data_8BL1 # _model_server_result.job_id VMwJ4FlFE4lW6J9fQ-bufg _model_server_result.datetime_utc '2025-01-10 08:52:40' _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 8bl1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8BL1 # _exptl.entry_id 8BL1 _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 8BL1 _cell.length_a 91.688 _cell.length_b 91.688 _cell.length_c 144.35 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BL1 _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,V 1 1 B,M,N,O,P,Q,R,S,T,U,W 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 M 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? # _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 8BL1 _atom_sites.fract_transf_matrix[1][1] 0.010907 _atom_sites.fract_transf_matrix[1][2] 0.006297 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012594 _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] 0.006928 _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 QY3 A 1 403 502 QY3 LIG . F 5 PEG A 1 404 503 PEG PEG . G 6 SO4 A 1 405 3 SO4 SO4 . H 6 SO4 A 1 406 4 SO4 SO4 . I 6 SO4 A 1 407 5 SO4 SO4 . J 6 SO4 A 1 408 7 SO4 SO4 . K 7 CL A 1 409 1 CL CL . L 7 CL A 1 410 2 CL CL . M 2 AR6 B 1 401 500 AR6 AR6 . N 3 ZN B 1 402 501 ZN ZN . O 5 PEG B 1 403 503 PEG PEG . P 4 QY3 B 1 404 504 QY3 LIG . Q 6 SO4 B 1 405 1 SO4 SO4 . R 6 SO4 B 1 406 2 SO4 SO4 . S 6 SO4 B 1 407 6 SO4 SO4 . T 6 SO4 B 1 408 8 SO4 SO4 . U 7 CL B 1 409 3 CL CL . V 8 HOH A 1 501 66 HOH HOH . V 8 HOH A 2 502 30 HOH HOH . V 8 HOH A 3 503 6 HOH HOH . V 8 HOH A 4 504 17 HOH HOH . V 8 HOH A 5 505 59 HOH HOH . V 8 HOH A 6 506 43 HOH HOH . V 8 HOH A 7 507 35 HOH HOH . V 8 HOH A 8 508 60 HOH HOH . V 8 HOH A 9 509 14 HOH HOH . V 8 HOH A 10 510 9 HOH HOH . V 8 HOH A 11 511 2 HOH HOH . V 8 HOH A 12 512 41 HOH HOH . V 8 HOH A 13 513 11 HOH HOH . V 8 HOH A 14 514 7 HOH HOH . V 8 HOH A 15 515 12 HOH HOH . V 8 HOH A 16 516 5 HOH HOH . V 8 HOH A 17 517 20 HOH HOH . V 8 HOH A 18 518 16 HOH HOH . V 8 HOH A 19 519 13 HOH HOH . V 8 HOH A 20 520 34 HOH HOH . V 8 HOH A 21 521 1 HOH HOH . V 8 HOH A 22 522 55 HOH HOH . V 8 HOH A 23 523 10 HOH HOH . V 8 HOH A 24 524 70 HOH HOH . V 8 HOH A 25 525 23 HOH HOH . V 8 HOH A 26 526 72 HOH HOH . V 8 HOH A 27 527 63 HOH HOH . V 8 HOH A 28 528 76 HOH HOH . V 8 HOH A 29 529 40 HOH HOH . V 8 HOH A 30 530 77 HOH HOH . V 8 HOH A 31 531 8 HOH HOH . V 8 HOH A 32 532 26 HOH HOH . V 8 HOH A 33 533 64 HOH HOH . V 8 HOH A 34 534 56 HOH HOH . V 8 HOH A 35 535 74 HOH HOH . V 8 HOH A 36 536 39 HOH HOH . V 8 HOH A 37 537 27 HOH HOH . V 8 HOH A 38 538 67 HOH HOH . V 8 HOH A 39 539 51 HOH HOH . V 8 HOH A 40 540 65 HOH HOH . V 8 HOH A 41 541 57 HOH HOH . V 8 HOH A 42 542 68 HOH HOH . W 8 HOH B 1 501 69 HOH HOH . W 8 HOH B 2 502 18 HOH HOH . W 8 HOH B 3 503 50 HOH HOH . W 8 HOH B 4 504 58 HOH HOH . W 8 HOH B 5 505 62 HOH HOH . W 8 HOH B 6 506 49 HOH HOH . W 8 HOH B 7 507 45 HOH HOH . W 8 HOH B 8 508 46 HOH HOH . W 8 HOH B 9 509 33 HOH HOH . W 8 HOH B 10 510 19 HOH HOH . W 8 HOH B 11 511 44 HOH HOH . W 8 HOH B 12 512 47 HOH HOH . W 8 HOH B 13 513 15 HOH HOH . W 8 HOH B 14 514 4 HOH HOH . W 8 HOH B 15 515 29 HOH HOH . W 8 HOH B 16 516 61 HOH HOH . W 8 HOH B 17 517 3 HOH HOH . W 8 HOH B 18 518 25 HOH HOH . W 8 HOH B 19 519 54 HOH HOH . W 8 HOH B 20 520 48 HOH HOH . W 8 HOH B 21 521 52 HOH HOH . W 8 HOH B 22 522 37 HOH HOH . W 8 HOH B 23 523 71 HOH HOH . W 8 HOH B 24 524 31 HOH HOH . W 8 HOH B 25 525 28 HOH HOH . W 8 HOH B 26 526 42 HOH HOH . W 8 HOH B 27 527 38 HOH HOH . W 8 HOH B 28 528 32 HOH HOH . W 8 HOH B 29 529 24 HOH HOH . W 8 HOH B 30 530 22 HOH HOH . W 8 HOH B 31 531 75 HOH HOH . W 8 HOH B 32 532 21 HOH HOH . W 8 HOH B 33 533 36 HOH HOH . W 8 HOH B 34 534 53 HOH HOH . W 8 HOH B 35 535 73 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 2 -29.903 9.701 24.445 1 31.08 ? N1 AR6 401 A 1 HETATM 2 C C2 AR6 . . . C 2 -30.614 9.53 23.32 1 26.9 ? C2 AR6 401 A 1 HETATM 3 N N3 AR6 . . . C 2 -31.244 10.424 22.584 1 31.82 ? N3 AR6 401 A 1 HETATM 4 C C4 AR6 . . . C 2 -31.051 11.658 23.088 1 31.06 ? C4 AR6 401 A 1 HETATM 5 C C5 AR6 . . . C 2 -30.354 11.993 24.228 1 29.39 ? C5 AR6 401 A 1 HETATM 6 C C6 AR6 . . . C 2 -29.723 10.943 24.93 1 28.63 ? C6 AR6 401 A 1 HETATM 7 N N6 AR6 . . . C 2 -28.96 11.088 26.021 1 29.29 ? N6 AR6 401 A 1 HETATM 8 N N7 AR6 . . . C 2 -30.403 13.371 24.419 1 32.33 ? N7 AR6 401 A 1 HETATM 9 C C8 AR6 . . . C 2 -31.121 13.822 23.42 1 32.68 ? C8 AR6 401 A 1 HETATM 10 N N9 AR6 . . . C 2 -31.56 12.827 22.593 1 28.91 ? N9 AR6 401 A 1 HETATM 11 P PA AR6 . . . C 2 -31.985 17.247 17.285 1 34.2 ? PA AR6 401 A 1 HETATM 12 P PB AR6 . . . C 2 -29.92 16.961 15.251 1 27.37 ? PB AR6 401 A 1 HETATM 13 C C1' AR6 . . . C 2 -32.376 12.946 21.379 1 27.62 ? C1' AR6 401 A 1 HETATM 14 O O1A AR6 . . . C 2 -32.941 17.558 16.188 1 36.88 ? O1A AR6 401 A 1 HETATM 15 O O1B AR6 . . . C 2 -28.52 16.453 15.365 1 28.08 ? O1B AR6 401 A 1 HETATM 16 C C1D AR6 . . . C 2 -29.922 21.846 13.659 1 27.99 ? C1D AR6 401 A 1 HETATM 17 O O1D AR6 . . . C 2 -30.572 22.983 13.094 1 26.71 ? O1D AR6 401 A 1 HETATM 18 C C2' AR6 . . . C 2 -33.451 14.019 21.394 1 23.58 ? C2' AR6 401 A 1 HETATM 19 O O2' AR6 . . . C 2 -34.668 13.475 21.818 1 21.58 ? O2' AR6 401 A 1 HETATM 20 O O2A AR6 . . . C 2 -31.992 18.019 18.578 1 30.1 ? O2A AR6 401 A 1 HETATM 21 O O2B AR6 . . . C 2 -30.901 15.959 14.745 1 23.2 ? O2B AR6 401 A 1 HETATM 22 C C2D AR6 . . . C 2 -28.402 21.832 13.453 1 29.09 ? C2D AR6 401 A 1 HETATM 23 O O2D AR6 . . . C 2 -28.055 22.271 12.166 1 30.88 ? O2D AR6 401 A 1 HETATM 24 C C3' AR6 . . . C 2 -33.53 14.491 19.93 1 24.96 ? C3' AR6 401 A 1 HETATM 25 O O3' AR6 . . . C 2 -34.672 13.983 19.276 1 20.11 ? O3' AR6 401 A 1 HETATM 26 O O3A AR6 . . . C 2 -30.476 17.444 16.705 1 29.43 ? O3A AR6 401 A 1 HETATM 27 C C3D AR6 . . . C 2 -28.055 20.338 13.546 1 29.57 ? C3D AR6 401 A 1 HETATM 28 O O3D AR6 . . . C 2 -26.815 19.964 12.948 1 26.26 ? O3D AR6 401 A 1 HETATM 29 C C4' AR6 . . . C 2 -32.221 14.006 19.294 1 26.75 ? C4' AR6 401 A 1 HETATM 30 O O4' AR6 . . . C 2 -31.507 13.301 20.337 1 25.46 ? O4' AR6 401 A 1 HETATM 31 C C4D AR6 . . . C 2 -29.224 19.764 12.744 1 27.4 ? C4D AR6 401 A 1 HETATM 32 O O4D AR6 . . . C 2 -30.351 20.645 12.991 1 27.15 ? O4D AR6 401 A 1 HETATM 33 C C5' AR6 . . . C 2 -31.344 15.096 18.738 1 28.28 ? C5' AR6 401 A 1 HETATM 34 O O5' AR6 . . . C 2 -32.036 15.689 17.575 1 30.94 ? O5' AR6 401 A 1 HETATM 35 C C5D AR6 . . . C 2 -29.634 18.35 13.061 1 33.85 ? C5D AR6 401 A 1 HETATM 36 O O5D AR6 . . . C 2 -30 18.325 14.452 1 31.18 ? O5D AR6 401 A 1 # _model_server_stats.io_time_ms 116 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #