data_6LOY # _model_server_result.job_id R6c8CQIXsQELH-0A2-RUfA _model_server_result.datetime_utc '2024-11-23 04:22:43' _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 6loy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6LOY # _exptl.entry_id 6LOY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 6LOY _cell.length_a 130.667 _cell.length_b 130.667 _cell.length_c 39.23 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LOY _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 H14 N5 O6 P' _chem_comp.formula_weight 331.222 _chem_comp.id D5M _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 O5' C5' D5M sing 70 n n O5' P D5M sing 71 n n C5' C4' D5M sing 72 n n C5' "H5'1" D5M sing 73 n n C5' "H5'2" D5M sing 74 n n C4' O4' D5M sing 75 n n C4' C3' D5M sing 76 n n C4' H4' D5M sing 77 n n O4' C1' D5M sing 78 n n C3' O3' D5M sing 79 n n C3' C2' D5M sing 80 n n C3' H1 D5M sing 81 n n O3' H3' D5M sing 82 n n C2' C1' D5M sing 83 n n C2' "H2'1" D5M sing 84 n n C2' "H2'2" D5M sing 85 n n C1' N9 D5M sing 86 n n C1' H1' D5M sing 87 n n N9 C8 D5M sing 88 n y N9 C4 D5M sing 89 n y C8 N7 D5M doub 90 n y C8 H8 D5M sing 91 n n N7 C5 D5M sing 92 n y C5 C6 D5M sing 93 n y C5 C4 D5M doub 94 n y C6 N6 D5M sing 95 n n C6 N1 D5M doub 96 n y N6 HN61 D5M sing 97 n n N6 HN62 D5M sing 98 n n N1 C2 D5M sing 99 n y C2 N3 D5M doub 100 n y C2 H2 D5M sing 101 n n N3 C4 D5M sing 102 n y P O1P D5M doub 103 n n P O3P D5M sing 104 n n P O2P D5M sing 105 n n O3P H3P D5M sing 106 n n O2P H2P D5M sing 107 n n # _atom_sites.entry_id 6LOY _atom_sites.fract_transf_matrix[1][1] 0.007653 _atom_sites.fract_transf_matrix[1][2] 0.004418 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008837 _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] 0.025491 _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 D5M A 1 301 1 D5M D5M . C 3 HOH A 1 401 154 HOH HOH . C 3 HOH A 2 402 37 HOH HOH . C 3 HOH A 3 403 80 HOH HOH . C 3 HOH A 4 404 41 HOH HOH . C 3 HOH A 5 405 23 HOH HOH . C 3 HOH A 6 406 67 HOH HOH . C 3 HOH A 7 407 142 HOH HOH . C 3 HOH A 8 408 84 HOH HOH . C 3 HOH A 9 409 95 HOH HOH . C 3 HOH A 10 410 40 HOH HOH . C 3 HOH A 11 411 110 HOH HOH . C 3 HOH A 12 412 51 HOH HOH . C 3 HOH A 13 413 82 HOH HOH . C 3 HOH A 14 414 76 HOH HOH . C 3 HOH A 15 415 153 HOH HOH . C 3 HOH A 16 416 96 HOH HOH . C 3 HOH A 17 417 22 HOH HOH . C 3 HOH A 18 418 151 HOH HOH . C 3 HOH A 19 419 56 HOH HOH . C 3 HOH A 20 420 18 HOH HOH . C 3 HOH A 21 421 150 HOH HOH . C 3 HOH A 22 422 36 HOH HOH . C 3 HOH A 23 423 120 HOH HOH . C 3 HOH A 24 424 35 HOH HOH . C 3 HOH A 25 425 44 HOH HOH . C 3 HOH A 26 426 12 HOH HOH . C 3 HOH A 27 427 158 HOH HOH . C 3 HOH A 28 428 54 HOH HOH . C 3 HOH A 29 429 128 HOH HOH . C 3 HOH A 30 430 53 HOH HOH . C 3 HOH A 31 431 3 HOH HOH . C 3 HOH A 32 432 10 HOH HOH . C 3 HOH A 33 433 118 HOH HOH . C 3 HOH A 34 434 62 HOH HOH . C 3 HOH A 35 435 79 HOH HOH . C 3 HOH A 36 436 11 HOH HOH . C 3 HOH A 37 437 4 HOH HOH . C 3 HOH A 38 438 145 HOH HOH . C 3 HOH A 39 439 149 HOH HOH . C 3 HOH A 40 440 147 HOH HOH . C 3 HOH A 41 441 171 HOH HOH . C 3 HOH A 42 442 16 HOH HOH . C 3 HOH A 43 443 34 HOH HOH . C 3 HOH A 44 444 68 HOH HOH . C 3 HOH A 45 445 5 HOH HOH . C 3 HOH A 46 446 136 HOH HOH . C 3 HOH A 47 447 13 HOH HOH . C 3 HOH A 48 448 72 HOH HOH . C 3 HOH A 49 449 57 HOH HOH . C 3 HOH A 50 450 49 HOH HOH . C 3 HOH A 51 451 114 HOH HOH . C 3 HOH A 52 452 14 HOH HOH . C 3 HOH A 53 453 32 HOH HOH . C 3 HOH A 54 454 69 HOH HOH . C 3 HOH A 55 455 104 HOH HOH . C 3 HOH A 56 456 107 HOH HOH . C 3 HOH A 57 457 78 HOH HOH . C 3 HOH A 58 458 113 HOH HOH . C 3 HOH A 59 459 74 HOH HOH . C 3 HOH A 60 460 109 HOH HOH . C 3 HOH A 61 461 30 HOH HOH . C 3 HOH A 62 462 174 HOH HOH . C 3 HOH A 63 463 8 HOH HOH . C 3 HOH A 64 464 1 HOH HOH . C 3 HOH A 65 465 52 HOH HOH . C 3 HOH A 66 466 108 HOH HOH . C 3 HOH A 67 467 90 HOH HOH . C 3 HOH A 68 468 98 HOH HOH . C 3 HOH A 69 469 33 HOH HOH . C 3 HOH A 70 470 24 HOH HOH . C 3 HOH A 71 471 6 HOH HOH . C 3 HOH A 72 472 127 HOH HOH . C 3 HOH A 73 473 71 HOH HOH . C 3 HOH A 74 474 117 HOH HOH . C 3 HOH A 75 475 143 HOH HOH . C 3 HOH A 76 476 7 HOH HOH . C 3 HOH A 77 477 100 HOH HOH . C 3 HOH A 78 478 106 HOH HOH . C 3 HOH A 79 479 46 HOH HOH . C 3 HOH A 80 480 75 HOH HOH . C 3 HOH A 81 481 29 HOH HOH . C 3 HOH A 82 482 25 HOH HOH . C 3 HOH A 83 483 47 HOH HOH . C 3 HOH A 84 484 125 HOH HOH . C 3 HOH A 85 485 112 HOH HOH . C 3 HOH A 86 486 15 HOH HOH . C 3 HOH A 87 487 139 HOH HOH . C 3 HOH A 88 488 111 HOH HOH . C 3 HOH A 89 489 101 HOH HOH . C 3 HOH A 90 490 38 HOH HOH . C 3 HOH A 91 491 50 HOH HOH . C 3 HOH A 92 492 115 HOH HOH . C 3 HOH A 93 493 102 HOH HOH . C 3 HOH A 94 494 27 HOH HOH . C 3 HOH A 95 495 59 HOH HOH . C 3 HOH A 96 496 43 HOH HOH . C 3 HOH A 97 497 94 HOH HOH . C 3 HOH A 98 498 2 HOH HOH . C 3 HOH A 99 499 31 HOH HOH . C 3 HOH A 100 500 131 HOH HOH . C 3 HOH A 101 501 137 HOH HOH . C 3 HOH A 102 502 105 HOH HOH . C 3 HOH A 103 503 65 HOH HOH . C 3 HOH A 104 504 167 HOH HOH . C 3 HOH A 105 505 21 HOH HOH . C 3 HOH A 106 506 19 HOH HOH . C 3 HOH A 107 507 88 HOH HOH . C 3 HOH A 108 508 91 HOH HOH . C 3 HOH A 109 509 9 HOH HOH . C 3 HOH A 110 510 160 HOH HOH . C 3 HOH A 111 511 99 HOH HOH . C 3 HOH A 112 512 164 HOH HOH . C 3 HOH A 113 513 70 HOH HOH . C 3 HOH A 114 514 28 HOH HOH . C 3 HOH A 115 515 48 HOH HOH . C 3 HOH A 116 516 144 HOH HOH . C 3 HOH A 117 517 165 HOH HOH . C 3 HOH A 118 518 93 HOH HOH . C 3 HOH A 119 519 103 HOH HOH . C 3 HOH A 120 520 97 HOH HOH . C 3 HOH A 121 521 17 HOH HOH . C 3 HOH A 122 522 141 HOH HOH . C 3 HOH A 123 523 60 HOH HOH . C 3 HOH A 124 524 66 HOH HOH . C 3 HOH A 125 525 89 HOH HOH . C 3 HOH A 126 526 140 HOH HOH . C 3 HOH A 127 527 121 HOH HOH . C 3 HOH A 128 528 85 HOH HOH . C 3 HOH A 129 529 39 HOH HOH . C 3 HOH A 130 530 81 HOH HOH . C 3 HOH A 131 531 138 HOH HOH . C 3 HOH A 132 532 42 HOH HOH . C 3 HOH A 133 533 129 HOH HOH . C 3 HOH A 134 534 119 HOH HOH . C 3 HOH A 135 535 133 HOH HOH . C 3 HOH A 136 536 177 HOH HOH . C 3 HOH A 137 537 61 HOH HOH . C 3 HOH A 138 538 45 HOH HOH . C 3 HOH A 139 539 20 HOH HOH . C 3 HOH A 140 540 64 HOH HOH . C 3 HOH A 141 541 83 HOH HOH . C 3 HOH A 142 542 179 HOH HOH . C 3 HOH A 143 543 55 HOH HOH . C 3 HOH A 144 544 87 HOH HOH . C 3 HOH A 145 545 162 HOH HOH . C 3 HOH A 146 546 159 HOH HOH . C 3 HOH A 147 547 126 HOH HOH . C 3 HOH A 148 548 132 HOH HOH . C 3 HOH A 149 549 123 HOH HOH . C 3 HOH A 150 550 148 HOH HOH . C 3 HOH A 151 551 86 HOH HOH . C 3 HOH A 152 552 175 HOH HOH . C 3 HOH A 153 553 73 HOH HOH . C 3 HOH A 154 554 26 HOH HOH . C 3 HOH A 155 555 166 HOH HOH . C 3 HOH A 156 556 173 HOH HOH . C 3 HOH A 157 557 146 HOH HOH . C 3 HOH A 158 558 122 HOH HOH . C 3 HOH A 159 559 155 HOH HOH . C 3 HOH A 160 560 124 HOH HOH . C 3 HOH A 161 561 163 HOH HOH . C 3 HOH A 162 562 130 HOH HOH . C 3 HOH A 163 563 77 HOH HOH . C 3 HOH A 164 564 58 HOH HOH . C 3 HOH A 165 565 178 HOH HOH . C 3 HOH A 166 566 63 HOH HOH . C 3 HOH A 167 567 152 HOH HOH . C 3 HOH A 168 568 170 HOH HOH . C 3 HOH A 169 569 161 HOH HOH . C 3 HOH A 170 570 157 HOH HOH . C 3 HOH A 171 571 92 HOH HOH . C 3 HOH A 172 572 135 HOH HOH . C 3 HOH A 173 573 116 HOH HOH . C 3 HOH A 174 574 172 HOH HOH . C 3 HOH A 175 575 156 HOH HOH . C 3 HOH A 176 576 168 HOH HOH . C 3 HOH A 177 577 134 HOH HOH . C 3 HOH A 178 578 169 HOH HOH . C 3 HOH A 179 579 176 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 O O5' D5M . . . B 2 -18.616 -13.965 9.379 1 37.95 ? O5' D5M 301 A 1 HETATM 2 C C5' D5M . . . B 2 -18.315 -14.908 8.399 1 33.48 ? C5' D5M 301 A 1 HETATM 3 C C4' D5M . . . B 2 -19.415 -14.763 7.341 1 37.79 ? C4' D5M 301 A 1 HETATM 4 O O4' D5M . . . B 2 -18.933 -13.668 6.336 1 36.22 ? O4' D5M 301 A 1 HETATM 5 C C3' D5M . . . B 2 -19.609 -15.848 6.679 1 36.69 ? C3' D5M 301 A 1 HETATM 6 O O3' D5M . . . B 2 -21.009 -16.295 6.8 1 39.98 ? O3' D5M 301 A 1 HETATM 7 C C2' D5M . . . B 2 -19.348 -15.489 5.12 1 36.62 ? C2' D5M 301 A 1 HETATM 8 C C1' D5M . . . B 2 -18.685 -14.34 5.009 1 34.67 ? C1' D5M 301 A 1 HETATM 9 N N9 D5M . . . B 2 -17.295 -14.626 4.626 1 28.98 ? N9 D5M 301 A 1 HETATM 10 C C8 D5M . . . B 2 -16.077 -14.681 5.213 1 31.11 ? C8 D5M 301 A 1 HETATM 11 N N7 D5M . . . B 2 -15.184 -15.074 4.278 1 28.14 ? N7 D5M 301 A 1 HETATM 12 C C5 D5M . . . B 2 -15.858 -15.265 3.095 1 26.18 ? C5 D5M 301 A 1 HETATM 13 C C6 D5M . . . B 2 -15.446 -15.649 1.824 1 24.65 ? C6 D5M 301 A 1 HETATM 14 N N6 D5M . . . B 2 -14.158 -16.009 1.322 1 24.68 ? N6 D5M 301 A 1 HETATM 15 N N1 D5M . . . B 2 -16.329 -15.727 0.852 1 22.14 ? N1 D5M 301 A 1 HETATM 16 C C2 D5M . . . B 2 -17.684 -15.438 1.08 1 22.86 ? C2 D5M 301 A 1 HETATM 17 N N3 D5M . . . B 2 -18.123 -15.108 2.299 1 24.1 ? N3 D5M 301 A 1 HETATM 18 C C4 D5M . . . B 2 -17.16 -14.977 3.308 1 26.31 ? C4 D5M 301 A 1 HETATM 19 P P D5M . . . B 2 -18.071 -14.097 10.832 1 39.58 ? P D5M 301 A 1 HETATM 20 O O1P D5M . . . B 2 -17.416 -15.447 10.96 1 44.44 ? O1P D5M 301 A 1 HETATM 21 O O3P D5M . . . B 2 -17.056 -13.026 11.045 1 44.37 ? O3P D5M 301 A 1 HETATM 22 O O2P D5M . . . B 2 -19.145 -13.999 11.905 1 43.68 ? O2P D5M 301 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #