data_6B4Y # _model_server_result.job_id 9IkByenQDJNdd96aWM5D3w _model_server_result.datetime_utc '2024-10-20 05:33:04' _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 6b4y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6B4Y # _exptl.entry_id 6B4Y _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 6B4Y _cell.length_a 140.217 _cell.length_b 39.41 _cell.length_c 53.504 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B4Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 6B4Y _atom_sites.fract_transf_matrix[1][1] 0.007132 _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] 0.025374 _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] 0.01869 _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 1 301 301 A3P A3P . C 3 OAQ A 1 302 302 OAQ OAQ . D 4 HOH A 1 401 401 HOH HOH . D 4 HOH A 2 402 402 HOH HOH . D 4 HOH A 3 403 403 HOH HOH . D 4 HOH A 4 404 496 HOH HOH . D 4 HOH A 5 405 405 HOH HOH . D 4 HOH A 6 406 406 HOH HOH . D 4 HOH A 7 407 407 HOH HOH . D 4 HOH A 8 408 408 HOH HOH . D 4 HOH A 9 409 409 HOH HOH . D 4 HOH A 10 410 410 HOH HOH . D 4 HOH A 11 411 411 HOH HOH . D 4 HOH A 12 412 412 HOH HOH . D 4 HOH A 13 413 413 HOH HOH . D 4 HOH A 14 414 414 HOH HOH . D 4 HOH A 15 415 415 HOH HOH . D 4 HOH A 16 416 416 HOH HOH . D 4 HOH A 17 417 417 HOH HOH . D 4 HOH A 18 418 418 HOH HOH . D 4 HOH A 19 419 419 HOH HOH . D 4 HOH A 20 420 420 HOH HOH . D 4 HOH A 21 421 421 HOH HOH . D 4 HOH A 22 422 422 HOH HOH . D 4 HOH A 23 423 423 HOH HOH . D 4 HOH A 24 424 424 HOH HOH . D 4 HOH A 25 425 425 HOH HOH . D 4 HOH A 26 426 426 HOH HOH . D 4 HOH A 27 427 427 HOH HOH . D 4 HOH A 28 428 428 HOH HOH . D 4 HOH A 29 429 429 HOH HOH . D 4 HOH A 30 430 430 HOH HOH . D 4 HOH A 31 431 432 HOH HOH . D 4 HOH A 32 432 433 HOH HOH . D 4 HOH A 33 433 434 HOH HOH . D 4 HOH A 34 434 435 HOH HOH . D 4 HOH A 35 435 436 HOH HOH . D 4 HOH A 36 436 437 HOH HOH . D 4 HOH A 37 437 438 HOH HOH . D 4 HOH A 38 438 439 HOH HOH . D 4 HOH A 39 439 440 HOH HOH . D 4 HOH A 40 440 441 HOH HOH . D 4 HOH A 41 441 442 HOH HOH . D 4 HOH A 42 442 443 HOH HOH . D 4 HOH A 43 443 444 HOH HOH . D 4 HOH A 44 444 445 HOH HOH . D 4 HOH A 45 445 446 HOH HOH . D 4 HOH A 46 446 447 HOH HOH . D 4 HOH A 47 447 448 HOH HOH . D 4 HOH A 48 448 449 HOH HOH . D 4 HOH A 49 449 450 HOH HOH . D 4 HOH A 50 450 451 HOH HOH . D 4 HOH A 51 451 452 HOH HOH . D 4 HOH A 52 452 431 HOH HOH . D 4 HOH A 53 453 453 HOH HOH . D 4 HOH A 54 454 454 HOH HOH . D 4 HOH A 55 455 455 HOH HOH . D 4 HOH A 56 456 456 HOH HOH . D 4 HOH A 57 457 457 HOH HOH . D 4 HOH A 58 458 458 HOH HOH . D 4 HOH A 59 459 459 HOH HOH . D 4 HOH A 60 460 460 HOH HOH . D 4 HOH A 61 461 461 HOH HOH . D 4 HOH A 62 462 462 HOH HOH . D 4 HOH A 63 463 463 HOH HOH . D 4 HOH A 64 464 464 HOH HOH . D 4 HOH A 65 465 465 HOH HOH . D 4 HOH A 66 466 466 HOH HOH . D 4 HOH A 67 467 467 HOH HOH . D 4 HOH A 68 468 468 HOH HOH . D 4 HOH A 69 469 469 HOH HOH . D 4 HOH A 70 470 470 HOH HOH . D 4 HOH A 71 471 471 HOH HOH . D 4 HOH A 72 472 472 HOH HOH . D 4 HOH A 73 473 473 HOH HOH . D 4 HOH A 74 474 474 HOH HOH . D 4 HOH A 75 475 475 HOH HOH . D 4 HOH A 76 476 476 HOH HOH . D 4 HOH A 77 477 477 HOH HOH . D 4 HOH A 78 478 478 HOH HOH . D 4 HOH A 79 479 479 HOH HOH . D 4 HOH A 80 480 480 HOH HOH . D 4 HOH A 81 481 481 HOH HOH . D 4 HOH A 82 482 482 HOH HOH . D 4 HOH A 83 483 483 HOH HOH . D 4 HOH A 84 484 484 HOH HOH . D 4 HOH A 85 485 485 HOH HOH . D 4 HOH A 86 486 486 HOH HOH . D 4 HOH A 87 487 487 HOH HOH . D 4 HOH A 88 488 488 HOH HOH . D 4 HOH A 89 489 489 HOH HOH . D 4 HOH A 90 490 490 HOH HOH . D 4 HOH A 91 491 493 HOH HOH . D 4 HOH A 92 492 491 HOH HOH . D 4 HOH A 93 493 492 HOH HOH . D 4 HOH A 94 494 494 HOH HOH . D 4 HOH A 95 495 495 HOH HOH . D 4 HOH A 96 496 404 HOH HOH . D 4 HOH A 97 497 497 HOH HOH . D 4 HOH A 98 498 498 HOH HOH . D 4 HOH A 99 499 499 HOH HOH . D 4 HOH A 100 500 500 HOH HOH . D 4 HOH A 101 501 501 HOH HOH . D 4 HOH A 102 502 502 HOH HOH . D 4 HOH A 103 503 503 HOH HOH . D 4 HOH A 104 504 504 HOH HOH . D 4 HOH A 105 505 505 HOH HOH . D 4 HOH A 106 506 506 HOH HOH . D 4 HOH A 107 507 507 HOH HOH . D 4 HOH A 108 508 508 HOH HOH . D 4 HOH A 109 509 509 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 2 110.065 -3.896 13.807 1 35.29 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . B 2 109.671 -4.666 12.581 1 33.07 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . B 2 109.405 -2.526 13.831 1 35.07 ? O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . B 2 109.711 -4.634 15.061 1 35.13 ? O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . B 2 115.413 1.057 14.111 1 33.25 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . B 2 116.427 1.384 13.04 1 33.96 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . B 2 115.935 1.125 15.512 1 29.43 ? O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . B 2 114.223 1.992 14.023 1 32.63 ? O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . B 2 114.953 -0.451 13.847 1 35.4 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . B 2 113.958 -1.046 14.693 1 31.27 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . B 2 113.6 -2.392 14.107 1 32.22 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . B 2 114.711 -3.304 14.283 1 31.08 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . B 2 112.411 -3.038 14.754 1 27.41 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . B 2 111.679 -3.746 13.753 1 33.92 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . B 2 113.005 -3.991 15.707 1 32.92 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . B 2 112.109 -5.062 15.924 1 34.67 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . B 2 114.18 -4.472 14.933 1 36.5 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . B 2 115.219 -4.98 15.727 1 35.71 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . B 2 115.987 -4.26 16.54 1 32.97 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . B 2 116.888 -5.053 17.121 1 35.09 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . B 2 116.694 -6.321 16.669 1 38.59 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . B 2 117.337 -7.566 16.913 1 39.48 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . B 2 118.417 -7.64 17.806 1 39.34 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . B 2 116.883 -8.649 16.28 1 38.03 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . B 2 115.858 -8.587 15.434 1 39.51 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . B 2 115.235 -7.436 15.168 1 40.18 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . B 2 115.623 -6.282 15.765 1 36.21 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #