data_7ON2 # _model_server_result.job_id OMC6paCJJnoGmo0H39DA6g _model_server_result.datetime_utc '2025-07-14 11:01:48' _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 7on2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7ON2 # _exptl.entry_id 7ON2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 111.418 _cell.angle_gamma 90 _cell.entry_id 7ON2 _cell.length_a 72.402 _cell.length_b 50.207 _cell.length_c 88.05 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ON2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 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,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 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 O LEU 193 A LEU 200 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc2 A O VAL 196 A VAL 203 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc3 A OD1 ASN 201 A ASN 208 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc4 A O LEU 202 A LEU 209 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc5 C K K . A K 402 1_555 E O HOH . A HOH 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 79 n n PB O2B GDP sing 80 n n PB O3B GDP sing 81 n n PB O3A GDP sing 82 n n O2B HOB2 GDP sing 83 n n O3B HOB3 GDP sing 84 n n O3A PA GDP sing 85 n n PA O1A GDP doub 86 n n PA O2A GDP sing 87 n n PA O5' GDP sing 88 n n O2A HOA2 GDP sing 89 n n O5' C5' GDP sing 90 n n C5' C4' GDP sing 91 n n C5' H5' GDP sing 92 n n C5' "H5''" GDP sing 93 n n C4' O4' GDP sing 94 n n C4' C3' GDP sing 95 n n C4' H4' GDP sing 96 n n O4' C1' GDP sing 97 n n C3' O3' GDP sing 98 n n C3' C2' GDP sing 99 n n C3' H3' GDP sing 100 n n O3' HO3' GDP sing 101 n n C2' O2' GDP sing 102 n n C2' C1' GDP sing 103 n n C2' H2' GDP sing 104 n n O2' HO2' GDP sing 105 n n C1' N9 GDP sing 106 n n C1' H1' GDP sing 107 n n N9 C8 GDP sing 108 n y N9 C4 GDP sing 109 n y C8 N7 GDP doub 110 n y C8 H8 GDP sing 111 n n N7 C5 GDP sing 112 n y C5 C6 GDP sing 113 n n C5 C4 GDP doub 114 n y C6 O6 GDP doub 115 n n C6 N1 GDP sing 116 n n N1 C2 GDP sing 117 n n N1 HN1 GDP sing 118 n n C2 N2 GDP sing 119 n n C2 N3 GDP doub 120 n n N2 HN21 GDP sing 121 n n N2 HN22 GDP sing 122 n n N3 C4 GDP sing 123 n n # _atom_sites.entry_id 7ON2 _atom_sites.fract_transf_matrix[1][1] 0.013812 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005418 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019918 _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] 0.0122 _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 GDP A 1 401 1 GDP GDP . C 3 K A 1 402 1 K K . D 4 EDO A 1 403 1 EDO EDO . E 5 HOH A 1 501 131 HOH HOH . E 5 HOH A 2 502 142 HOH HOH . E 5 HOH A 3 503 162 HOH HOH . E 5 HOH A 4 504 37 HOH HOH . E 5 HOH A 5 505 113 HOH HOH . E 5 HOH A 6 506 49 HOH HOH . E 5 HOH A 7 507 118 HOH HOH . E 5 HOH A 8 508 44 HOH HOH . E 5 HOH A 9 509 26 HOH HOH . E 5 HOH A 10 510 123 HOH HOH . E 5 HOH A 11 511 59 HOH HOH . E 5 HOH A 12 512 150 HOH HOH . E 5 HOH A 13 513 14 HOH HOH . E 5 HOH A 14 514 88 HOH HOH . E 5 HOH A 15 515 19 HOH HOH . E 5 HOH A 16 516 54 HOH HOH . E 5 HOH A 17 517 163 HOH HOH . E 5 HOH A 18 518 42 HOH HOH . E 5 HOH A 19 519 52 HOH HOH . E 5 HOH A 20 520 95 HOH HOH . E 5 HOH A 21 521 53 HOH HOH . E 5 HOH A 22 522 43 HOH HOH . E 5 HOH A 23 523 79 HOH HOH . E 5 HOH A 24 524 34 HOH HOH . E 5 HOH A 25 525 65 HOH HOH . E 5 HOH A 26 526 128 HOH HOH . E 5 HOH A 27 527 121 HOH HOH . E 5 HOH A 28 528 110 HOH HOH . E 5 HOH A 29 529 48 HOH HOH . E 5 HOH A 30 530 7 HOH HOH . E 5 HOH A 31 531 27 HOH HOH . E 5 HOH A 32 532 6 HOH HOH . E 5 HOH A 33 533 8 HOH HOH . E 5 HOH A 34 534 119 HOH HOH . E 5 HOH A 35 535 158 HOH HOH . E 5 HOH A 36 536 93 HOH HOH . E 5 HOH A 37 537 45 HOH HOH . E 5 HOH A 38 538 10 HOH HOH . E 5 HOH A 39 539 57 HOH HOH . E 5 HOH A 40 540 97 HOH HOH . E 5 HOH A 41 541 126 HOH HOH . E 5 HOH A 42 542 71 HOH HOH . E 5 HOH A 43 543 47 HOH HOH . E 5 HOH A 44 544 78 HOH HOH . E 5 HOH A 45 545 122 HOH HOH . E 5 HOH A 46 546 28 HOH HOH . E 5 HOH A 47 547 86 HOH HOH . E 5 HOH A 48 548 5 HOH HOH . E 5 HOH A 49 549 9 HOH HOH . E 5 HOH A 50 550 24 HOH HOH . E 5 HOH A 51 551 73 HOH HOH . E 5 HOH A 52 552 22 HOH HOH . E 5 HOH A 53 553 130 HOH HOH . E 5 HOH A 54 554 17 HOH HOH . E 5 HOH A 55 555 69 HOH HOH . E 5 HOH A 56 556 18 HOH HOH . E 5 HOH A 57 557 11 HOH HOH . E 5 HOH A 58 558 29 HOH HOH . E 5 HOH A 59 559 109 HOH HOH . E 5 HOH A 60 560 55 HOH HOH . E 5 HOH A 61 561 99 HOH HOH . E 5 HOH A 62 562 83 HOH HOH . E 5 HOH A 63 563 91 HOH HOH . E 5 HOH A 64 564 12 HOH HOH . E 5 HOH A 65 565 81 HOH HOH . E 5 HOH A 66 566 33 HOH HOH . E 5 HOH A 67 567 15 HOH HOH . E 5 HOH A 68 568 146 HOH HOH . E 5 HOH A 69 569 50 HOH HOH . E 5 HOH A 70 570 87 HOH HOH . E 5 HOH A 71 571 77 HOH HOH . E 5 HOH A 72 572 2 HOH HOH . E 5 HOH A 73 573 31 HOH HOH . E 5 HOH A 74 574 135 HOH HOH . E 5 HOH A 75 575 112 HOH HOH . E 5 HOH A 76 576 80 HOH HOH . E 5 HOH A 77 577 20 HOH HOH . E 5 HOH A 78 578 63 HOH HOH . E 5 HOH A 79 579 56 HOH HOH . E 5 HOH A 80 580 148 HOH HOH . E 5 HOH A 81 581 35 HOH HOH . E 5 HOH A 82 582 72 HOH HOH . E 5 HOH A 83 583 144 HOH HOH . E 5 HOH A 84 584 36 HOH HOH . E 5 HOH A 85 585 1 HOH HOH . E 5 HOH A 86 586 68 HOH HOH . E 5 HOH A 87 587 129 HOH HOH . E 5 HOH A 88 588 21 HOH HOH . E 5 HOH A 89 589 116 HOH HOH . E 5 HOH A 90 590 136 HOH HOH . E 5 HOH A 91 591 60 HOH HOH . E 5 HOH A 92 592 66 HOH HOH . E 5 HOH A 93 593 84 HOH HOH . E 5 HOH A 94 594 32 HOH HOH . E 5 HOH A 95 595 152 HOH HOH . E 5 HOH A 96 596 74 HOH HOH . E 5 HOH A 97 597 3 HOH HOH . E 5 HOH A 98 598 46 HOH HOH . E 5 HOH A 99 599 139 HOH HOH . E 5 HOH A 100 600 61 HOH HOH . E 5 HOH A 101 601 40 HOH HOH . E 5 HOH A 102 602 16 HOH HOH . E 5 HOH A 103 603 4 HOH HOH . E 5 HOH A 104 604 70 HOH HOH . E 5 HOH A 105 605 76 HOH HOH . E 5 HOH A 106 606 124 HOH HOH . E 5 HOH A 107 607 38 HOH HOH . E 5 HOH A 108 608 67 HOH HOH . E 5 HOH A 109 609 96 HOH HOH . E 5 HOH A 110 610 62 HOH HOH . E 5 HOH A 111 611 100 HOH HOH . E 5 HOH A 112 612 147 HOH HOH . E 5 HOH A 113 613 13 HOH HOH . E 5 HOH A 114 614 41 HOH HOH . E 5 HOH A 115 615 51 HOH HOH . E 5 HOH A 116 616 108 HOH HOH . E 5 HOH A 117 617 125 HOH HOH . E 5 HOH A 118 618 117 HOH HOH . E 5 HOH A 119 619 23 HOH HOH . E 5 HOH A 120 620 145 HOH HOH . E 5 HOH A 121 621 30 HOH HOH . E 5 HOH A 122 622 25 HOH HOH . E 5 HOH A 123 623 107 HOH HOH . E 5 HOH A 124 624 75 HOH HOH . E 5 HOH A 125 625 89 HOH HOH . E 5 HOH A 126 626 115 HOH HOH . E 5 HOH A 127 627 151 HOH HOH . E 5 HOH A 128 628 153 HOH HOH . E 5 HOH A 129 629 159 HOH HOH . E 5 HOH A 130 630 39 HOH HOH . E 5 HOH A 131 631 164 HOH HOH . E 5 HOH A 132 632 90 HOH HOH . E 5 HOH A 133 633 133 HOH HOH . E 5 HOH A 134 634 140 HOH HOH . E 5 HOH A 135 635 98 HOH HOH . E 5 HOH A 136 636 149 HOH HOH . E 5 HOH A 137 637 105 HOH HOH . E 5 HOH A 138 638 157 HOH HOH . E 5 HOH A 139 639 143 HOH HOH . E 5 HOH A 140 640 127 HOH HOH . E 5 HOH A 141 641 138 HOH HOH . E 5 HOH A 142 642 85 HOH HOH . E 5 HOH A 143 643 155 HOH HOH . E 5 HOH A 144 644 156 HOH HOH . E 5 HOH A 145 645 58 HOH HOH . E 5 HOH A 146 646 103 HOH HOH . E 5 HOH A 147 647 154 HOH HOH . E 5 HOH A 148 648 114 HOH HOH . E 5 HOH A 149 649 64 HOH HOH . E 5 HOH A 150 650 101 HOH HOH . E 5 HOH A 151 651 160 HOH HOH . E 5 HOH A 152 652 132 HOH HOH . E 5 HOH A 153 653 106 HOH HOH . E 5 HOH A 154 654 120 HOH HOH . E 5 HOH A 155 655 82 HOH HOH . E 5 HOH A 156 656 94 HOH HOH . E 5 HOH A 157 657 104 HOH HOH . E 5 HOH A 158 658 161 HOH HOH . E 5 HOH A 159 659 111 HOH HOH . E 5 HOH A 160 660 137 HOH HOH . E 5 HOH A 161 661 141 HOH HOH . E 5 HOH A 162 662 102 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 PB GDP . . . B 2 5.025 -9.084 26.852 1 25.08 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 5.876 -7.916 27.139 1 24.06 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 5.504 -10.31 27.605 1 32.09 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 3.563 -8.827 27.194 1 33.16 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 4.991 -9.336 25.27 1 20.24 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 4.911 -8.338 24.041 1 22.64 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 6.249 -7.737 23.636 1 26.72 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 3.856 -7.231 24.282 1 24.55 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 4.461 -9.346 22.916 1 21.69 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 3.137 -9.907 22.94 1 21.22 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 2.557 -9.873 21.571 1 27.02 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 2.3 -8.533 21.186 1 21.67 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 3.487 -10.438 20.502 1 24.81 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 3.316 -11.839 20.45 1 25.72 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 3.034 -9.767 19.219 1 21.59 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 1.86 -10.365 18.611 1 21.56 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 2.501 -8.463 19.693 1 21.61 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 3.27 -7.235 19.627 1 22.11 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 4.376 -6.939 20.328 1 23.17 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 4.706 -5.663 20.112 1 23.43 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 3.824 -5.107 19.251 1 27.27 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 3.591 -3.797 18.607 1 24.7 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 4.315 -2.763 18.762 1 27.42 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 2.522 -3.695 17.808 1 26.21 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 1.706 -4.75 17.551 1 25.55 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 0.642 -4.594 16.748 1 23.19 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 1.841 -5.96 18.118 1 20.67 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 2.872 -6.174 18.957 1 27.9 ? C4 GDP 401 A 1 HETATM 29 H H4' GDP . . . B 2 1.645 -10.483 21.628 1 32.25 ? H4' GDP 401 A 1 HETATM 30 H H3' GDP . . . B 2 4.554 -10.256 20.69 1 29.6 ? H3' GDP 401 A 1 HETATM 31 H HO3' GDP . . . B 2 4.182 -12.268 20.421 1 30.7 ? HO3' GDP 401 A 1 HETATM 32 H H2' GDP . . . B 2 3.864 -9.792 18.5 1 25.74 ? H2' GDP 401 A 1 HETATM 33 H HO2' GDP . . . B 2 2.015 -10.489 17.665 1 25.71 ? HO2' GDP 401 A 1 HETATM 34 H H1' GDP . . . B 2 1.661 -8.391 18.988 1 25.76 ? H1' GDP 401 A 1 HETATM 35 H H8 GDP . . . B 2 4.916 -7.627 20.967 1 27.63 ? H8 GDP 401 A 1 HETATM 36 H HN1 GDP . . . B 2 2.31 -2.777 17.368 1 31.28 ? HN1 GDP 401 A 1 HETATM 37 H HN21 GDP . . . B 2 0.026 -5.365 16.614 1 27.66 ? HN21 GDP 401 A 1 HETATM 38 H HN22 GDP . . . B 2 0.459 -3.721 16.285 1 27.66 ? HN22 GDP 401 A 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #