data_8AK9 # _model_server_result.job_id BQyXFa27hv6_6-pZkHPX8g _model_server_result.datetime_utc '2025-01-10 08:32:37' _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 8ak9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":402}' # _entry.id 8AK9 # _exptl.entry_id 8AK9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _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 2 _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 8AK9 _cell.length_a 91.047 _cell.length_b 91.047 _cell.length_c 143.934 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AK9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,Y 1 1 B,M,N,O,P,Q,R,S,T,U,V,W,X,Z 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 N N 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 SG CYS 135 A CYS 141 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 O ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 O ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 O ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 O ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? # _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 13 n y N1 C6 AR6 sing 14 n y C2 N3 AR6 sing 15 n y N3 C4 AR6 doub 16 n y C4 C5 AR6 sing 17 n y C4 N9 AR6 sing 18 n y C5 C6 AR6 doub 19 n y C5 N7 AR6 sing 20 n y C6 N6 AR6 sing 21 n n N7 C8 AR6 doub 22 n y C8 N9 AR6 sing 23 n y N9 C1' AR6 sing 24 n n PA O1A AR6 sing 25 n n PA O2A AR6 doub 26 n n PA O3A AR6 sing 27 n n PA O5' AR6 sing 28 n n PB O1B AR6 sing 29 n n PB O2B AR6 doub 30 n n PB O3A AR6 sing 31 n n PB O5D AR6 sing 32 n n C1' C2' AR6 sing 33 n n C1' O4' AR6 sing 34 n n C1D O1D AR6 sing 35 n n C1D C2D AR6 sing 36 n n C1D O4D AR6 sing 37 n n C2' O2' AR6 sing 38 n n C2' C3' AR6 sing 39 n n C2D O2D AR6 sing 40 n n C2D C3D AR6 sing 41 n n C3' O3' AR6 sing 42 n n C3' C4' AR6 sing 43 n n C3D O3D AR6 sing 44 n n C3D C4D AR6 sing 45 n n C4' O4' AR6 sing 46 n n C4' C5' AR6 sing 47 n n C4D O4D AR6 sing 48 n n C4D C5D AR6 sing 49 n n C5' O5' AR6 sing 50 n n C5D O5D AR6 sing 51 n n C2 H2 AR6 sing 52 n n N6 HN6 AR6 sing 53 n n N6 HN6A AR6 sing 54 n n C8 H8 AR6 sing 55 n n C1' H1' AR6 sing 56 n n C1D H1D AR6 sing 57 n n C2' H2' AR6 sing 58 n n O2' HO2' AR6 sing 59 n n C2D H2D AR6 sing 60 n n O2D HO2D AR6 sing 61 n n C3' H3' AR6 sing 62 n n O3' HO3' AR6 sing 63 n n C3D H3D AR6 sing 64 n n O3D HO3D AR6 sing 65 n n C4' H4' AR6 sing 66 n n C4D H4D AR6 sing 67 n n C5' H5' AR6 sing 68 n n C5' "H5'A" AR6 sing 69 n n C5D H5D AR6 sing 70 n n C5D H5DA AR6 sing 71 n n O1A H1A AR6 sing 72 n n O1B H1B AR6 sing 73 n n O1D HD1 AR6 sing 74 n n # _atom_sites.entry_id 8AK9 _atom_sites.fract_transf_matrix[1][1] 0.010983 _atom_sites.fract_transf_matrix[1][2] 0.006341 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012682 _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] 0.006948 _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 2 AR6 A 1 401 500 AR6 AR6 . D 3 ZN A 1 402 501 ZN ZN . E 4 EDO A 1 403 503 EDO EDO . F 5 PG4 A 1 404 504 PG4 PG4 . G 6 SO4 A 1 405 3 SO4 SO4 . H 6 SO4 A 1 406 5 SO4 SO4 . I 6 SO4 A 1 407 7 SO4 SO4 . J 6 SO4 A 1 408 9 SO4 SO4 . K 7 ISN A 1 409 1 ISN ISN . L 8 CL A 1 410 1 CL CL . M 9 PEG B 1 401 502 PEG PEG . N 2 AR6 B 1 402 500 AR6 AR6 . O 3 ZN B 1 403 501 ZN ZN . P 9 PEG B 1 404 502 PEG PEG . Q 5 PG4 B 1 405 503 PG4 PG4 . R 6 SO4 B 1 406 1 SO4 SO4 . S 6 SO4 B 1 407 2 SO4 SO4 . T 6 SO4 B 1 408 4 SO4 SO4 . U 6 SO4 B 1 409 6 SO4 SO4 . V 6 SO4 B 1 410 8 SO4 SO4 . W 7 ISN B 1 411 2 ISN ISN . X 8 CL B 1 412 2 CL CL . Y 10 HOH A 1 501 82 HOH HOH . Y 10 HOH A 2 502 64 HOH HOH . Y 10 HOH A 3 503 8 HOH HOH . Y 10 HOH A 4 504 12 HOH HOH . Y 10 HOH A 5 505 85 HOH HOH . Y 10 HOH A 6 506 54 HOH HOH . Y 10 HOH A 7 507 50 HOH HOH . Y 10 HOH A 8 508 75 HOH HOH . Y 10 HOH A 9 509 65 HOH HOH . Y 10 HOH A 10 510 35 HOH HOH . Y 10 HOH A 11 511 74 HOH HOH . Y 10 HOH A 12 512 46 HOH HOH . Y 10 HOH A 13 513 81 HOH HOH . Y 10 HOH A 14 514 48 HOH HOH . Y 10 HOH A 15 515 77 HOH HOH . Y 10 HOH A 16 516 30 HOH HOH . Y 10 HOH A 17 517 5 HOH HOH . Y 10 HOH A 18 518 28 HOH HOH . Y 10 HOH A 19 519 43 HOH HOH . Y 10 HOH A 20 520 20 HOH HOH . Y 10 HOH A 21 521 40 HOH HOH . Y 10 HOH A 22 522 38 HOH HOH . Y 10 HOH A 23 523 60 HOH HOH . Y 10 HOH A 24 524 4 HOH HOH . Y 10 HOH A 25 525 63 HOH HOH . Y 10 HOH A 26 526 25 HOH HOH . Y 10 HOH A 27 527 45 HOH HOH . Y 10 HOH A 28 528 58 HOH HOH . Y 10 HOH A 29 529 1 HOH HOH . Y 10 HOH A 30 530 34 HOH HOH . Y 10 HOH A 31 531 31 HOH HOH . Y 10 HOH A 32 532 100 HOH HOH . Y 10 HOH A 33 533 84 HOH HOH . Y 10 HOH A 34 534 78 HOH HOH . Y 10 HOH A 35 535 94 HOH HOH . Y 10 HOH A 36 536 37 HOH HOH . Y 10 HOH A 37 537 91 HOH HOH . Y 10 HOH A 38 538 79 HOH HOH . Y 10 HOH A 39 539 73 HOH HOH . Y 10 HOH A 40 540 9 HOH HOH . Y 10 HOH A 41 541 29 HOH HOH . Y 10 HOH A 42 542 14 HOH HOH . Y 10 HOH A 43 543 42 HOH HOH . Y 10 HOH A 44 544 44 HOH HOH . Y 10 HOH A 45 545 57 HOH HOH . Y 10 HOH A 46 546 56 HOH HOH . Y 10 HOH A 47 547 47 HOH HOH . Y 10 HOH A 48 548 23 HOH HOH . Y 10 HOH A 49 549 76 HOH HOH . Y 10 HOH A 50 550 24 HOH HOH . Y 10 HOH A 51 551 90 HOH HOH . Y 10 HOH A 52 552 98 HOH HOH . Y 10 HOH A 53 553 88 HOH HOH . Y 10 HOH A 54 554 2 HOH HOH . Y 10 HOH A 55 555 86 HOH HOH . Y 10 HOH A 56 556 83 HOH HOH . Y 10 HOH A 57 557 13 HOH HOH . Y 10 HOH A 58 558 80 HOH HOH . Y 10 HOH A 59 559 92 HOH HOH . Y 10 HOH A 60 560 93 HOH HOH . Y 10 HOH A 61 561 66 HOH HOH . Y 10 HOH A 62 562 67 HOH HOH . Z 10 HOH B 1 501 68 HOH HOH . Z 10 HOH B 2 502 71 HOH HOH . Z 10 HOH B 3 503 96 HOH HOH . Z 10 HOH B 4 504 95 HOH HOH . Z 10 HOH B 5 505 62 HOH HOH . Z 10 HOH B 6 506 11 HOH HOH . Z 10 HOH B 7 507 7 HOH HOH . Z 10 HOH B 8 508 19 HOH HOH . Z 10 HOH B 9 509 55 HOH HOH . Z 10 HOH B 10 510 33 HOH HOH . Z 10 HOH B 11 511 26 HOH HOH . Z 10 HOH B 12 512 72 HOH HOH . Z 10 HOH B 13 513 15 HOH HOH . Z 10 HOH B 14 514 87 HOH HOH . Z 10 HOH B 15 515 17 HOH HOH . Z 10 HOH B 16 516 41 HOH HOH . Z 10 HOH B 17 517 53 HOH HOH . Z 10 HOH B 18 518 39 HOH HOH . Z 10 HOH B 19 519 10 HOH HOH . Z 10 HOH B 20 520 97 HOH HOH . Z 10 HOH B 21 521 99 HOH HOH . Z 10 HOH B 22 522 27 HOH HOH . Z 10 HOH B 23 523 101 HOH HOH . Z 10 HOH B 24 524 6 HOH HOH . Z 10 HOH B 25 525 32 HOH HOH . Z 10 HOH B 26 526 70 HOH HOH . Z 10 HOH B 27 527 36 HOH HOH . Z 10 HOH B 28 528 51 HOH HOH . Z 10 HOH B 29 529 89 HOH HOH . Z 10 HOH B 30 530 22 HOH HOH . Z 10 HOH B 31 531 49 HOH HOH . Z 10 HOH B 32 532 52 HOH HOH . Z 10 HOH B 33 533 21 HOH HOH . Z 10 HOH B 34 534 16 HOH HOH . Z 10 HOH B 35 535 18 HOH HOH . Z 10 HOH B 36 536 61 HOH HOH . Z 10 HOH B 37 537 59 HOH HOH . Z 10 HOH B 38 538 3 HOH HOH . Z 10 HOH B 39 539 69 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 . . . N 2 -19.248 24.643 36.895 1 48.12 ? N1 AR6 402 B 1 HETATM 2 C C2 AR6 . . . N 2 -19.358 25.483 37.942 1 46.49 ? C2 AR6 402 B 1 HETATM 3 N N3 AR6 . . . N 2 -20.426 25.765 38.687 1 44.09 ? N3 AR6 402 B 1 HETATM 4 C C4 AR6 . . . N 2 -21.492 25.066 38.251 1 39.84 ? C4 AR6 402 B 1 HETATM 5 C C5 AR6 . . . N 2 -21.545 24.211 37.171 1 39.86 ? C5 AR6 402 B 1 HETATM 6 C C6 AR6 . . . N 2 -20.353 23.988 36.459 1 43.75 ? C6 AR6 402 B 1 HETATM 7 N N6 AR6 . . . N 2 -20.249 23.149 35.421 1 43.3 ? N6 AR6 402 B 1 HETATM 8 N N7 AR6 . . . N 2 -22.836 23.71 37.019 1 46.82 ? N7 AR6 402 B 1 HETATM 9 C C8 AR6 . . . N 2 -23.524 24.245 37.998 1 42.26 ? C8 AR6 402 B 1 HETATM 10 N N9 AR6 . . . N 2 -22.764 25.11 38.747 1 45.03 ? N9 AR6 402 B 1 HETATM 11 P PA AR6 . . . N 2 -27.121 24.029 43.948 1 52.15 ? PA AR6 402 B 1 HETATM 12 P PB AR6 . . . N 2 -26.034 22.288 45.938 1 43.86 ? PB AR6 402 B 1 HETATM 13 C C1' AR6 . . . N 2 -23.186 25.85 39.932 1 41.85 ? C1' AR6 402 B 1 HETATM 14 O O1A AR6 . . . N 2 -27.682 24.915 45.012 1 53.72 ? O1A AR6 402 B 1 HETATM 15 O O1B AR6 . . . N 2 -25.323 20.969 45.853 1 45.73 ? O1B AR6 402 B 1 HETATM 16 C C1D AR6 . . . N 2 -30.653 20.537 47.729 1 54.52 ? C1D AR6 402 B 1 HETATM 17 O O1D AR6 . . . N 2 -31.758 20.627 48.552 1 63.61 ? O1D AR6 402 B 1 HETATM 18 C C2' AR6 . . . N 2 -24.493 26.619 39.807 1 37.88 ? C2' AR6 402 B 1 HETATM 19 O O2' AR6 . . . N 2 -24.133 27.936 39.458 1 36.06 ? O2' AR6 402 B 1 HETATM 20 O O2A AR6 . . . N 2 -27.841 23.858 42.648 1 52.65 ? O2A AR6 402 B 1 HETATM 21 O O2B AR6 . . . N 2 -25.249 23.487 46.339 1 42.04 ? O2B AR6 402 B 1 HETATM 22 C C2D AR6 . . . N 2 -30.001 19.155 47.868 1 50.13 ? C2D AR6 402 B 1 HETATM 23 O O2D AR6 . . . N 2 -30.14 18.565 49.14 1 58.16 ? O2D AR6 402 B 1 HETATM 24 C C3' AR6 . . . N 2 -25.107 26.503 41.217 1 38.04 ? C3' AR6 402 B 1 HETATM 25 O O3' AR6 . . . N 2 -24.89 27.712 41.936 1 37.84 ? O3' AR6 402 B 1 HETATM 26 O O3A AR6 . . . N 2 -26.808 22.593 44.567 1 46.98 ? O3A AR6 402 B 1 HETATM 27 C C3D AR6 . . . N 2 -28.529 19.462 47.644 1 53.69 ? C3D AR6 402 B 1 HETATM 28 O O3D AR6 . . . N 2 -27.667 18.444 48.139 1 49.54 ? O3D AR6 402 B 1 HETATM 29 C C4' AR6 . . . N 2 -24.315 25.379 41.907 1 40.07 ? C4' AR6 402 B 1 HETATM 30 O O4' AR6 . . . N 2 -23.394 24.881 40.924 1 40.66 ? O4' AR6 402 B 1 HETATM 31 C C4D AR6 . . . N 2 -28.426 20.758 48.453 1 48.75 ? C4D AR6 402 B 1 HETATM 32 O O4D AR6 . . . N 2 -29.633 21.489 48.119 1 51.93 ? O4D AR6 402 B 1 HETATM 33 C C5' AR6 . . . N 2 -25.079 24.184 42.394 1 48.16 ? C5' AR6 402 B 1 HETATM 34 O O5' AR6 . . . N 2 -25.627 24.489 43.678 1 49.88 ? O5' AR6 402 B 1 HETATM 35 C C5D AR6 . . . N 2 -27.22 21.606 48.175 1 50.26 ? C5D AR6 402 B 1 HETATM 36 O O5D AR6 . . . N 2 -27.337 22.137 46.84 1 44.81 ? O5D AR6 402 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 42 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 543 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 36 #