data_3F5F # _model_server_result.job_id mVTfs-SNAgEX6-GFYYK1mw _model_server_result.datetime_utc '2025-04-26 21:15:05' _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 3f5f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":673}' # _entry.id 3F5F # _exptl.entry_id 3F5F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-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 90 _cell.angle_gamma 120 _cell.entry_id 3F5F _cell.length_a 152.647 _cell.length_b 152.647 _cell.length_c 85.686 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3F5F _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 152.647 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 76.3235 132.19618 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 GLC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC ? 672 GLC 2 n B GLC 2 B 2 GLC ? 671 GLC # 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 503 A CYS 1201 1_555 A SG CYS 511 A CYS 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 524 A CYS 1222 1_555 A SG CYS 530 A CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 B O4 GLC . B GLC 1 1_555 B C1 GLC . B GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 3F5F _atom_sites.fract_transf_matrix[1][1] 0.006551 _atom_sites.fract_transf_matrix[1][2] 0.003782 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007565 _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] 0.011671 _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 C 3 A3P A 1 673 673 A3P A3P . D 4 HOH A 1 501 501 HOH TIP . D 4 HOH A 2 502 502 HOH TIP . D 4 HOH A 3 503 503 HOH TIP . D 4 HOH A 4 504 504 HOH TIP . D 4 HOH A 5 505 505 HOH TIP . D 4 HOH A 6 506 506 HOH TIP . D 4 HOH A 7 507 507 HOH TIP . D 4 HOH A 8 508 508 HOH TIP . D 4 HOH A 9 509 509 HOH TIP . D 4 HOH A 10 510 510 HOH TIP . D 4 HOH A 11 511 511 HOH TIP . D 4 HOH A 12 512 512 HOH TIP . D 4 HOH A 13 513 513 HOH TIP . D 4 HOH A 14 514 514 HOH TIP . D 4 HOH A 15 515 515 HOH TIP . D 4 HOH A 16 516 516 HOH TIP . D 4 HOH A 17 517 517 HOH TIP . D 4 HOH A 18 518 518 HOH TIP . D 4 HOH A 19 519 519 HOH TIP . D 4 HOH A 20 520 520 HOH TIP . D 4 HOH A 21 521 521 HOH TIP . D 4 HOH A 22 522 522 HOH TIP . D 4 HOH A 23 523 523 HOH TIP . D 4 HOH A 24 524 524 HOH TIP . D 4 HOH A 25 525 525 HOH TIP . D 4 HOH A 26 526 526 HOH TIP . D 4 HOH A 27 527 527 HOH TIP . D 4 HOH A 28 528 528 HOH TIP . D 4 HOH A 29 529 529 HOH TIP . D 4 HOH A 30 530 530 HOH TIP . D 4 HOH A 31 531 531 HOH TIP . D 4 HOH A 32 532 532 HOH TIP . D 4 HOH A 33 533 533 HOH TIP . D 4 HOH A 34 534 534 HOH TIP . D 4 HOH A 35 535 535 HOH TIP . D 4 HOH A 36 536 536 HOH TIP . D 4 HOH A 37 537 537 HOH TIP . D 4 HOH A 38 538 538 HOH TIP . D 4 HOH A 39 539 539 HOH TIP . D 4 HOH A 40 540 540 HOH TIP . D 4 HOH A 41 541 541 HOH TIP . D 4 HOH A 42 542 542 HOH TIP . D 4 HOH A 43 543 543 HOH TIP . D 4 HOH A 44 544 544 HOH TIP . D 4 HOH A 45 545 545 HOH TIP . D 4 HOH A 46 546 546 HOH TIP . D 4 HOH A 47 547 547 HOH TIP . D 4 HOH A 48 548 548 HOH TIP . D 4 HOH A 49 549 549 HOH TIP . D 4 HOH A 50 550 550 HOH TIP . D 4 HOH A 51 551 551 HOH TIP . D 4 HOH A 52 552 552 HOH TIP . D 4 HOH A 53 553 553 HOH TIP . D 4 HOH A 54 554 554 HOH TIP . D 4 HOH A 55 555 555 HOH TIP . D 4 HOH A 56 556 556 HOH TIP . D 4 HOH A 57 557 557 HOH TIP . D 4 HOH A 58 558 558 HOH TIP . D 4 HOH A 59 559 559 HOH TIP . D 4 HOH A 60 560 560 HOH TIP . D 4 HOH A 61 561 561 HOH TIP . D 4 HOH A 62 562 562 HOH TIP . D 4 HOH A 63 563 563 HOH TIP . D 4 HOH A 64 564 564 HOH TIP . D 4 HOH A 65 565 565 HOH TIP . D 4 HOH A 66 566 566 HOH TIP . D 4 HOH A 67 567 567 HOH TIP . D 4 HOH A 68 568 568 HOH TIP . D 4 HOH A 69 569 569 HOH TIP . D 4 HOH A 70 570 570 HOH TIP . D 4 HOH A 71 571 571 HOH TIP . D 4 HOH A 72 572 572 HOH TIP . D 4 HOH A 73 573 573 HOH TIP . D 4 HOH A 74 574 574 HOH TIP . D 4 HOH A 75 575 575 HOH TIP . D 4 HOH A 76 576 576 HOH TIP . D 4 HOH A 77 577 577 HOH TIP . D 4 HOH A 78 578 578 HOH TIP . D 4 HOH A 79 579 579 HOH TIP . D 4 HOH A 80 580 580 HOH TIP . D 4 HOH A 81 581 581 HOH TIP . D 4 HOH A 82 582 582 HOH TIP . D 4 HOH A 83 583 583 HOH TIP . D 4 HOH A 84 584 584 HOH TIP . D 4 HOH A 85 585 585 HOH TIP . D 4 HOH A 86 586 586 HOH TIP . D 4 HOH A 87 587 587 HOH TIP . D 4 HOH A 88 588 588 HOH TIP . D 4 HOH A 89 589 589 HOH TIP . D 4 HOH A 90 590 590 HOH TIP . D 4 HOH A 91 591 591 HOH TIP . D 4 HOH A 92 592 592 HOH TIP . D 4 HOH A 93 593 593 HOH TIP . D 4 HOH A 94 594 594 HOH TIP . D 4 HOH A 95 595 595 HOH TIP . D 4 HOH A 96 596 596 HOH TIP . D 4 HOH A 97 597 597 HOH TIP . D 4 HOH A 98 598 598 HOH TIP . D 4 HOH A 99 599 599 HOH TIP . D 4 HOH A 100 600 600 HOH TIP . D 4 HOH A 101 601 601 HOH TIP . D 4 HOH A 102 602 602 HOH TIP . D 4 HOH A 103 603 603 HOH TIP . D 4 HOH A 104 604 604 HOH TIP . D 4 HOH A 105 605 605 HOH TIP . D 4 HOH A 106 606 606 HOH TIP . D 4 HOH A 107 607 607 HOH TIP . D 4 HOH A 108 608 608 HOH TIP . D 4 HOH A 109 609 609 HOH TIP . D 4 HOH A 110 610 610 HOH TIP . D 4 HOH A 111 611 611 HOH TIP . D 4 HOH A 112 612 612 HOH TIP . D 4 HOH A 113 613 613 HOH TIP . D 4 HOH A 114 614 614 HOH TIP . D 4 HOH A 115 615 615 HOH TIP . D 4 HOH A 116 616 616 HOH TIP . D 4 HOH A 117 617 617 HOH TIP . D 4 HOH A 118 618 618 HOH TIP . D 4 HOH A 119 619 619 HOH TIP . D 4 HOH A 120 620 620 HOH TIP . D 4 HOH A 121 621 621 HOH TIP . D 4 HOH A 122 622 622 HOH TIP . D 4 HOH A 123 623 623 HOH TIP . D 4 HOH A 124 624 624 HOH TIP . D 4 HOH A 125 625 625 HOH TIP . D 4 HOH A 126 626 626 HOH TIP . D 4 HOH A 127 627 627 HOH TIP . D 4 HOH A 128 628 628 HOH TIP . D 4 HOH A 129 629 629 HOH TIP . D 4 HOH A 130 630 630 HOH TIP . D 4 HOH A 131 631 631 HOH TIP . D 4 HOH A 132 632 632 HOH TIP . D 4 HOH A 133 633 633 HOH TIP . D 4 HOH A 134 634 634 HOH TIP . D 4 HOH A 135 635 635 HOH TIP . D 4 HOH A 136 636 636 HOH TIP . D 4 HOH A 137 637 637 HOH TIP . D 4 HOH A 138 638 638 HOH TIP . D 4 HOH A 139 639 639 HOH TIP . D 4 HOH A 140 640 640 HOH TIP . D 4 HOH A 141 641 641 HOH TIP . D 4 HOH A 142 642 642 HOH TIP . D 4 HOH A 143 643 643 HOH TIP . D 4 HOH A 144 644 644 HOH TIP . D 4 HOH A 145 645 645 HOH TIP . D 4 HOH A 146 646 646 HOH TIP . D 4 HOH A 147 647 647 HOH TIP . D 4 HOH A 148 648 648 HOH TIP . D 4 HOH A 149 649 649 HOH TIP . D 4 HOH A 150 650 650 HOH TIP . D 4 HOH A 151 651 651 HOH TIP . D 4 HOH A 152 652 652 HOH TIP . D 4 HOH A 153 653 653 HOH TIP . D 4 HOH A 154 654 654 HOH TIP . D 4 HOH A 155 655 655 HOH TIP . D 4 HOH A 156 656 656 HOH TIP . D 4 HOH A 157 657 657 HOH TIP . D 4 HOH A 158 658 658 HOH TIP . D 4 HOH A 159 659 659 HOH TIP . D 4 HOH A 160 660 660 HOH TIP . D 4 HOH A 161 661 661 HOH TIP . D 4 HOH A 162 662 662 HOH TIP . D 4 HOH A 163 663 663 HOH TIP . D 4 HOH A 164 664 664 HOH TIP . D 4 HOH A 165 665 665 HOH TIP . D 4 HOH A 166 666 666 HOH TIP . D 4 HOH A 167 667 667 HOH TIP . # 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 P1 A3P . . . C 3 58.093 73.05 43.903 1 46 ? P1 A3P 673 A 1 HETATM 2 O O1P A3P . . . C 3 56.802 72.374 43.972 1 41.09 ? O1P A3P 673 A 1 HETATM 3 O O2P A3P . . . C 3 57.952 74.432 43.458 1 47.34 ? O2P A3P 673 A 1 HETATM 4 O O3P A3P . . . C 3 58.753 72.976 45.217 1 46.11 ? O3P A3P 673 A 1 HETATM 5 P P2 A3P . . . C 3 58.473 68.015 38.303 1 47.93 ? P2 A3P 673 A 1 HETATM 6 O O4P A3P . . . C 3 59.053 68.68 37.119 1 48.18 ? O4P A3P 673 A 1 HETATM 7 O O5P A3P . . . C 3 59.089 66.711 38.538 1 47.48 ? O5P A3P 673 A 1 HETATM 8 O O6P A3P . . . C 3 57.004 67.864 38.13 1 46.02 ? O6P A3P 673 A 1 HETATM 9 O O5' A3P . . . C 3 58.787 68.9 39.589 1 45.24 ? O5' A3P 673 A 1 HETATM 10 C C5' A3P . . . C 3 58.363 70.249 39.784 1 43.53 ? C5' A3P 673 A 1 HETATM 11 C C4' A3P . . . C 3 59.191 70.871 40.939 1 43.27 ? C4' A3P 673 A 1 HETATM 12 O O4' A3P . . . C 3 60.51 71.223 40.414 1 44.64 ? O4' A3P 673 A 1 HETATM 13 C C3' A3P . . . C 3 58.645 72.18 41.481 1 43.48 ? C3' A3P 673 A 1 HETATM 14 O O3' A3P . . . C 3 58.979 72.276 42.866 1 44.72 ? O3' A3P 673 A 1 HETATM 15 C C2' A3P . . . C 3 59.354 73.201 40.629 1 41.33 ? C2' A3P 673 A 1 HETATM 16 O O2' A3P . . . C 3 59.288 74.544 41.057 1 41.02 ? O2' A3P 673 A 1 HETATM 17 C C1' A3P . . . C 3 60.757 72.613 40.6 1 39.15 ? C1' A3P 673 A 1 HETATM 18 N N9 A3P . . . C 3 61.582 73.135 39.487 1 34.74 ? N9 A3P 673 A 1 HETATM 19 C C8 A3P . . . C 3 61.228 73.341 38.171 1 34.15 ? C8 A3P 673 A 1 HETATM 20 N N7 A3P . . . C 3 62.181 73.819 37.415 1 34.42 ? N7 A3P 673 A 1 HETATM 21 C C5 A3P . . . C 3 63.245 73.942 38.269 1 30.96 ? C5 A3P 673 A 1 HETATM 22 C C6 A3P . . . C 3 64.576 74.401 38.082 1 29.43 ? C6 A3P 673 A 1 HETATM 23 N N6 A3P . . . C 3 65.039 74.834 36.892 1 32.54 ? N6 A3P 673 A 1 HETATM 24 N N1 A3P . . . C 3 65.428 74.397 39.172 1 29.23 ? N1 A3P 673 A 1 HETATM 25 C C2 A3P . . . C 3 64.988 73.965 40.39 1 30.25 ? C2 A3P 673 A 1 HETATM 26 N N3 A3P . . . C 3 63.728 73.506 40.685 1 32.39 ? N3 A3P 673 A 1 HETATM 27 C C4 A3P . . . C 3 62.905 73.523 39.573 1 31.33 ? C4 A3P 673 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #