sing 131 n n PG O3G GSP sing 132 n n O3B PB GSP sing 133 n n O2G HOG2 GSP sing 134 n n O3G HOG3 GSP sing 135 n n PB O1B GSP doub 136 n n PB O2B GSP sing 137 n n PB O3A GSP sing 138 n n O2B HOB2 GSP sing 139 n n PA O1A GSP doub 140 n n PA O2A GSP sing 141 n n PA O3A GSP sing 142 n n PA O5' GSP sing 143 n n O2A HOA2 GSP sing 144 n n O5' C5' GSP sing 145 n n C5' C4' GSP sing 146 n n C5' "H5'1" GSP sing 147 n n C5' "H5'2" GSP sing 148 n n C4' O4' GSP sing 149 n n C4' C3' GSP sing 150 n n C4' H4' GSP sing 151 n n O4' C1' GSP sing 152 n n C3' O3' GSP sing 153 n n C3' C2' GSP sing 154 n n C3' H3' GSP sing 155 n n O3' HO3' GSP sing 156 n n C2' O2' GSP sing 157 n n C2' C1' GSP sing 158 n n C2' H2' GSP sing 159 n n O2' HO2' GSP sing 160 n n C1' N9 GSP sing 161 n n C1' H1' GSP sing 162 n n N9 C8 GSP sing 163 n y N9 C4 GSP sing 164 n y C8 N7 GSP doub 165 n y C8 H8 GSP sing 166 n n N7 C5 GSP sing 167 n y C5 C6 GSP sing 168 n n C5 C4 GSP doub 169 n y C6 O6 GSP doub 170 n n C6 N1 GSP sing 171 n n N1 C2 GSP sing 172 n n N1 HN1 GSP sing 173 n n C2 N2 GSP sing 174 n n C2 N3 GSP doub 175 n n N2 HN21 GSP sing 176 n n N2 HN22 GSP sing 177 n n N3 C4 GSP sing 178 n n # _atom_sites.entry_id 4PAO _atom_sites.fract_transf_matrix[1][1] 0.01263 _atom_sites.fract_transf_matrix[1][2] 0.007292 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014584 _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] 0.009534 _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 B 2 GSP A 1 401 1 GSP GSP . C 3 MG A 1 402 1 MG MG . D 4 HOH A 1 501 115 HOH HOH . D 4 HOH A 2 502 172 HOH HOH . D 4 HOH A 3 503 14 HOH HOH . D 4 HOH A 4 504 4 HOH HOH . D 4 HOH A 5 505 61 HOH HOH . D 4 HOH A 6 506 95 HOH HOH . D 4 HOH A 7 507 114 HOH HOH . D 4 HOH A 8 508 184 HOH HOH . D 4 HOH A 9 509 153 HOH HOH . D 4 HOH A 10 510 83 HOH HOH . D 4 HOH A 11 511 188 HOH HOH . D 4 HOH A 12 512 43 HOH HOH . D 4 HOH A 13 513 128 HOH HOH . D 4 HOH A 14 514 149 HOH HOH . D 4 HOH A 15 515 116 HOH HOH . D 4 HOH A 16 516 123 HOH HOH . D 4 HOH A 17 517 12 HOH HOH . D 4 HOH A 18 518 168 HOH HOH . D 4 HOH A 19 519 100 HOH HOH . D 4 HOH A 20 520 52 HOH HOH . D 4 HOH A 21 521 41 HOH HOH . D 4 HOH A 22 522 51 HOH HOH . D 4 HOH A 23 523 185 HOH HOH . D 4 HOH A 24 524 181 HOH HOH . D 4 HOH A 25 525 53 HOH HOH . D 4 HOH A 26 526 57 HOH HOH . D 4 HOH A 27 527 175 HOH HOH . D 4 HOH A 28 528 42 HOH HOH . D 4 HOH A 29 529 137 HOH HOH . D 4 HOH A 30 530 129 HOH HOH . D 4 HOH A 31 531 40 HOH HOH . D 4 HOH A 32 532 48 HOH HOH . D 4 HOH A 33 533 98 HOH HOH . D 4 HOH A 34 534 62 HOH HOH . D 4 HOH A 35 535 125 HOH HOH . D 4 HOH A 36 536 119 HOH HOH . D 4 HOH A 37 537 92 HOH HOH . D 4 HOH A 38 538 147 HOH HOH . D 4 HOH A 39 539 60 HOH HOH . D 4 HOH A 40 540 107 HOH HOH . D 4 HOH A 41 541 3 HOH HOH . D 4 HOH A 42 542 157 HOH HOH . D 4 HOH A 43 543 124 HOH HOH . D 4 HOH A 44 544 54 HOH HOH . D 4 HOH A 45 545 50 HOH HOH . D 4 HOH A 46 546 74 HOH HOH . D 4 HOH A 47 547 182 HOH HOH . D 4 HOH A 48 548 31 HOH HOH . D 4 HOH A 49 549 195 HOH HOH . D 4 HOH A 50 550 30 HOH HOH . D 4 HOH A 51 551 80 HOH HOH . D 4 HOH A 52 552 144 HOH HOH . D 4 HOH A 53 553 122 HOH HOH . D 4 HOH A 54 554 56 HOH HOH . D 4 HOH A 55 555 33 HOH HOH . D 4 HOH A 56 556 154 HOH HOH . D 4 HOH A 57 557 150 HOH HOH . D 4 HOH A 58 558 135 HOH HOH . D 4 HOH A 59 559 171 HOH HOH . D 4 HOH A 60 560 112 HOH HOH . D 4 HOH A 61 561 126 HOH HOH . D 4 HOH A 62 562 155 HOH HOH . D 4 HOH A 63 563 136 HOH HOH . D 4 HOH A 64 564 63 HOH HOH . D 4 HOH A 65 565 1 HOH HOH . D 4 HOH A 66 566 2 HOH HOH . D 4 HOH A 67 567 6 HOH HOH . D 4 HOH A 68 568 7 HOH HOH . D 4 HOH A 69 569 8 HOH HOH . D 4 HOH A 70 570 9 HOH HOH . D 4 HOH A 71 571 10 HOH HOH . D 4 HOH A 72 572 11 HOH HOH . D 4 HOH A 73 573 13 HOH HOH . D 4 HOH A 74 574 15 HOH HOH . D 4 HOH A 75 575 16 HOH HOH . D 4 HOH A 76 576 17 HOH HOH . D 4 HOH A 77 577 18 HOH HOH . D 4 HOH A 78 578 19 HOH HOH . D 4 HOH A 79 579 20 HOH HOH . D 4 HOH A 80 580 21 HOH HOH . D 4 HOH A 81 581 22 HOH HOH . D 4 HOH A 82 582 23 HOH HOH . D 4 HOH A 83 583 24 HOH HOH . D 4 HOH A 84 584 25 HOH HOH . D 4 HOH A 85 585 26 HOH HOH . D 4 HOH A 86 586 27 HOH HOH . D 4 HOH A 87 587 28 HOH HOH . D 4 HOH A 88 588 29 HOH HOH . D 4 HOH A 89 589 32 HOH HOH . D 4 HOH A 90 590 34 HOH HOH . D 4 HOH A 91 591 35 HOH HOH . D 4 HOH A 92 592 36 HOH HOH . D 4 HOH A 93 593 37 HOH HOH . D 4 HOH A 94 594 38 HOH HOH . D 4 HOH A 95 595 39 HOH HOH . D 4 HOH A 96 596 44 HOH HOH . D 4 HOH A 97 597 45 HOH HOH . D 4 HOH A 98 598 46 HOH HOH . D 4 HOH A 99 599 47 HOH HOH . D 4 HOH A 100 600 49 HOH HOH . D 4 HOH A 101 601 55 HOH HOH . D 4 HOH A 102 602 58 HOH HOH . D 4 HOH A 103 603 59 HOH HOH . D 4 HOH A 104 604 64 HOH HOH . D 4 HOH A 105 605 65 HOH HOH . D 4 HOH A 106 606 66 HOH HOH . D 4 HOH A 107 607 67 HOH HOH . D 4 HOH A 108 608 68 HOH HOH . D 4 HOH A 109 609 69 HOH HOH . D 4 HOH A 110 610 70 HOH HOH . D 4 HOH A 111 611 71 HOH HOH . D 4 HOH A 112 612 75 HOH HOH . D 4 HOH A 113 613 76 HOH HOH . D 4 HOH A 114 614 77 HOH HOH . D 4 HOH A 115 615 78 HOH HOH . D 4 HOH A 116 616 79 HOH HOH . D 4 HOH A 117 617 81 HOH HOH . D 4 HOH A 118 618 84 HOH HOH . D 4 HOH A 119 619 86 HOH HOH . D 4 HOH A 120 620 87 HOH HOH . D 4 HOH A 121 621 88 HOH HOH . D 4 HOH A 122 622 89 HOH HOH . D 4 HOH A 123 623 90 HOH HOH . D 4 HOH A 124 624 91 HOH HOH . D 4 HOH A 125 625 93 HOH HOH . D 4 HOH A 126 626 96 HOH HOH . D 4 HOH A 127 627 97 HOH HOH . D 4 HOH A 128 628 99 HOH HOH . D 4 HOH A 129 629 101 HOH HOH . D 4 HOH A 130 630 102 HOH HOH . D 4 HOH A 131 631 103 HOH HOH . D 4 HOH A 132 632 104 HOH HOH . D 4 HOH A 133 633 105 HOH HOH . D 4 HOH A 134 634 106 HOH HOH . D 4 HOH A 135 635 110 HOH HOH . D 4 HOH A 136 636 111 HOH HOH . D 4 HOH A 137 637 113 HOH HOH . D 4 HOH A 138 638 117 HOH HOH . D 4 HOH A 139 639 118 HOH HOH . D 4 HOH A 140 640 120 HOH HOH . D 4 HOH A 141 641 121 HOH HOH . D 4 HOH A 142 642 127 HOH HOH . D 4 HOH A 143 643 130 HOH HOH . D 4 HOH A 144 644 131 HOH HOH . D 4 HOH A 145 645 132 HOH HOH . D 4 HOH A 146 646 133 HOH HOH . D 4 HOH A 147 647 134 HOH HOH . D 4 HOH A 148 648 138 HOH HOH . D 4 HOH A 149 649 139 HOH HOH . D 4 HOH A 150 650 140 HOH HOH . D 4 HOH A 151 651 143 HOH HOH . D 4 HOH A 152 652 145 HOH HOH . D 4 HOH A 153 653 146 HOH HOH . D 4 HOH A 154 654 148 HOH HOH . D 4 HOH A 155 655 151 HOH HOH . D 4 HOH A 156 656 152 HOH HOH . D 4 HOH A 157 657 156 HOH HOH . D 4 HOH A 158 658 158 HOH HOH . D 4 HOH A 159 659 159 HOH HOH . D 4 HOH A 160 660 160 HOH HOH . D 4 HOH A 161 661 161 HOH HOH . D 4 HOH A 162 662 162 HOH HOH . D 4 HOH A 163 663 163 HOH HOH . D 4 HOH A 164 664 164 HOH HOH . D 4 HOH A 165 665 165 HOH HOH . D 4 HOH A 166 666 166 HOH HOH . D 4 HOH A 167 667 167 HOH HOH . D 4 HOH A 168 668 169 HOH HOH . D 4 HOH A 169 669 170 HOH HOH . D 4 HOH A 170 670 173 HOH HOH . D 4 HOH A 171 671 174 HOH HOH . D 4 HOH A 172 672 176 HOH HOH . D 4 HOH A 173 673 177 HOH HOH . D 4 HOH A 174 674 178 HOH HOH . D 4 HOH A 175 675 179 HOH HOH . D 4 HOH A 176 676 180 HOH HOH . D 4 HOH A 177 677 183 HOH HOH . D 4 HOH A 178 678 186 HOH HOH . D 4 HOH A 179 679 187 HOH HOH . D 4 HOH A 180 680 190 HOH HOH . D 4 HOH A 181 681 192 HOH HOH . D 4 HOH A 182 682 193 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 GSP . . . B 2 115.708 105.073 12.175 1 12 ? PG GSP 401 A 1 HETATM 2 O O3B GSP . . . B 2 116.053 105.946 10.854 1 4.16 ? O3B GSP 401 A 1 HETATM 3 S S1G GSP . . . B 2 117.255 104.62 12.878 1 10.83 ? S1G GSP 401 A 1 HETATM 4 O O2G GSP . . . B 2 114.913 105.961 13.146 1 7.91 ? O2G GSP 401 A 1 HETATM 5 O O3G GSP . . . B 2 114.845 103.87 11.775 1 6.98 ? O3G GSP 401 A 1 HETATM 6 P PB GSP . . . B 2 114.981 106.702 9.914 1 3.97 ? PB GSP 401 A 1 HETATM 7 O O1B GSP . . . B 2 114.387 105.75 8.954 1 5.31 ? O1B GSP 401 A 1 HETATM 8 O O2B GSP . . . B 2 113.95 107.455 10.652 1 4.23 ? O2B GSP 401 A 1 HETATM 9 P PA GSP . . . B 2 116.037 109.284 9.305 1 5.65 ? PA GSP 401 A 1 HETATM 10 O O1A GSP . . . B 2 114.777 109.946 8.876 1 6.1 ? O1A GSP 401 A 1 HETATM 11 O O2A GSP . . . B 2 116.387 109.615 10.712 1 5.19 ? O2A GSP 401 A 1 HETATM 12 O O3A GSP . . . B 2 115.951 107.693 9.094 1 4.3 ? O3A GSP 401 A 1 HETATM 13 O O5' GSP . . . B 2 117.194 109.642 8.249 1 5.49 ? O5' GSP 401 A 1 HETATM 14 C C5' GSP . . . B 2 118.551 109.398 8.588 1 4.39 ? C5' GSP 401 A 1 HETATM 15 C C4' GSP . . . B 2 119.418 110.551 8.115 1 3.07 ? C4' GSP 401 A 1 HETATM 16 O O4' GSP . . . B 2 119.392 110.609 6.7 1 2.97 ? O4' GSP 401 A 1 HETATM 17 C C3' GSP . . . B 2 118.878 111.881 8.608 1 3 ? C3' GSP 401 A 1 HETATM 18 O O3' GSP . . . B 2 119.996 112.673 8.914 1 4.53 ? O3' GSP 401 A 1 HETATM 19 C C2' GSP . . . B 2 118.184 112.492 7.413 1 2.2 ? C2' GSP 401 A 1 HETATM 20 O O2' GSP . . . B 2 118.299 113.897 7.394 1 3.94 ? O2' GSP 401 A 1 HETATM 21 C C1' GSP . . . B 2 118.948 111.886 6.255 1 2.95 ? C1' GSP 401 A 1 HETATM 22 N N9 GSP . . . B 2 118.105 111.672 5.069 1 4.8 ? N9 GSP 401 A 1 HETATM 23 C C8 GSP . . . B 2 116.897 111.015 4.994 1 6.24 ? C8 GSP 401 A 1 HETATM 24 N N7 GSP . . . B 2 116.505 111.012 3.698 1 6.34 ? N7 GSP 401 A 1 HETATM 25 C C5 GSP . . . B 2 117.437 111.65 2.956 1 5.03 ? C5 GSP 401 A 1 HETATM 26 C C6 GSP . . . B 2 117.531 111.93 1.595 1 7.26 ? C6 GSP 401 A 1 HETATM 27 O O6 GSP . . . B 2 116.65 111.579 0.803 1 6.86 ? O6 GSP 401 A 1 HETATM 28 N N1 GSP . . . B 2 118.64 112.603 1.135 1 5.78 ? N1 GSP 401 A 1 HETATM 29 C C2 GSP . . . B 2 119.635 113.004 2.006 1 6.59 ? C2 GSP 401 A 1 HETATM 30 N N2 GSP . . . B 2 120.695 113.662 1.544 1 3.22 ? N2 GSP 401 A 1 HETATM 31 N N3 GSP . . . B 2 119.542 112.715 3.35 1 4.48 ? N3 GSP 401 A 1 HETATM 32 C C4 GSP . . . B 2 118.455 112.053 3.809 1 6.38 ? C4 GSP 401 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #