data_6CY7 # _model_server_result.job_id eo1Iz4UDjxaHj2NOtFTFlg _model_server_result.datetime_utc '2024-10-19 03:49:52' _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 6cy7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6CY7 # _exptl.entry_id 6CY7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 658.412 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide" _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 6CY7 _cell.length_a 111.457 _cell.length_b 111.457 _cell.length_c 35.424 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6CY7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_643 y+1,x-1,-z-2 0 1 0 1 0 0 0 0 -1 111.457 -111.457 -70.848 # _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 # _chem_comp.formula 'C20 H24 N10 O12 P2' _chem_comp.formula_weight 658.412 _chem_comp.id 2BA _chem_comp.mon_nstd_flag . _chem_comp.name "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate" # 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 P O1P 2BA doub 1 n n P O2P 2BA sing 2 n n P O5' 2BA sing 3 n n P "O3'1" 2BA sing 4 n n O5' C5' 2BA sing 5 n n C5' C4' 2BA sing 6 n n C4' O4' 2BA sing 7 n n C4' C3' 2BA sing 8 n n O4' C1' 2BA sing 9 n n C3' O3' 2BA sing 10 n n C3' C2' 2BA sing 11 n n O3' P1 2BA sing 12 n n C2' O2' 2BA sing 13 n n C2' C1' 2BA sing 14 n n C1' N9 2BA sing 15 n n N9 C8 2BA sing 16 n y N9 C4 2BA sing 17 n y C8 N7 2BA doub 18 n y N7 C5 2BA sing 19 n y C5 C6 2BA doub 20 n y C5 C4 2BA sing 21 n y C6 N6 2BA sing 22 n n C6 N1 2BA sing 23 n y N1 C2 2BA doub 24 n y C2 N3 2BA sing 25 n y N3 C4 2BA doub 26 n y P1 O1P1 2BA doub 27 n n P1 O2P1 2BA sing 28 n n P1 "O5'1" 2BA sing 29 n n "O5'1" "C5'1" 2BA sing 30 n n "C5'1" "C4'1" 2BA sing 31 n n "C4'1" "O4'1" 2BA sing 32 n n "C4'1" "C3'1" 2BA sing 33 n n "O4'1" "C1'1" 2BA sing 34 n n "C3'1" "O3'1" 2BA sing 35 n n "C3'1" "C2'1" 2BA sing 36 n n "C2'1" "O2'1" 2BA sing 37 n n "C2'1" "C1'1" 2BA sing 38 n n "C1'1" N91 2BA sing 39 n n N91 C81 2BA sing 40 n y N91 C41 2BA sing 41 n y C81 N71 2BA doub 42 n y N71 C51 2BA sing 43 n y C51 C61 2BA doub 44 n y C51 C41 2BA sing 45 n y C61 N61 2BA sing 46 n n C61 N11 2BA sing 47 n y N11 C21 2BA doub 48 n y C21 N31 2BA sing 49 n y N31 C41 2BA doub 50 n y C5' H5' 2BA sing 51 n n C5' "H5'A" 2BA sing 52 n n C4' H4' 2BA sing 53 n n C3' H3' 2BA sing 54 n n C2' H2' 2BA sing 55 n n O2' HO2' 2BA sing 56 n n C1' H1' 2BA sing 57 n n C8 H8 2BA sing 58 n n N6 HN6 2BA sing 59 n n N6 HN6A 2BA sing 60 n n C2 H2 2BA sing 61 n n "C5'1" HC5' 2BA sing 62 n n "C5'1" HC5A 2BA sing 63 n n "C4'1" HC4' 2BA sing 64 n n "C3'1" HC3' 2BA sing 65 n n "C2'1" HC2' 2BA sing 66 n n "O2'1" HO2A 2BA sing 67 n n "C1'1" HC1' 2BA sing 68 n n C81 HC8 2BA sing 69 n n N61 H1N6 2BA sing 70 n n N61 H1NA 2BA sing 71 n n C21 HC2 2BA sing 72 n n O2P H2P 2BA sing 73 n n O2P1 H2OP 2BA sing 74 n n # _atom_sites.entry_id 6CY7 _atom_sites.fract_transf_matrix[1][1] 0.008972 _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] 0.008972 _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] 0.028229 _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 2BA A 1 401 401 2BA SED . C 3 IMD A 1 402 403 IMD IMD . D 4 GOL A 1 403 402 GOL GOL . E 5 HOH A 1 501 19 HOH HOH . E 5 HOH A 2 502 5 HOH HOH . E 5 HOH A 3 503 58 HOH HOH . E 5 HOH A 4 504 63 HOH HOH . E 5 HOH A 5 505 27 HOH HOH . E 5 HOH A 6 506 14 HOH HOH . E 5 HOH A 7 507 6 HOH HOH . E 5 HOH A 8 508 12 HOH HOH . E 5 HOH A 9 509 61 HOH HOH . E 5 HOH A 10 510 28 HOH HOH . E 5 HOH A 11 511 31 HOH HOH . E 5 HOH A 12 512 11 HOH HOH . E 5 HOH A 13 513 10 HOH HOH . E 5 HOH A 14 514 1 HOH HOH . E 5 HOH A 15 515 30 HOH HOH . E 5 HOH A 16 516 26 HOH HOH . E 5 HOH A 17 517 54 HOH HOH . E 5 HOH A 18 518 22 HOH HOH . E 5 HOH A 19 519 4 HOH HOH . E 5 HOH A 20 520 2 HOH HOH . E 5 HOH A 21 521 34 HOH HOH . E 5 HOH A 22 522 46 HOH HOH . E 5 HOH A 23 523 65 HOH HOH . E 5 HOH A 24 524 13 HOH HOH . E 5 HOH A 25 525 25 HOH HOH . E 5 HOH A 26 526 9 HOH HOH . E 5 HOH A 27 527 7 HOH HOH . E 5 HOH A 28 528 20 HOH HOH . E 5 HOH A 29 529 44 HOH HOH . E 5 HOH A 30 530 64 HOH HOH . E 5 HOH A 31 531 16 HOH HOH . E 5 HOH A 32 532 52 HOH HOH . E 5 HOH A 33 533 24 HOH HOH . E 5 HOH A 34 534 38 HOH HOH . E 5 HOH A 35 535 47 HOH HOH . E 5 HOH A 36 536 48 HOH HOH . E 5 HOH A 37 537 60 HOH HOH . E 5 HOH A 38 538 62 HOH HOH . E 5 HOH A 39 539 42 HOH HOH . E 5 HOH A 40 540 8 HOH HOH . E 5 HOH A 41 541 66 HOH HOH . E 5 HOH A 42 542 18 HOH HOH . E 5 HOH A 43 543 33 HOH HOH . E 5 HOH A 44 544 37 HOH HOH . E 5 HOH A 45 545 49 HOH HOH . E 5 HOH A 46 546 40 HOH HOH . E 5 HOH A 47 547 68 HOH HOH . E 5 HOH A 48 548 39 HOH HOH . E 5 HOH A 49 549 17 HOH HOH . E 5 HOH A 50 550 43 HOH HOH . E 5 HOH A 51 551 67 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 P 2BA . . . B 2 133.732 19.984 -37.883 1 36.64 ? P 2BA 401 A 1 HETATM 2 O O1P 2BA . . . B 2 134.698 20.411 -38.875 1 37.23 ? O1P 2BA 401 A 1 HETATM 3 O O2P 2BA . . . B 2 133.176 18.57 -37.909 1 43.42 ? O2P 2BA 401 A 1 HETATM 4 O O5' 2BA . . . B 2 132.59 21.054 -37.519 1 35.75 ? O5' 2BA 401 A 1 HETATM 5 C C5' 2BA . . . B 2 132.938 22.461 -37.472 1 33.45 ? C5' 2BA 401 A 1 HETATM 6 C C4' 2BA . . . B 2 131.721 23.218 -37.008 1 35.11 ? C4' 2BA 401 A 1 HETATM 7 O O4' 2BA . . . B 2 130.643 22.932 -37.858 1 30.69 ? O4' 2BA 401 A 1 HETATM 8 C C3' 2BA . . . B 2 131.349 22.899 -35.586 1 31.91 ? C3' 2BA 401 A 1 HETATM 9 O O3' 2BA . . . B 2 131.648 23.217 -34.278 1 31.88 ? O3' 2BA 401 A 1 HETATM 10 C C2' 2BA . . . B 2 129.829 23.16 -35.642 1 36.55 ? C2' 2BA 401 A 1 HETATM 11 O O2' 2BA . . . B 2 129.313 24.429 -35.135 1 40.9 ? O2' 2BA 401 A 1 HETATM 12 C C1' 2BA . . . B 2 129.425 22.894 -37.07 1 39.39 ? C1' 2BA 401 A 1 HETATM 13 N N9 2BA . . . B 2 128.803 21.563 -37.054 1 39.66 ? N9 2BA 401 A 1 HETATM 14 C C8 2BA . . . B 2 129.412 20.441 -37.481 1 38.42 ? C8 2BA 401 A 1 HETATM 15 N N7 2BA . . . B 2 128.582 19.421 -37.384 1 34.96 ? N7 2BA 401 A 1 HETATM 16 C C5 2BA . . . B 2 127.428 19.916 -36.867 1 37.75 ? C5 2BA 401 A 1 HETATM 17 C C6 2BA . . . B 2 126.167 19.332 -36.434 1 41.31 ? C6 2BA 401 A 1 HETATM 18 N N6 2BA . . . B 2 125.96 18.007 -36.623 1 45.62 ? N6 2BA 401 A 1 HETATM 19 N N1 2BA . . . B 2 125.223 20.158 -35.926 1 45.31 ? N1 2BA 401 A 1 HETATM 20 C C2 2BA . . . B 2 125.442 21.494 -35.787 1 44.69 ? C2 2BA 401 A 1 HETATM 21 N N3 2BA . . . B 2 126.583 22.063 -36.148 1 44.77 ? N3 2BA 401 A 1 HETATM 22 C C4 2BA . . . B 2 127.593 21.313 -36.627 1 39.53 ? C4 2BA 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 22 #