data_8XGZ # _model_server_result.job_id 1LDp6S7TFnApEYCDliixQA _model_server_result.datetime_utc '2024-12-25 07:50:03' _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 8xgz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 8XGZ # _exptl.entry_id 8XGZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 8XGZ _cell.length_a 77.719 _cell.length_b 77.719 _cell.length_c 141.209 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XGZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 8XGZ _atom_sites.fract_transf_matrix[1][1] 0.012867 _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] 0.012867 _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] 0.007082 _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 A3P A 1 301 307 A3P A3P . C 3 HOH A 1 401 112 HOH HOH . C 3 HOH A 2 402 54 HOH HOH . C 3 HOH A 3 403 77 HOH HOH . C 3 HOH A 4 404 41 HOH HOH . C 3 HOH A 5 405 99 HOH HOH . C 3 HOH A 6 406 42 HOH HOH . C 3 HOH A 7 407 109 HOH HOH . C 3 HOH A 8 408 102 HOH HOH . C 3 HOH A 9 409 2 HOH HOH . C 3 HOH A 10 410 14 HOH HOH . C 3 HOH A 11 411 72 HOH HOH . C 3 HOH A 12 412 71 HOH HOH . C 3 HOH A 13 413 26 HOH HOH . C 3 HOH A 14 414 20 HOH HOH . C 3 HOH A 15 415 38 HOH HOH . C 3 HOH A 16 416 36 HOH HOH . C 3 HOH A 17 417 13 HOH HOH . C 3 HOH A 18 418 45 HOH HOH . C 3 HOH A 19 419 64 HOH HOH . C 3 HOH A 20 420 93 HOH HOH . C 3 HOH A 21 421 59 HOH HOH . C 3 HOH A 22 422 23 HOH HOH . C 3 HOH A 23 423 37 HOH HOH . C 3 HOH A 24 424 25 HOH HOH . C 3 HOH A 25 425 31 HOH HOH . C 3 HOH A 26 426 32 HOH HOH . C 3 HOH A 27 427 51 HOH HOH . C 3 HOH A 28 428 34 HOH HOH . C 3 HOH A 29 429 5 HOH HOH . C 3 HOH A 30 430 73 HOH HOH . C 3 HOH A 31 431 39 HOH HOH . C 3 HOH A 32 432 104 HOH HOH . C 3 HOH A 33 433 43 HOH HOH . C 3 HOH A 34 434 9 HOH HOH . C 3 HOH A 35 435 22 HOH HOH . C 3 HOH A 36 436 46 HOH HOH . C 3 HOH A 37 437 17 HOH HOH . C 3 HOH A 38 438 40 HOH HOH . C 3 HOH A 39 439 53 HOH HOH . C 3 HOH A 40 440 11 HOH HOH . C 3 HOH A 41 441 63 HOH HOH . C 3 HOH A 42 442 8 HOH HOH . C 3 HOH A 43 443 19 HOH HOH . C 3 HOH A 44 444 58 HOH HOH . C 3 HOH A 45 445 47 HOH HOH . C 3 HOH A 46 446 4 HOH HOH . C 3 HOH A 47 447 27 HOH HOH . C 3 HOH A 48 448 98 HOH HOH . C 3 HOH A 49 449 48 HOH HOH . C 3 HOH A 50 450 7 HOH HOH . C 3 HOH A 51 451 24 HOH HOH . C 3 HOH A 52 452 10 HOH HOH . C 3 HOH A 53 453 97 HOH HOH . C 3 HOH A 54 454 18 HOH HOH . C 3 HOH A 55 455 1 HOH HOH . C 3 HOH A 56 456 100 HOH HOH . C 3 HOH A 57 457 3 HOH HOH . C 3 HOH A 58 458 88 HOH HOH . C 3 HOH A 59 459 62 HOH HOH . C 3 HOH A 60 460 57 HOH HOH . C 3 HOH A 61 461 70 HOH HOH . C 3 HOH A 62 462 61 HOH HOH . C 3 HOH A 63 463 33 HOH HOH . C 3 HOH A 64 464 52 HOH HOH . C 3 HOH A 65 465 87 HOH HOH . C 3 HOH A 66 466 90 HOH HOH . C 3 HOH A 67 467 6 HOH HOH . C 3 HOH A 68 468 103 HOH HOH . C 3 HOH A 69 469 49 HOH HOH . C 3 HOH A 70 470 68 HOH HOH . C 3 HOH A 71 471 101 HOH HOH . C 3 HOH A 72 472 95 HOH HOH . C 3 HOH A 73 473 96 HOH HOH . C 3 HOH A 74 474 92 HOH HOH . C 3 HOH A 75 475 12 HOH HOH . C 3 HOH A 76 476 107 HOH HOH . C 3 HOH A 77 477 79 HOH HOH . C 3 HOH A 78 478 83 HOH HOH . C 3 HOH A 79 479 94 HOH HOH . C 3 HOH A 80 480 28 HOH HOH . C 3 HOH A 81 481 78 HOH HOH . C 3 HOH A 82 482 30 HOH HOH . C 3 HOH A 83 483 108 HOH HOH . C 3 HOH A 84 484 65 HOH HOH . C 3 HOH A 85 485 15 HOH HOH . C 3 HOH A 86 486 82 HOH HOH . C 3 HOH A 87 487 21 HOH HOH . C 3 HOH A 88 488 16 HOH HOH . C 3 HOH A 89 489 84 HOH HOH . C 3 HOH A 90 490 89 HOH HOH . C 3 HOH A 91 491 80 HOH HOH . C 3 HOH A 92 492 56 HOH HOH . C 3 HOH A 93 493 91 HOH HOH . C 3 HOH A 94 494 111 HOH HOH . C 3 HOH A 95 495 44 HOH HOH . C 3 HOH A 96 496 55 HOH HOH . C 3 HOH A 97 497 69 HOH HOH . C 3 HOH A 98 498 67 HOH HOH . C 3 HOH A 99 499 86 HOH HOH . C 3 HOH A 100 500 85 HOH HOH . C 3 HOH A 101 501 50 HOH HOH . C 3 HOH A 102 502 66 HOH HOH . C 3 HOH A 103 503 35 HOH HOH . C 3 HOH A 104 504 81 HOH HOH . C 3 HOH A 105 505 113 HOH HOH . C 3 HOH A 106 506 74 HOH HOH . C 3 HOH A 107 507 106 HOH HOH . C 3 HOH A 108 508 110 HOH HOH . C 3 HOH A 109 509 75 HOH HOH . C 3 HOH A 110 510 60 HOH HOH . C 3 HOH A 111 511 105 HOH HOH . C 3 HOH A 112 512 76 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 P1 A3P . . . B 2 -18.323 5.482 -2.067 1 29.08 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . B 2 -18.533 4.167 -2.717 1 35.26 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . B 2 -19.021 5.489 -0.62 1 32.53 -1 O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . B 2 -16.745 5.751 -1.896 1 35.45 -1 O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . B 2 -22.481 7.826 -7.775 1 28.4 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . B 2 -21.995 8.501 -8.999 1 27.98 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . B 2 -22.814 6.284 -8.105 1 30.16 -1 O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . B 2 -23.804 8.566 -7.233 1 34.77 -1 O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . B 2 -21.311 7.933 -6.67 1 33.57 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . B 2 -21.565 7.084 -5.548 1 21.93 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . B 2 -20.448 7.397 -4.583 1 28.45 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . B 2 -20.65 8.719 -4.026 1 30.59 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . B 2 -20.298 6.48 -3.37 1 31.22 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . B 2 -18.91 6.664 -2.984 1 33.08 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . B 2 -21.186 7.176 -2.345 1 35.03 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . B 2 -20.895 6.803 -1.004 1 33.36 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . B 2 -20.762 8.617 -2.618 1 34.57 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . B 2 -21.687 9.637 -2.136 1 33.86 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . B 2 -23.028 9.744 -2.401 1 36.56 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . B 2 -23.607 10.77 -1.825 1 35.97 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . B 2 -22.573 11.38 -1.125 1 31.98 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . B 2 -22.527 12.52 -0.301 1 31.28 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . B 2 -23.588 13.287 -0.03 1 36.21 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . B 2 -21.334 12.855 0.243 1 33.08 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . B 2 -20.27 12.094 -0.023 1 31.85 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . B 2 -20.195 10.999 -0.783 1 36.87 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . B 2 -21.387 10.691 -1.31 1 33.25 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #