data_5Y2F # _model_server_result.job_id s8_O0j1Nfj5nqJkEUCdZUQ _model_server_result.datetime_utc '2025-06-21 23:17:40' _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 5y2f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5Y2F # _exptl.entry_id 5Y2F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _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 90 _cell.entry_id 5Y2F _cell.length_a 162.422 _cell.length_b 162.422 _cell.length_c 162.422 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y2F _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 3 _struct_asym.id C _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 covale ? covale1 B NZ LYS 5 C LYS 5 1_555 R C1 HDR . C HDR 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? metalc ? metalc1 A SG CYS 139 A CYS 139 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc2 A SG CYS 142 A CYS 142 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc3 A SG CYS 164 A CYS 164 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc4 A SG CYS 175 A CYS 175 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id AR6 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Adenosine-5-Diphosphoribose # 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 N1 C2 AR6 doub 63 n y N1 C6 AR6 sing 64 n y C2 N3 AR6 sing 65 n y N3 C4 AR6 doub 66 n y C4 C5 AR6 sing 67 n y C4 N9 AR6 sing 68 n y C5 C6 AR6 doub 69 n y C5 N7 AR6 sing 70 n y C6 N6 AR6 sing 71 n n N7 C8 AR6 doub 72 n y C8 N9 AR6 sing 73 n y N9 C1' AR6 sing 74 n n PA O1A AR6 sing 75 n n PA O2A AR6 doub 76 n n PA O3A AR6 sing 77 n n PA O5' AR6 sing 78 n n PB O1B AR6 sing 79 n n PB O2B AR6 doub 80 n n PB O3A AR6 sing 81 n n PB O5D AR6 sing 82 n n C1' C2' AR6 sing 83 n n C1' O4' AR6 sing 84 n n C1D O1D AR6 sing 85 n n C1D C2D AR6 sing 86 n n C1D O4D AR6 sing 87 n n C2' O2' AR6 sing 88 n n C2' C3' AR6 sing 89 n n C2D O2D AR6 sing 90 n n C2D C3D AR6 sing 91 n n C3' O3' AR6 sing 92 n n C3' C4' AR6 sing 93 n n C3D O3D AR6 sing 94 n n C3D C4D AR6 sing 95 n n C4' O4' AR6 sing 96 n n C4' C5' AR6 sing 97 n n C4D O4D AR6 sing 98 n n C4D C5D AR6 sing 99 n n C5' O5' AR6 sing 100 n n C5D O5D AR6 sing 101 n n C2 H2 AR6 sing 102 n n N6 HN6 AR6 sing 103 n n N6 HN6A AR6 sing 104 n n C8 H8 AR6 sing 105 n n C1' H1' AR6 sing 106 n n C1D H1D AR6 sing 107 n n C2' H2' AR6 sing 108 n n O2' HO2' AR6 sing 109 n n C2D H2D AR6 sing 110 n n O2D HO2D AR6 sing 111 n n C3' H3' AR6 sing 112 n n O3' HO3' AR6 sing 113 n n C3D H3D AR6 sing 114 n n O3D HO3D AR6 sing 115 n n C4' H4' AR6 sing 116 n n C4D H4D AR6 sing 117 n n C5' H5' AR6 sing 118 n n C5' "H5'A" AR6 sing 119 n n C5D H5D AR6 sing 120 n n C5D H5DA AR6 sing 121 n n O1A H1A AR6 sing 122 n n O1B H1B AR6 sing 123 n n O1D HD1 AR6 sing 124 n n # _atom_sites.entry_id 5Y2F _atom_sites.fract_transf_matrix[1][1] 0.006157 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006157 _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] 0.006157 _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 AR6 A 1 401 1 AR6 AR6 . D 4 8L9 A 1 402 1 8L9 318 . E 5 ZN A 1 403 1 ZN ZN . F 6 GOL A 1 404 1 GOL GOL . G 6 GOL A 1 405 2 GOL GOL . H 6 GOL A 1 406 3 GOL GOL . I 6 GOL A 1 407 4 GOL GOL . J 6 GOL A 1 408 5 GOL GOL . K 7 SO4 A 1 409 6 SO4 SO4 . L 7 SO4 A 1 410 7 SO4 SO4 . M 7 SO4 A 1 411 8 SO4 SO4 . N 7 SO4 A 1 412 10 SO4 SO4 . O 7 SO4 A 1 413 11 SO4 SO4 . P 7 SO4 A 1 414 12 SO4 SO4 . Q 8 PEG A 1 415 13 PEG PEG . R 9 HDR C 1 101 1 HDR MYR . S 7 SO4 C 1 102 9 SO4 SO4 . T 10 HOH A 1 501 1 HOH HOH . T 10 HOH A 2 502 87 HOH HOH . T 10 HOH A 3 503 108 HOH HOH . T 10 HOH A 4 504 4 HOH HOH . T 10 HOH A 5 505 25 HOH HOH . T 10 HOH A 6 506 98 HOH HOH . T 10 HOH A 7 507 9 HOH HOH . T 10 HOH A 8 508 68 HOH HOH . T 10 HOH A 9 509 91 HOH HOH . T 10 HOH A 10 510 47 HOH HOH . T 10 HOH A 11 511 28 HOH HOH . T 10 HOH A 12 512 3 HOH HOH . T 10 HOH A 13 513 73 HOH HOH . T 10 HOH A 14 514 115 HOH HOH . T 10 HOH A 15 515 8 HOH HOH . T 10 HOH A 16 516 33 HOH HOH . T 10 HOH A 17 517 6 HOH HOH . T 10 HOH A 18 518 74 HOH HOH . T 10 HOH A 19 519 66 HOH HOH . T 10 HOH A 20 520 30 HOH HOH . T 10 HOH A 21 521 75 HOH HOH . T 10 HOH A 22 522 43 HOH HOH . T 10 HOH A 23 523 76 HOH HOH . T 10 HOH A 24 524 45 HOH HOH . T 10 HOH A 25 525 80 HOH HOH . T 10 HOH A 26 526 50 HOH HOH . T 10 HOH A 27 527 67 HOH HOH . T 10 HOH A 28 528 11 HOH HOH . T 10 HOH A 29 529 5 HOH HOH . T 10 HOH A 30 530 22 HOH HOH . T 10 HOH A 31 531 34 HOH HOH . T 10 HOH A 32 532 127 HOH HOH . T 10 HOH A 33 533 71 HOH HOH . T 10 HOH A 34 534 53 HOH HOH . T 10 HOH A 35 535 100 HOH HOH . T 10 HOH A 36 536 37 HOH HOH . T 10 HOH A 37 537 62 HOH HOH . T 10 HOH A 38 538 26 HOH HOH . T 10 HOH A 39 539 113 HOH HOH . T 10 HOH A 40 540 58 HOH HOH . T 10 HOH A 41 541 17 HOH HOH . T 10 HOH A 42 542 70 HOH HOH . T 10 HOH A 43 543 104 HOH HOH . T 10 HOH A 44 544 51 HOH HOH . T 10 HOH A 45 545 49 HOH HOH . T 10 HOH A 46 546 112 HOH HOH . T 10 HOH A 47 547 134 HOH HOH . T 10 HOH A 48 548 39 HOH HOH . T 10 HOH A 49 549 10 HOH HOH . T 10 HOH A 50 550 97 HOH HOH . T 10 HOH A 51 551 96 HOH HOH . T 10 HOH A 52 552 122 HOH HOH . T 10 HOH A 53 553 31 HOH HOH . T 10 HOH A 54 554 12 HOH HOH . T 10 HOH A 55 555 52 HOH HOH . T 10 HOH A 56 556 72 HOH HOH . T 10 HOH A 57 557 21 HOH HOH . T 10 HOH A 58 558 55 HOH HOH . T 10 HOH A 59 559 23 HOH HOH . T 10 HOH A 60 560 84 HOH HOH . T 10 HOH A 61 561 105 HOH HOH . T 10 HOH A 62 562 142 HOH HOH . T 10 HOH A 63 563 110 HOH HOH . T 10 HOH A 64 564 24 HOH HOH . T 10 HOH A 65 565 7 HOH HOH . T 10 HOH A 66 566 36 HOH HOH . T 10 HOH A 67 567 65 HOH HOH . T 10 HOH A 68 568 42 HOH HOH . T 10 HOH A 69 569 16 HOH HOH . T 10 HOH A 70 570 102 HOH HOH . T 10 HOH A 71 571 114 HOH HOH . T 10 HOH A 72 572 77 HOH HOH . T 10 HOH A 73 573 20 HOH HOH . T 10 HOH A 74 574 35 HOH HOH . T 10 HOH A 75 575 83 HOH HOH . T 10 HOH A 76 576 2 HOH HOH . T 10 HOH A 77 577 40 HOH HOH . T 10 HOH A 78 578 41 HOH HOH . T 10 HOH A 79 579 90 HOH HOH . T 10 HOH A 80 580 29 HOH HOH . T 10 HOH A 81 581 128 HOH HOH . T 10 HOH A 82 582 94 HOH HOH . T 10 HOH A 83 583 32 HOH HOH . T 10 HOH A 84 584 116 HOH HOH . T 10 HOH A 85 585 109 HOH HOH . T 10 HOH A 86 586 54 HOH HOH . T 10 HOH A 87 587 99 HOH HOH . T 10 HOH A 88 588 56 HOH HOH . T 10 HOH A 89 589 93 HOH HOH . T 10 HOH A 90 590 135 HOH HOH . T 10 HOH A 91 591 46 HOH HOH . T 10 HOH A 92 592 48 HOH HOH . T 10 HOH A 93 593 89 HOH HOH . T 10 HOH A 94 594 27 HOH HOH . T 10 HOH A 95 595 61 HOH HOH . T 10 HOH A 96 596 19 HOH HOH . T 10 HOH A 97 597 59 HOH HOH . T 10 HOH A 98 598 13 HOH HOH . T 10 HOH A 99 599 78 HOH HOH . T 10 HOH A 100 600 44 HOH HOH . T 10 HOH A 101 601 92 HOH HOH . T 10 HOH A 102 602 38 HOH HOH . T 10 HOH A 103 603 138 HOH HOH . T 10 HOH A 104 604 81 HOH HOH . T 10 HOH A 105 605 119 HOH HOH . T 10 HOH A 106 606 60 HOH HOH . T 10 HOH A 107 607 143 HOH HOH . T 10 HOH A 108 608 15 HOH HOH . T 10 HOH A 109 609 82 HOH HOH . T 10 HOH A 110 610 117 HOH HOH . T 10 HOH A 111 611 129 HOH HOH . T 10 HOH A 112 612 85 HOH HOH . T 10 HOH A 113 613 137 HOH HOH . T 10 HOH A 114 614 145 HOH HOH . T 10 HOH A 115 615 64 HOH HOH . T 10 HOH A 116 616 111 HOH HOH . T 10 HOH A 117 617 101 HOH HOH . T 10 HOH A 118 618 139 HOH HOH . T 10 HOH A 119 619 144 HOH HOH . T 10 HOH A 120 620 103 HOH HOH . T 10 HOH A 121 621 63 HOH HOH . T 10 HOH A 122 622 69 HOH HOH . T 10 HOH A 123 623 106 HOH HOH . T 10 HOH A 124 624 57 HOH HOH . T 10 HOH A 125 625 88 HOH HOH . U 10 HOH C 1 201 107 HOH HOH . U 10 HOH C 2 202 124 HOH HOH . U 10 HOH C 3 203 125 HOH HOH . U 10 HOH C 4 204 95 HOH HOH . U 10 HOH C 5 205 136 HOH HOH . U 10 HOH C 6 206 14 HOH HOH . U 10 HOH C 7 207 86 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 N N1 AR6 . . . C 3 8.722 135.267 140.94 1 49.82 ? N1 AR6 401 A 1 HETATM 2 C C2 AR6 . . . C 3 8.564 136.601 141.087 1 50.12 ? C2 AR6 401 A 1 HETATM 3 N N3 AR6 . . . C 3 7.476 137.141 141.667 1 45.84 ? N3 AR6 401 A 1 HETATM 4 C C4 AR6 . . . C 3 6.49 136.363 142.142 1 42.73 ? C4 AR6 401 A 1 HETATM 5 C C5 AR6 . . . C 3 6.603 134.926 142.036 1 44.07 ? C5 AR6 401 A 1 HETATM 6 C C6 AR6 . . . C 3 7.803 134.392 141.395 1 47.38 ? C6 AR6 401 A 1 HETATM 7 N N6 AR6 . . . C 3 7.928 133.057 141.254 1 50.02 ? N6 AR6 401 A 1 HETATM 8 N N7 AR6 . . . C 3 5.518 134.387 142.575 1 44.05 ? N7 AR6 401 A 1 HETATM 9 C C8 AR6 . . . C 3 4.761 135.424 143.018 1 48.59 ? C8 AR6 401 A 1 HETATM 10 N N9 AR6 . . . C 3 5.349 136.6 142.753 1 46.39 ? N9 AR6 401 A 1 HETATM 11 P PA AR6 . . . C 3 1.975 139.587 148.101 1 44.23 ? PA AR6 401 A 1 HETATM 12 P PB AR6 . . . C 3 3.804 140.024 150.262 1 42.14 ? PB AR6 401 A 1 HETATM 13 C C1' AR6 . . . C 3 4.886 137.961 143.125 1 47.8 ? C1' AR6 401 A 1 HETATM 14 O O1A AR6 . . . C 3 1.25 140.921 148.247 1 46.13 ? O1A AR6 401 A 1 HETATM 15 O O1B AR6 . . . C 3 4.718 138.923 150.664 1 45.18 ? O1B AR6 401 A 1 HETATM 16 C C1D AR6 . . . C 3 0.018 139.683 153.962 1 41.55 ? C1D AR6 401 A 1 HETATM 17 O O1D AR6 . . . C 3 -1.155 140.101 154.637 1 39.08 ? O1D AR6 401 A 1 HETATM 18 C C2' AR6 . . . C 3 3.418 138.291 142.93 1 49.41 ? C2' AR6 401 A 1 HETATM 19 O O2' AR6 . . . C 3 3.244 138.817 141.622 1 49.03 ? O2' AR6 401 A 1 HETATM 20 O O2A AR6 . . . C 3 1.203 138.348 147.738 1 40.24 ? O2A AR6 401 A 1 HETATM 21 O O2B AR6 . . . C 3 4.268 141.26 149.517 1 40.42 ? O2B AR6 401 A 1 HETATM 22 C C2D AR6 . . . C 3 1.022 138.941 154.839 1 43.33 ? C2D AR6 401 A 1 HETATM 23 O O2D AR6 . . . C 3 1.013 139.576 156.132 1 44.16 ? O2D AR6 401 A 1 HETATM 24 C C3' AR6 . . . C 3 3.103 139.278 144.053 1 48.65 ? C3' AR6 401 A 1 HETATM 25 O O3' AR6 . . . C 3 3.046 140.648 143.648 1 44.09 ? O3' AR6 401 A 1 HETATM 26 O O3A AR6 . . . C 3 2.615 139.243 149.551 1 46.53 ? O3A AR6 401 A 1 HETATM 27 C C3D AR6 . . . C 3 2.326 139.222 154.116 1 42.37 ? C3D AR6 401 A 1 HETATM 28 O O3D AR6 . . . C 3 3.508 139.147 154.922 1 36.62 ? O3D AR6 401 A 1 HETATM 29 C C4' AR6 . . . C 3 4.253 139.127 145.049 1 46.84 ? C4' AR6 401 A 1 HETATM 30 O O4' AR6 . . . C 3 5.121 138.121 144.534 1 46.71 ? O4' AR6 401 A 1 HETATM 31 C C4D AR6 . . . C 3 2.083 140.646 153.588 1 41.98 ? C4D AR6 401 A 1 HETATM 32 O O4D AR6 . . . C 3 0.676 140.879 153.611 1 43.06 ? O4D AR6 401 A 1 HETATM 33 C C5' AR6 . . . C 3 3.753 138.718 146.411 1 47.09 ? C5' AR6 401 A 1 HETATM 34 O O5' AR6 . . . C 3 3.154 139.836 147.062 1 43.03 ? O5' AR6 401 A 1 HETATM 35 C C5D AR6 . . . C 3 2.25 140.791 152.129 1 43.52 ? C5D AR6 401 A 1 HETATM 36 O O5D AR6 . . . C 3 3.524 140.533 151.732 1 49.45 ? O5D AR6 401 A 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 43 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 1104 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 36 #