data_6E0L # _model_server_result.job_id aZz8Zd1J80jU4aqJBPZ1_g _model_server_result.datetime_utc '2024-12-15 22:36:44' _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 6e0l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 6E0L # _exptl.entry_id 6E0L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _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 6E0L _cell.length_a 51.647 _cell.length_b 65.652 _cell.length_c 88.855 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E0L _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,D,E _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD2 ASP 62 A ASP 62 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc2 B MG MG . A MG 301 1_555 C O3G APC . A APC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc3 B MG MG . A MG 301 1_555 C O1B APC . A APC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc4 B MG MG . A MG 301 1_555 C O1A APC . A APC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 B MG MG . A MG 301 1_555 E O HOH . A HOH 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc6 B MG MG . A MG 301 1_555 E O HOH . A HOH 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id 2KH _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _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 O2' C2' 2KH sing 1 n n O3' C3' 2KH sing 2 n n C2' C3' 2KH sing 3 n n C2' C1' 2KH sing 4 n n O2 C2 2KH doub 5 n n C3' C4' 2KH sing 6 n n C1' N1 2KH sing 7 n n C1' O4' 2KH sing 8 n n C2 N1 2KH sing 9 n n C2 N3 2KH sing 10 n n C4' O4' 2KH sing 11 n n C4' C5' 2KH sing 12 n n N1 C6 2KH sing 13 n n N3 C4 2KH sing 14 n n C5' O5' 2KH sing 15 n n C6 C5 2KH doub 16 n n C4 C5 2KH sing 17 n n C4 O4 2KH doub 18 n n O2B PB 2KH doub 19 n n O5' PA 2KH sing 20 n n N3A PB 2KH sing 21 n n N3A PA 2KH sing 22 n n PB O1B 2KH sing 23 n n PB O3B 2KH sing 24 n n PA O1A 2KH doub 25 n n PA O2A 2KH sing 26 n n O3B PG 2KH sing 27 n n PG O2G 2KH doub 28 n n PG O1G 2KH sing 29 n n PG O3G 2KH sing 30 n n O2A H1 2KH sing 31 n n N3A H2 2KH sing 32 n n O1B H3 2KH sing 33 n n O1G H4 2KH sing 34 n n O3G H5 2KH sing 35 n n C5' H6 2KH sing 36 n n C5' H7 2KH sing 37 n n C4' H8 2KH sing 38 n n C1' H9 2KH sing 39 n n C2' H10 2KH sing 40 n n O2' H11 2KH sing 41 n n C3' H12 2KH sing 42 n n O3' H13 2KH sing 43 n n C6 H14 2KH sing 44 n n N3 H15 2KH sing 45 n n C5 H16 2KH sing 46 n n # _atom_sites.entry_id 6E0L _atom_sites.fract_transf_matrix[1][1] 0.019362 _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] 0.015232 _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] 0.011254 _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 MG A 1 301 1 MG MG . C 3 APC A 1 302 1 APC APC . D 4 2KH A 1 303 1 2KH 2KH . E 5 HOH A 1 401 18 HOH HOH . E 5 HOH A 2 402 75 HOH HOH . E 5 HOH A 3 403 114 HOH HOH . E 5 HOH A 4 404 69 HOH HOH . E 5 HOH A 5 405 158 HOH HOH . E 5 HOH A 6 406 61 HOH HOH . E 5 HOH A 7 407 73 HOH HOH . E 5 HOH A 8 408 71 HOH HOH . E 5 HOH A 9 409 63 HOH HOH . E 5 HOH A 10 410 56 HOH HOH . E 5 HOH A 11 411 54 HOH HOH . E 5 HOH A 12 412 24 HOH HOH . E 5 HOH A 13 413 60 HOH HOH . E 5 HOH A 14 414 25 HOH HOH . E 5 HOH A 15 415 173 HOH HOH . E 5 HOH A 16 416 139 HOH HOH . E 5 HOH A 17 417 79 HOH HOH . E 5 HOH A 18 418 161 HOH HOH . E 5 HOH A 19 419 52 HOH HOH . E 5 HOH A 20 420 26 HOH HOH . E 5 HOH A 21 421 96 HOH HOH . E 5 HOH A 22 422 43 HOH HOH . E 5 HOH A 23 423 80 HOH HOH . E 5 HOH A 24 424 20 HOH HOH . E 5 HOH A 25 425 33 HOH HOH . E 5 HOH A 26 426 36 HOH HOH . E 5 HOH A 27 427 13 HOH HOH . E 5 HOH A 28 428 40 HOH HOH . E 5 HOH A 29 429 47 HOH HOH . E 5 HOH A 30 430 77 HOH HOH . E 5 HOH A 31 431 170 HOH HOH . E 5 HOH A 32 432 141 HOH HOH . E 5 HOH A 33 433 8 HOH HOH . E 5 HOH A 34 434 70 HOH HOH . E 5 HOH A 35 435 48 HOH HOH . E 5 HOH A 36 436 28 HOH HOH . E 5 HOH A 37 437 16 HOH HOH . E 5 HOH A 38 438 66 HOH HOH . E 5 HOH A 39 439 142 HOH HOH . E 5 HOH A 40 440 121 HOH HOH . E 5 HOH A 41 441 136 HOH HOH . E 5 HOH A 42 442 162 HOH HOH . E 5 HOH A 43 443 6 HOH HOH . E 5 HOH A 44 444 50 HOH HOH . E 5 HOH A 45 445 58 HOH HOH . E 5 HOH A 46 446 21 HOH HOH . E 5 HOH A 47 447 116 HOH HOH . E 5 HOH A 48 448 2 HOH HOH . E 5 HOH A 49 449 102 HOH HOH . E 5 HOH A 50 450 35 HOH HOH . E 5 HOH A 51 451 97 HOH HOH . E 5 HOH A 52 452 12 HOH HOH . E 5 HOH A 53 453 49 HOH HOH . E 5 HOH A 54 454 34 HOH HOH . E 5 HOH A 55 455 124 HOH HOH . E 5 HOH A 56 456 81 HOH HOH . E 5 HOH A 57 457 32 HOH HOH . E 5 HOH A 58 458 84 HOH HOH . E 5 HOH A 59 459 10 HOH HOH . E 5 HOH A 60 460 38 HOH HOH . E 5 HOH A 61 461 14 HOH HOH . E 5 HOH A 62 462 57 HOH HOH . E 5 HOH A 63 463 128 HOH HOH . E 5 HOH A 64 464 94 HOH HOH . E 5 HOH A 65 465 151 HOH HOH . E 5 HOH A 66 466 78 HOH HOH . E 5 HOH A 67 467 65 HOH HOH . E 5 HOH A 68 468 68 HOH HOH . E 5 HOH A 69 469 23 HOH HOH . E 5 HOH A 70 470 109 HOH HOH . E 5 HOH A 71 471 67 HOH HOH . E 5 HOH A 72 472 55 HOH HOH . E 5 HOH A 73 473 7 HOH HOH . E 5 HOH A 74 474 174 HOH HOH . E 5 HOH A 75 475 27 HOH HOH . E 5 HOH A 76 476 29 HOH HOH . E 5 HOH A 77 477 45 HOH HOH . E 5 HOH A 78 478 5 HOH HOH . E 5 HOH A 79 479 76 HOH HOH . E 5 HOH A 80 480 53 HOH HOH . E 5 HOH A 81 481 11 HOH HOH . E 5 HOH A 82 482 99 HOH HOH . E 5 HOH A 83 483 19 HOH HOH . E 5 HOH A 84 484 17 HOH HOH . E 5 HOH A 85 485 46 HOH HOH . E 5 HOH A 86 486 37 HOH HOH . E 5 HOH A 87 487 85 HOH HOH . E 5 HOH A 88 488 39 HOH HOH . E 5 HOH A 89 489 168 HOH HOH . E 5 HOH A 90 490 15 HOH HOH . E 5 HOH A 91 491 41 HOH HOH . E 5 HOH A 92 492 1 HOH HOH . E 5 HOH A 93 493 4 HOH HOH . E 5 HOH A 94 494 165 HOH HOH . E 5 HOH A 95 495 44 HOH HOH . E 5 HOH A 96 496 176 HOH HOH . E 5 HOH A 97 497 103 HOH HOH . E 5 HOH A 98 498 105 HOH HOH . E 5 HOH A 99 499 123 HOH HOH . E 5 HOH A 100 500 86 HOH HOH . E 5 HOH A 101 501 138 HOH HOH . E 5 HOH A 102 502 92 HOH HOH . E 5 HOH A 103 503 95 HOH HOH . E 5 HOH A 104 504 82 HOH HOH . E 5 HOH A 105 505 42 HOH HOH . E 5 HOH A 106 506 51 HOH HOH . E 5 HOH A 107 507 129 HOH HOH . E 5 HOH A 108 508 137 HOH HOH . E 5 HOH A 109 509 108 HOH HOH . E 5 HOH A 110 510 149 HOH HOH . E 5 HOH A 111 511 119 HOH HOH . E 5 HOH A 112 512 3 HOH HOH . E 5 HOH A 113 513 122 HOH HOH . E 5 HOH A 114 514 30 HOH HOH . E 5 HOH A 115 515 22 HOH HOH . E 5 HOH A 116 516 120 HOH HOH . E 5 HOH A 117 517 111 HOH HOH . E 5 HOH A 118 518 83 HOH HOH . E 5 HOH A 119 519 9 HOH HOH . E 5 HOH A 120 520 110 HOH HOH . E 5 HOH A 121 521 134 HOH HOH . E 5 HOH A 122 522 175 HOH HOH . E 5 HOH A 123 523 131 HOH HOH . E 5 HOH A 124 524 157 HOH HOH . E 5 HOH A 125 525 115 HOH HOH . E 5 HOH A 126 526 90 HOH HOH . E 5 HOH A 127 527 59 HOH HOH . E 5 HOH A 128 528 118 HOH HOH . E 5 HOH A 129 529 135 HOH HOH . E 5 HOH A 130 530 93 HOH HOH . E 5 HOH A 131 531 148 HOH HOH . E 5 HOH A 132 532 166 HOH HOH . E 5 HOH A 133 533 100 HOH HOH . E 5 HOH A 134 534 163 HOH HOH . E 5 HOH A 135 535 64 HOH HOH . E 5 HOH A 136 536 153 HOH HOH . E 5 HOH A 137 537 117 HOH HOH . E 5 HOH A 138 538 62 HOH HOH . E 5 HOH A 139 539 125 HOH HOH . E 5 HOH A 140 540 144 HOH HOH . E 5 HOH A 141 541 155 HOH HOH . E 5 HOH A 142 542 88 HOH HOH . E 5 HOH A 143 543 98 HOH HOH . E 5 HOH A 144 544 113 HOH HOH . E 5 HOH A 145 545 91 HOH HOH . E 5 HOH A 146 546 101 HOH HOH . E 5 HOH A 147 547 154 HOH HOH . E 5 HOH A 148 548 143 HOH HOH . E 5 HOH A 149 549 146 HOH HOH . E 5 HOH A 150 550 172 HOH HOH . E 5 HOH A 151 551 140 HOH HOH . E 5 HOH A 152 552 31 HOH HOH . E 5 HOH A 153 553 164 HOH HOH . E 5 HOH A 154 554 72 HOH HOH . E 5 HOH A 155 555 132 HOH HOH . E 5 HOH A 156 556 87 HOH HOH . E 5 HOH A 157 557 126 HOH HOH . E 5 HOH A 158 558 89 HOH HOH . E 5 HOH A 159 559 156 HOH HOH . E 5 HOH A 160 560 127 HOH HOH . E 5 HOH A 161 561 112 HOH HOH . E 5 HOH A 162 562 130 HOH HOH . E 5 HOH A 163 563 159 HOH HOH . E 5 HOH A 164 564 150 HOH HOH . E 5 HOH A 165 565 133 HOH HOH . E 5 HOH A 166 566 145 HOH HOH . E 5 HOH A 167 567 169 HOH HOH . E 5 HOH A 168 568 104 HOH HOH . E 5 HOH A 169 569 106 HOH HOH . E 5 HOH A 170 570 74 HOH HOH . E 5 HOH A 171 571 167 HOH HOH . E 5 HOH A 172 572 107 HOH HOH . E 5 HOH A 173 573 160 HOH HOH . E 5 HOH A 174 574 177 HOH HOH . E 5 HOH A 175 575 171 HOH HOH . E 5 HOH A 176 576 147 HOH HOH . E 5 HOH A 177 577 152 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 PA 2KH . . . D 4 19.443 41.147 60.863 1 67.01 ? PA 2KH 303 A 1 HETATM 2 O O1A 2KH . . . D 4 19.21 41.755 59.485 1 68.43 ? O1A 2KH 303 A 1 HETATM 3 O O2A 2KH . . . D 4 18.352 40.147 61.171 1 67.4 -1 O2A 2KH 303 A 1 HETATM 4 N N3A 2KH . . . D 4 19.454 42.345 62.071 1 70.5 ? N3A 2KH 303 A 1 HETATM 5 O O5' 2KH . . . D 4 20.906 40.372 60.911 1 59.79 ? O5' 2KH 303 A 1 HETATM 6 P PB 2KH . . . D 4 19.761 43.971 61.659 1 74.89 ? PB 2KH 303 A 1 HETATM 7 O O1B 2KH . . . D 4 18.887 44.87 62.512 1 74.94 ? O1B 2KH 303 A 1 HETATM 8 O O2B 2KH . . . D 4 19.479 44.205 60.181 1 74.93 -1 O2B 2KH 303 A 1 HETATM 9 O O3B 2KH . . . D 4 21.354 44.292 61.997 1 74.39 ? O3B 2KH 303 A 1 HETATM 10 P PG 2KH . . . D 4 22.549 44.687 60.914 1 74.18 ? PG 2KH 303 A 1 HETATM 11 O O1G 2KH . . . D 4 22.785 46.19 60.935 1 73.67 -1 O1G 2KH 303 A 1 HETATM 12 O O2G 2KH . . . D 4 22.103 44.258 59.529 1 71.67 ? O2G 2KH 303 A 1 HETATM 13 O O3G 2KH . . . D 4 23.819 43.954 61.322 1 74.63 -1 O3G 2KH 303 A 1 HETATM 14 C C5' 2KH . . . D 4 22.017 40.938 60.255 1 52.52 ? C5' 2KH 303 A 1 HETATM 15 C C4' 2KH . . . D 4 23.086 39.856 60.076 1 45.07 ? C4' 2KH 303 A 1 HETATM 16 O O4' 2KH . . . D 4 23.423 39.396 61.263 1 41.21 ? O4' 2KH 303 A 1 HETATM 17 C C1' 2KH . . . D 4 23.701 37.822 61.116 1 37.76 ? C1' 2KH 303 A 1 HETATM 18 C C2' 2KH . . . D 4 23.314 37.457 59.858 1 40.02 ? C2' 2KH 303 A 1 HETATM 19 O O2' 2KH . . . D 4 24.501 37.235 58.974 1 39.44 ? O2' 2KH 303 A 1 HETATM 20 C C3' 2KH . . . D 4 22.474 38.615 59.331 1 41.87 ? C3' 2KH 303 A 1 HETATM 21 O O3' 2KH . . . D 4 22.599 38.761 57.994 1 41.49 ? O3' 2KH 303 A 1 HETATM 22 N N1 2KH . . . D 4 23.01 37.165 62.177 1 33.12 ? N1 2KH 303 A 1 HETATM 23 C C6 2KH . . . D 4 21.732 37.692 62.633 1 31.2 ? C6 2KH 303 A 1 HETATM 24 C C2 2KH . . . D 4 23.576 35.964 62.86 1 31.05 ? C2 2KH 303 A 1 HETATM 25 O O2 2KH . . . D 4 24.616 35.506 62.52 1 30.93 ? O2 2KH 303 A 1 HETATM 26 N N3 2KH . . . D 4 22.832 35.307 63.979 1 29.94 ? N3 2KH 303 A 1 HETATM 27 C C4 2KH . . . D 4 21.551 35.834 64.435 1 29.37 ? C4 2KH 303 A 1 HETATM 28 O O4 2KH . . . D 4 20.96 35.317 65.326 1 29.16 ? O4 2KH 303 A 1 HETATM 29 C C5 2KH . . . D 4 20.985 37.037 63.756 1 29.75 ? C5 2KH 303 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 373 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #