data_4YXM # _model_server_result.job_id P2RlpXZKaAgYV6T61-ZZ_A _model_server_result.datetime_utc '2024-11-19 10:20:22' _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 4yxm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4YXM # _exptl.entry_id 4YXM _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 4YXM _cell.length_a 108.55 _cell.length_b 108.55 _cell.length_c 165.92 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YXM _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -108.55 0 3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -54.275 -54.275 0 4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 54.275 -54.275 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 4YXM _atom_sites.fract_transf_matrix[1][1] 0.009212 _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] 0.009212 _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] 0.006027 _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 2BA B 1 401 1 2BA 2BA . D 3 MPD B 1 402 1 MPD MPD . E 4 HOH A 1 401 67 HOH HOH . E 4 HOH A 2 402 72 HOH HOH . E 4 HOH A 3 403 33 HOH HOH . E 4 HOH A 4 404 133 HOH HOH . E 4 HOH A 5 405 139 HOH HOH . E 4 HOH A 6 406 134 HOH HOH . E 4 HOH A 7 407 77 HOH HOH . E 4 HOH A 8 408 34 HOH HOH . E 4 HOH A 9 409 112 HOH HOH . E 4 HOH A 10 410 22 HOH HOH . E 4 HOH A 11 411 59 HOH HOH . E 4 HOH A 12 412 20 HOH HOH . E 4 HOH A 13 413 16 HOH HOH . E 4 HOH A 14 414 45 HOH HOH . E 4 HOH A 15 415 40 HOH HOH . E 4 HOH A 16 416 36 HOH HOH . E 4 HOH A 17 417 51 HOH HOH . E 4 HOH A 18 418 10 HOH HOH . E 4 HOH A 19 419 30 HOH HOH . E 4 HOH A 20 420 26 HOH HOH . E 4 HOH A 21 421 88 HOH HOH . E 4 HOH A 22 422 37 HOH HOH . E 4 HOH A 23 423 62 HOH HOH . E 4 HOH A 24 424 14 HOH HOH . E 4 HOH A 25 425 6 HOH HOH . E 4 HOH A 26 426 11 HOH HOH . E 4 HOH A 27 427 21 HOH HOH . E 4 HOH A 28 428 28 HOH HOH . E 4 HOH A 29 429 2 HOH HOH . E 4 HOH A 30 430 48 HOH HOH . E 4 HOH A 31 431 132 HOH HOH . E 4 HOH A 32 432 66 HOH HOH . E 4 HOH A 33 433 18 HOH HOH . E 4 HOH A 34 434 53 HOH HOH . E 4 HOH A 35 435 140 HOH HOH . E 4 HOH A 36 436 70 HOH HOH . E 4 HOH A 37 437 65 HOH HOH . E 4 HOH A 38 438 8 HOH HOH . E 4 HOH A 39 439 104 HOH HOH . E 4 HOH A 40 440 128 HOH HOH . E 4 HOH A 41 441 54 HOH HOH . E 4 HOH A 42 442 123 HOH HOH . E 4 HOH A 43 443 23 HOH HOH . E 4 HOH A 44 444 89 HOH HOH . E 4 HOH A 45 445 105 HOH HOH . E 4 HOH A 46 446 86 HOH HOH . E 4 HOH A 47 447 94 HOH HOH . E 4 HOH A 48 448 55 HOH HOH . E 4 HOH A 49 449 24 HOH HOH . E 4 HOH A 50 450 129 HOH HOH . E 4 HOH A 51 451 58 HOH HOH . E 4 HOH A 52 452 137 HOH HOH . E 4 HOH A 53 453 113 HOH HOH . E 4 HOH A 54 454 125 HOH HOH . E 4 HOH A 55 455 127 HOH HOH . E 4 HOH A 56 456 108 HOH HOH . E 4 HOH A 57 457 46 HOH HOH . E 4 HOH A 58 458 50 HOH HOH . E 4 HOH A 59 459 96 HOH HOH . E 4 HOH A 60 460 56 HOH HOH . E 4 HOH A 61 461 97 HOH HOH . E 4 HOH A 62 462 101 HOH HOH . E 4 HOH A 63 463 35 HOH HOH . E 4 HOH A 64 464 43 HOH HOH . E 4 HOH A 65 465 31 HOH HOH . E 4 HOH A 66 466 82 HOH HOH . E 4 HOH A 67 467 135 HOH HOH . E 4 HOH A 68 468 76 HOH HOH . E 4 HOH A 69 469 121 HOH HOH . E 4 HOH A 70 470 131 HOH HOH . E 4 HOH A 71 471 138 HOH HOH . E 4 HOH A 72 472 87 HOH HOH . E 4 HOH A 73 473 78 HOH HOH . E 4 HOH A 74 474 114 HOH HOH . E 4 HOH A 75 475 136 HOH HOH . E 4 HOH A 76 476 99 HOH HOH . E 4 HOH A 77 477 130 HOH HOH . E 4 HOH A 78 478 80 HOH HOH . F 4 HOH B 1 501 152 HOH HOH . F 4 HOH B 2 502 141 HOH HOH . F 4 HOH B 3 503 19 HOH HOH . F 4 HOH B 4 504 144 HOH HOH . F 4 HOH B 5 505 15 HOH HOH . F 4 HOH B 6 506 85 HOH HOH . F 4 HOH B 7 507 106 HOH HOH . F 4 HOH B 8 508 69 HOH HOH . F 4 HOH B 9 509 61 HOH HOH . F 4 HOH B 10 510 42 HOH HOH . F 4 HOH B 11 511 117 HOH HOH . F 4 HOH B 12 512 83 HOH HOH . F 4 HOH B 13 513 3 HOH HOH . F 4 HOH B 14 514 9 HOH HOH . F 4 HOH B 15 515 41 HOH HOH . F 4 HOH B 16 516 13 HOH HOH . F 4 HOH B 17 517 1 HOH HOH . F 4 HOH B 18 518 44 HOH HOH . F 4 HOH B 19 519 150 HOH HOH . F 4 HOH B 20 520 27 HOH HOH . F 4 HOH B 21 521 90 HOH HOH . F 4 HOH B 22 522 29 HOH HOH . F 4 HOH B 23 523 98 HOH HOH . F 4 HOH B 24 524 17 HOH HOH . F 4 HOH B 25 525 49 HOH HOH . F 4 HOH B 26 526 147 HOH HOH . F 4 HOH B 27 527 109 HOH HOH . F 4 HOH B 28 528 124 HOH HOH . F 4 HOH B 29 529 38 HOH HOH . F 4 HOH B 30 530 64 HOH HOH . F 4 HOH B 31 531 75 HOH HOH . F 4 HOH B 32 532 4 HOH HOH . F 4 HOH B 33 533 39 HOH HOH . F 4 HOH B 34 534 60 HOH HOH . F 4 HOH B 35 535 5 HOH HOH . F 4 HOH B 36 536 73 HOH HOH . F 4 HOH B 37 537 84 HOH HOH . F 4 HOH B 38 538 148 HOH HOH . F 4 HOH B 39 539 63 HOH HOH . F 4 HOH B 40 540 47 HOH HOH . F 4 HOH B 41 541 57 HOH HOH . F 4 HOH B 42 542 25 HOH HOH . F 4 HOH B 43 543 74 HOH HOH . F 4 HOH B 44 544 93 HOH HOH . F 4 HOH B 45 545 120 HOH HOH . F 4 HOH B 46 546 32 HOH HOH . F 4 HOH B 47 547 122 HOH HOH . F 4 HOH B 48 548 12 HOH HOH . F 4 HOH B 49 549 52 HOH HOH . F 4 HOH B 50 550 149 HOH HOH . F 4 HOH B 51 551 7 HOH HOH . F 4 HOH B 52 552 71 HOH HOH . F 4 HOH B 53 553 126 HOH HOH . F 4 HOH B 54 554 151 HOH HOH . F 4 HOH B 55 555 110 HOH HOH . F 4 HOH B 56 556 153 HOH HOH . F 4 HOH B 57 557 118 HOH HOH . F 4 HOH B 58 558 143 HOH HOH . F 4 HOH B 59 559 119 HOH HOH . F 4 HOH B 60 560 145 HOH HOH . F 4 HOH B 61 561 81 HOH HOH . F 4 HOH B 62 562 142 HOH HOH . F 4 HOH B 63 563 68 HOH HOH . F 4 HOH B 64 564 111 HOH HOH . F 4 HOH B 65 565 146 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 . . . C 2 13.924 -40.304 -37.952 1 131.42 ? P 2BA 401 B 1 HETATM 2 O O1P 2BA . . . C 2 15.305 -39.932 -37.502 1 95.98 ? O1P 2BA 401 B 1 HETATM 3 O O2P 2BA . . . C 2 13.445 -41.468 -37.015 1 62.75 ? O2P 2BA 401 B 1 HETATM 4 O O5' 2BA . . . C 2 13.065 -38.982 -37.793 1 52 ? O5' 2BA 401 B 1 HETATM 5 C C5' 2BA . . . C 2 11.779 -39.088 -37.221 1 53.41 ? C5' 2BA 401 B 1 HETATM 6 C C4' 2BA . . . C 2 10.879 -37.814 -37.421 1 37.56 ? C4' 2BA 401 B 1 HETATM 7 O O4' 2BA . . . C 2 11.168 -36.901 -36.496 1 50.9 ? O4' 2BA 401 B 1 HETATM 8 C C3' 2BA . . . C 2 11.035 -37.096 -38.738 1 46.48 ? C3' 2BA 401 B 1 HETATM 9 O O3' 2BA . . . C 2 10.295 -37.732 -39.705 1 50.93 ? O3' 2BA 401 B 1 HETATM 10 C C2' 2BA . . . C 2 10.367 -35.724 -38.323 1 52.49 ? C2' 2BA 401 B 1 HETATM 11 O O2' 2BA . . . C 2 8.938 -35.842 -38.574 1 47.2 ? O2' 2BA 401 B 1 HETATM 12 C C1' 2BA . . . C 2 10.645 -35.496 -37.062 1 43.48 ? C1' 2BA 401 B 1 HETATM 13 N N9 2BA . . . C 2 11.648 -34.487 -37.084 1 44.36 ? N9 2BA 401 B 1 HETATM 14 C C8 2BA . . . C 2 12.884 -35.003 -36.946 1 42.6 ? C8 2BA 401 B 1 HETATM 15 N N7 2BA . . . C 2 13.798 -33.986 -37.029 1 39.64 ? N7 2BA 401 B 1 HETATM 16 C C5 2BA . . . C 2 13.103 -32.829 -37.238 1 39.3 ? C5 2BA 401 B 1 HETATM 17 C C6 2BA . . . C 2 13.505 -31.485 -37.413 1 43.4 ? C6 2BA 401 B 1 HETATM 18 N N6 2BA . . . C 2 14.797 -30.88 -37.433 1 40.36 ? N6 2BA 401 B 1 HETATM 19 N N1 2BA . . . C 2 12.589 -30.531 -37.612 1 40.02 ? N1 2BA 401 B 1 HETATM 20 C C2 2BA . . . C 2 11.266 -30.841 -37.635 1 39.67 ? C2 2BA 401 B 1 HETATM 21 N N3 2BA . . . C 2 10.874 -32.153 -37.477 1 39.14 ? N3 2BA 401 B 1 HETATM 22 C C4 2BA . . . C 2 11.794 -33.129 -37.282 1 38.96 ? C4 2BA 401 B 1 HETATM 23 P P1 2BA . . . C 2 10.753 -37.617 -41.265 1 63.25 ? P1 2BA 401 B 1 HETATM 24 O O1P1 2BA . . . C 2 10.953 -36.165 -41.643 1 49.43 ? O1P1 2BA 401 B 1 HETATM 25 O O2P1 2BA . . . C 2 9.766 -38.157 -42.269 1 68.97 ? O2P1 2BA 401 B 1 HETATM 26 O "O5'1" 2BA . . . C 2 12.293 -38.3 -41.335 1 57.88 ? "O5'1" 2BA 401 B 1 HETATM 27 C "C5'1" 2BA . . . C 2 12.294 -39.633 -41.777 1 49.57 ? "C5'1" 2BA 401 B 1 HETATM 28 C "C4'1" 2BA . . . C 2 13.7 -40.156 -41.852 1 49.72 ? "C4'1" 2BA 401 B 1 HETATM 29 O "O4'1" 2BA . . . C 2 14.397 -39.554 -42.759 1 46.93 ? "O4'1" 2BA 401 B 1 HETATM 30 C "C3'1" 2BA . . . C 2 14.523 -39.865 -40.461 1 46.49 ? "C3'1" 2BA 401 B 1 HETATM 31 O "O3'1" 2BA . . . C 2 14.081 -40.869 -39.496 1 63.14 ? "O3'1" 2BA 401 B 1 HETATM 32 C "C2'1" 2BA . . . C 2 15.741 -40.017 -40.77 1 38.17 ? "C2'1" 2BA 401 B 1 HETATM 33 O "O2'1" 2BA . . . C 2 16.163 -41.465 -40.72 1 38.08 ? "O2'1" 2BA 401 B 1 HETATM 34 C "C1'1" 2BA . . . C 2 15.85 -39.51 -42.263 1 38.32 ? "C1'1" 2BA 401 B 1 HETATM 35 N N91 2BA . . . C 2 16.33 -38.289 -42.266 1 38.67 ? N91 2BA 401 B 1 HETATM 36 C C81 2BA . . . C 2 15.676 -37.118 -42.4 1 38.75 ? C81 2BA 401 B 1 HETATM 37 N N71 2BA . . . C 2 16.604 -36.134 -42.297 1 39.44 ? N71 2BA 401 B 1 HETATM 38 C C51 2BA . . . C 2 17.838 -36.7 -42.109 1 39.45 ? C51 2BA 401 B 1 HETATM 39 C C61 2BA . . . C 2 19.117 -36.145 -41.954 1 40 ? C61 2BA 401 B 1 HETATM 40 N N61 2BA . . . C 2 19.398 -34.73 -41.961 1 40.47 ? N61 2BA 401 B 1 HETATM 41 N N11 2BA . . . C 2 20.193 -36.954 -41.756 1 40.17 ? N11 2BA 401 B 1 HETATM 42 C C21 2BA . . . C 2 20.01 -38.305 -41.725 1 41.58 ? C21 2BA 401 B 1 HETATM 43 N N31 2BA . . . C 2 18.755 -38.851 -41.88 1 39.28 ? N31 2BA 401 B 1 HETATM 44 C C41 2BA . . . C 2 17.664 -38.035 -42.069 1 41.15 ? C41 2BA 401 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #