data_4PAQ # _model_server_result.job_id J4atOjLl8Ll0WKly9ml8wA _model_server_result.datetime_utc '2024-11-26 02:52:33' _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 4paq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4PAQ # _exptl.entry_id 4PAQ _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 4PAQ _cell.length_a 79.3 _cell.length_b 79.3 _cell.length_c 105.141 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PAQ _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc2 A OG1 THR 181 A THR 181 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc3 B O2G GSP . A GSP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc4 B O2B GSP . A GSP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc5 C MG MG . A MG 402 1_555 D O HOH . A HOH 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 C MG MG . A MG 402 1_555 D O HOH . A HOH 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? # _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 4PAQ _atom_sites.fract_transf_matrix[1][1] 0.01261 _atom_sites.fract_transf_matrix[1][2] 0.007281 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014561 _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] 0.009511 _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 1 501 114 HOH HOH . D 4 HOH A 2 502 123 HOH HOH . D 4 HOH A 3 503 115 HOH HOH . D 4 HOH A 4 504 174 HOH HOH . D 4 HOH A 5 505 52 HOH HOH . D 4 HOH A 6 506 83 HOH HOH . D 4 HOH A 7 507 95 HOH HOH . D 4 HOH A 8 508 61 HOH HOH . D 4 HOH A 9 509 41 HOH HOH . D 4 HOH A 10 510 116 HOH HOH . D 4 HOH A 11 511 153 HOH HOH . D 4 HOH A 12 512 100 HOH HOH . D 4 HOH A 13 513 48 HOH HOH . D 4 HOH A 14 514 183 HOH HOH . D 4 HOH A 15 515 186 HOH HOH . D 4 HOH A 16 516 14 HOH HOH . D 4 HOH A 17 517 43 HOH HOH . D 4 HOH A 18 518 155 HOH HOH . D 4 HOH A 19 519 51 HOH HOH . D 4 HOH A 20 520 140 HOH HOH . D 4 HOH A 21 521 12 HOH HOH . D 4 HOH A 22 522 4 HOH HOH . D 4 HOH A 23 523 60 HOH HOH . D 4 HOH A 24 524 194 HOH HOH . D 4 HOH A 25 525 152 HOH HOH . D 4 HOH A 26 526 42 HOH HOH . D 4 HOH A 27 527 57 HOH HOH . D 4 HOH A 28 528 40 HOH HOH . D 4 HOH A 29 529 62 HOH HOH . D 4 HOH A 30 530 136 HOH HOH . D 4 HOH A 31 531 169 HOH HOH . D 4 HOH A 32 532 142 HOH HOH . D 4 HOH A 33 533 3 HOH HOH . D 4 HOH A 34 534 50 HOH HOH . D 4 HOH A 35 535 173 HOH HOH . D 4 HOH A 36 536 107 HOH HOH . D 4 HOH A 37 537 125 HOH HOH . D 4 HOH A 38 538 53 HOH HOH . D 4 HOH A 39 539 137 HOH HOH . D 4 HOH A 40 540 119 HOH HOH . D 4 HOH A 41 541 170 HOH HOH . D 4 HOH A 42 542 124 HOH HOH . D 4 HOH A 43 543 74 HOH HOH . D 4 HOH A 44 544 31 HOH HOH . D 4 HOH A 45 545 54 HOH HOH . D 4 HOH A 46 546 92 HOH HOH . D 4 HOH A 47 547 30 HOH HOH . D 4 HOH A 48 548 80 HOH HOH . D 4 HOH A 49 549 122 HOH HOH . D 4 HOH A 50 550 143 HOH HOH . D 4 HOH A 51 551 56 HOH HOH . D 4 HOH A 52 552 139 HOH HOH . D 4 HOH A 53 553 33 HOH HOH . D 4 HOH A 54 554 187 HOH HOH . D 4 HOH A 55 555 135 HOH HOH . D 4 HOH A 56 556 141 HOH HOH . D 4 HOH A 57 557 167 HOH HOH . D 4 HOH A 58 558 112 HOH HOH . D 4 HOH A 59 559 188 HOH HOH . D 4 HOH A 60 560 138 HOH HOH . D 4 HOH A 61 561 63 HOH HOH . D 4 HOH A 62 562 154 HOH HOH . D 4 HOH A 63 563 172 HOH HOH . D 4 HOH A 64 564 1 HOH HOH . D 4 HOH A 65 565 2 HOH HOH . D 4 HOH A 66 566 6 HOH HOH . D 4 HOH A 67 567 10 HOH HOH . D 4 HOH A 68 568 11 HOH HOH . D 4 HOH A 69 569 13 HOH HOH . D 4 HOH A 70 570 15 HOH HOH . D 4 HOH A 71 571 17 HOH HOH . D 4 HOH A 72 572 18 HOH HOH . D 4 HOH A 73 573 19 HOH HOH . D 4 HOH A 74 574 20 HOH HOH . D 4 HOH A 75 575 22 HOH HOH . D 4 HOH A 76 576 24 HOH HOH . D 4 HOH A 77 577 25 HOH HOH . D 4 HOH A 78 578 26 HOH HOH . D 4 HOH A 79 579 28 HOH HOH . D 4 HOH A 80 580 29 HOH HOH . D 4 HOH A 81 581 32 HOH HOH . D 4 HOH A 82 582 34 HOH HOH . D 4 HOH A 83 583 35 HOH HOH . D 4 HOH A 84 584 36 HOH HOH . D 4 HOH A 85 585 37 HOH HOH . D 4 HOH A 86 586 39 HOH HOH . D 4 HOH A 87 587 44 HOH HOH . D 4 HOH A 88 588 45 HOH HOH . D 4 HOH A 89 589 46 HOH HOH . D 4 HOH A 90 590 47 HOH HOH . D 4 HOH A 91 591 49 HOH HOH . D 4 HOH A 92 592 55 HOH HOH . D 4 HOH A 93 593 58 HOH HOH . D 4 HOH A 94 594 59 HOH HOH . D 4 HOH A 95 595 64 HOH HOH . D 4 HOH A 96 596 66 HOH HOH . D 4 HOH A 97 597 67 HOH HOH . D 4 HOH A 98 598 68 HOH HOH . D 4 HOH A 99 599 69 HOH HOH . D 4 HOH A 100 600 70 HOH HOH . D 4 HOH A 101 601 71 HOH HOH . D 4 HOH A 102 602 75 HOH HOH . D 4 HOH A 103 603 76 HOH HOH . D 4 HOH A 104 604 77 HOH HOH . D 4 HOH A 105 605 78 HOH HOH . D 4 HOH A 106 606 79 HOH HOH . D 4 HOH A 107 607 81 HOH HOH . D 4 HOH A 108 608 84 HOH HOH . D 4 HOH A 109 609 85 HOH HOH . D 4 HOH A 110 610 86 HOH HOH . D 4 HOH A 111 611 87 HOH HOH . D 4 HOH A 112 612 88 HOH HOH . D 4 HOH A 113 613 89 HOH HOH . D 4 HOH A 114 614 90 HOH HOH . D 4 HOH A 115 615 91 HOH HOH . D 4 HOH A 116 616 93 HOH HOH . D 4 HOH A 117 617 96 HOH HOH . D 4 HOH A 118 618 97 HOH HOH . D 4 HOH A 119 619 99 HOH HOH . D 4 HOH A 120 620 101 HOH HOH . D 4 HOH A 121 621 102 HOH HOH . D 4 HOH A 122 622 103 HOH HOH . D 4 HOH A 123 623 104 HOH HOH . D 4 HOH A 124 624 105 HOH HOH . D 4 HOH A 125 625 106 HOH HOH . D 4 HOH A 126 626 109 HOH HOH . D 4 HOH A 127 627 110 HOH HOH . D 4 HOH A 128 628 111 HOH HOH . D 4 HOH A 129 629 113 HOH HOH . D 4 HOH A 130 630 117 HOH HOH . D 4 HOH A 131 631 118 HOH HOH . D 4 HOH A 132 632 120 HOH HOH . D 4 HOH A 133 633 121 HOH HOH . D 4 HOH A 134 634 133 HOH HOH . D 4 HOH A 135 635 134 HOH HOH . D 4 HOH A 136 636 146 HOH HOH . D 4 HOH A 137 637 147 HOH HOH . D 4 HOH A 138 638 148 HOH HOH . D 4 HOH A 139 639 149 HOH HOH . D 4 HOH A 140 640 150 HOH HOH . D 4 HOH A 141 641 151 HOH HOH . D 4 HOH A 142 642 156 HOH HOH . D 4 HOH A 143 643 157 HOH HOH . D 4 HOH A 144 644 158 HOH HOH . D 4 HOH A 145 645 159 HOH HOH . D 4 HOH A 146 646 160 HOH HOH . D 4 HOH A 147 647 161 HOH HOH . D 4 HOH A 148 648 162 HOH HOH . D 4 HOH A 149 649 163 HOH HOH . D 4 HOH A 150 650 164 HOH HOH . D 4 HOH A 151 651 165 HOH HOH . D 4 HOH A 152 652 166 HOH HOH . D 4 HOH A 153 653 168 HOH HOH . D 4 HOH A 154 654 171 HOH HOH . D 4 HOH A 155 655 176 HOH HOH . D 4 HOH A 156 656 177 HOH HOH . D 4 HOH A 157 657 178 HOH HOH . D 4 HOH A 158 658 179 HOH HOH . D 4 HOH A 159 659 181 HOH HOH . D 4 HOH A 160 660 182 HOH HOH . D 4 HOH A 161 661 185 HOH HOH . D 4 HOH A 162 662 189 HOH HOH . D 4 HOH A 163 663 190 HOH HOH . D 4 HOH A 164 664 191 HOH HOH . D 4 HOH A 165 665 192 HOH HOH . D 4 HOH A 166 666 193 HOH HOH . D 4 HOH A 167 667 195 HOH HOH . D 4 HOH A 168 668 196 HOH HOH . D 4 HOH A 169 669 197 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 -33.149 15.644 -5.369 1 15.44 ? PG GSP 401 A 1 HETATM 2 O O3B GSP . . . B 2 -33.732 16.38 -6.69 1 7.8 ? O3B GSP 401 A 1 HETATM 3 S S1G GSP . . . B 2 -31.989 16.765 -4.658 1 16.32 ? S1G GSP 401 A 1 HETATM 4 O O2G GSP . . . B 2 -34.331 15.386 -4.422 1 12.34 ? O2G GSP 401 A 1 HETATM 5 O O3G GSP . . . B 2 -32.546 14.276 -5.73 1 12.18 ? O3G GSP 401 A 1 HETATM 6 P PB GSP . . . B 2 -34.955 15.84 -7.601 1 9.25 ? PB GSP 401 A 1 HETATM 7 O O1B GSP . . . B 2 -34.424 14.872 -8.595 1 8.02 ? O1B GSP 401 A 1 HETATM 8 O O2B GSP . . . B 2 -36.103 15.293 -6.863 1 9.07 ? O2B GSP 401 A 1 HETATM 9 P PA GSP . . . B 2 -36.676 18.039 -8.214 1 9.71 ? PA GSP 401 A 1 HETATM 10 O O1A GSP . . . B 2 -37.903 17.323 -8.623 1 6.95 ? O1A GSP 401 A 1 HETATM 11 O O2A GSP . . . B 2 -36.711 18.493 -6.8 1 9.9 ? O2A GSP 401 A 1 HETATM 12 O O3A GSP . . . B 2 -35.368 17.132 -8.475 1 8.48 ? O3A GSP 401 A 1 HETATM 13 O O5' GSP . . . B 2 -36.432 19.243 -9.244 1 9.53 ? O5' GSP 401 A 1 HETATM 14 C C5' GSP . . . B 2 -35.468 20.258 -8.989 1 10.77 ? C5' GSP 401 A 1 HETATM 15 C C4' GSP . . . B 2 -36.02 21.604 -9.452 1 8.25 ? C4' GSP 401 A 1 HETATM 16 O O4' GSP . . . B 2 -36.112 21.617 -10.868 1 7.2 ? O4' GSP 401 A 1 HETATM 17 C C3' GSP . . . B 2 -37.435 21.812 -8.936 1 8.35 ? C3' GSP 401 A 1 HETATM 18 O O3' GSP . . . B 2 -37.561 23.176 -8.634 1 7.21 ? O3' GSP 401 A 1 HETATM 19 C C2' GSP . . . B 2 -38.328 21.482 -10.117 1 7.01 ? C2' GSP 401 A 1 HETATM 20 O O2' GSP . . . B 2 -39.516 22.246 -10.138 1 8.91 ? O2' GSP 401 A 1 HETATM 21 C C1' GSP . . . B 2 -37.449 21.852 -11.295 1 7.97 ? C1' GSP 401 A 1 HETATM 22 N N9 GSP . . . B 2 -37.699 21.006 -12.473 1 7.24 ? N9 GSP 401 A 1 HETATM 23 C C8 GSP . . . B 2 -37.773 19.629 -12.534 1 8.97 ? C8 GSP 401 A 1 HETATM 24 N N7 GSP . . . B 2 -37.98 19.265 -13.825 1 8.75 ? N7 GSP 401 A 1 HETATM 25 C C5 GSP . . . B 2 -38.028 20.386 -14.584 1 10.18 ? C5 GSP 401 A 1 HETATM 26 C C6 GSP . . . B 2 -38.217 20.599 -15.944 1 11.78 ? C6 GSP 401 A 1 HETATM 27 O O6 GSP . . . B 2 -38.38 19.659 -16.734 1 11.57 ? O6 GSP 401 A 1 HETATM 28 N N1 GSP . . . B 2 -38.214 21.896 -16.415 1 9.65 ? N1 GSP 401 A 1 HETATM 29 C C2 GSP . . . B 2 -38.036 22.961 -15.561 1 9.43 ? C2 GSP 401 A 1 HETATM 30 N N2 GSP . . . B 2 -38.044 24.205 -16.041 1 7.35 ? N2 GSP 401 A 1 HETATM 31 N N3 GSP . . . B 2 -37.841 22.75 -14.213 1 10.27 ? N3 GSP 401 A 1 HETATM 32 C C4 GSP . . . B 2 -37.843 21.485 -13.739 1 10.11 ? C4 GSP 401 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #