data_1D0V # _model_server_result.job_id 4PPlfvSig1GMXvjmS_gmFQ _model_server_result.datetime_utc '2024-11-24 07:20:44' _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 1d0v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":990}' # _entry.id 1D0V # _exptl.entry_id 1D0V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 358.284 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ALPHA-RIBAZOLE-5'-PHOSPHATE" _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 1D0V _cell.length_a 72.1 _cell.length_b 90 _cell.length_c 47.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D0V _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 PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 72.1 90 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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 160 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 160 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 256 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 256 _struct_conn.ptnr2_symmetry 1_555 _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 2.005 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C14 H19 N2 O7 P' _chem_comp.formula_weight 358.284 _chem_comp.id RBZ _chem_comp.mon_nstd_flag . _chem_comp.name "ALPHA-RIBAZOLE-5'-PHOSPHATE" _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 N3 C2 RBZ doub 291 n y N3 C3A RBZ sing 292 n y N1 C2 RBZ sing 293 n y N1 C7A RBZ sing 294 n y N1 C1' RBZ sing 295 n n C2 H2 RBZ sing 296 n n C7A C3A RBZ doub 297 n y C7A C7 RBZ sing 298 n y C3A C4 RBZ sing 299 n y C4 C5 RBZ doub 300 n y C4 H4 RBZ sing 301 n n C5 C6 RBZ sing 302 n y C5 C8 RBZ sing 303 n n C6 C7 RBZ doub 304 n y C6 C9 RBZ sing 305 n n C7 H7 RBZ sing 306 n n C8 H81 RBZ sing 307 n n C8 H82 RBZ sing 308 n n C8 H83 RBZ sing 309 n n C9 H91 RBZ sing 310 n n C9 H92 RBZ sing 311 n n C9 H93 RBZ sing 312 n n P O1P RBZ doub 313 n n P O2P RBZ sing 314 n n P O3P RBZ sing 315 n n P O5' RBZ sing 316 n n O2P HOP2 RBZ sing 317 n n O3P HOP3 RBZ sing 318 n n O5' C5' RBZ sing 319 n n C5' C4' RBZ sing 320 n n C5' "H5'1" RBZ sing 321 n n C5' "H5'2" RBZ sing 322 n n C4' O4' RBZ sing 323 n n C4' C3' RBZ sing 324 n n C4' H4' RBZ sing 325 n n O4' C1' RBZ sing 326 n n C3' O3' RBZ sing 327 n n C3' C2' RBZ sing 328 n n C3' H3' RBZ sing 329 n n O3' "HO'3" RBZ sing 330 n n C2' O2' RBZ sing 331 n n C2' C1' RBZ sing 332 n n C2' H2' RBZ sing 333 n n O2' "HO'2" RBZ sing 334 n n C1' H1' RBZ sing 335 n n # _atom_sites.entry_id 1D0V _atom_sites.fract_transf_matrix[1][1] 0.01387 _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] 0.011111 _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] 0.021008 _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 RBZ A 1 990 990 RBZ RIB . C 3 NIO A 1 991 991 NIO NIC . D 4 HOH A 1 401 401 HOH WAT . D 4 HOH A 2 402 402 HOH WAT . D 4 HOH A 3 403 403 HOH WAT . D 4 HOH A 4 404 404 HOH WAT . D 4 HOH A 5 406 406 HOH WAT . D 4 HOH A 6 407 407 HOH WAT . D 4 HOH A 7 408 408 HOH WAT . D 4 HOH A 8 409 409 HOH WAT . D 4 HOH A 9 410 410 HOH WAT . D 4 HOH A 10 412 412 HOH WAT . D 4 HOH A 11 414 414 HOH WAT . D 4 HOH A 12 415 415 HOH WAT . D 4 HOH A 13 416 416 HOH WAT . D 4 HOH A 14 417 417 HOH WAT . D 4 HOH A 15 423 423 HOH WAT . D 4 HOH A 16 425 425 HOH WAT . D 4 HOH A 17 427 427 HOH WAT . D 4 HOH A 18 429 429 HOH WAT . D 4 HOH A 19 430 430 HOH WAT . D 4 HOH A 20 432 432 HOH WAT . D 4 HOH A 21 433 433 HOH WAT . D 4 HOH A 22 435 435 HOH WAT . D 4 HOH A 23 442 442 HOH WAT . D 4 HOH A 24 444 444 HOH WAT . D 4 HOH A 25 445 445 HOH WAT . D 4 HOH A 26 446 446 HOH WAT . D 4 HOH A 27 447 447 HOH WAT . D 4 HOH A 28 448 448 HOH WAT . D 4 HOH A 29 450 450 HOH WAT . D 4 HOH A 30 451 451 HOH WAT . D 4 HOH A 31 452 452 HOH WAT . D 4 HOH A 32 454 454 HOH WAT . D 4 HOH A 33 455 455 HOH WAT . D 4 HOH A 34 458 458 HOH WAT . D 4 HOH A 35 460 460 HOH WAT . D 4 HOH A 36 461 461 HOH WAT . D 4 HOH A 37 462 462 HOH WAT . D 4 HOH A 38 464 464 HOH WAT . D 4 HOH A 39 465 465 HOH WAT . D 4 HOH A 40 466 466 HOH WAT . D 4 HOH A 41 468 468 HOH WAT . D 4 HOH A 42 469 469 HOH WAT . D 4 HOH A 43 470 470 HOH WAT . D 4 HOH A 44 471 471 HOH WAT . D 4 HOH A 45 472 472 HOH WAT . D 4 HOH A 46 473 473 HOH WAT . D 4 HOH A 47 475 475 HOH WAT . D 4 HOH A 48 477 477 HOH WAT . D 4 HOH A 49 478 478 HOH WAT . D 4 HOH A 50 479 479 HOH WAT . D 4 HOH A 51 481 481 HOH WAT . D 4 HOH A 52 482 482 HOH WAT . D 4 HOH A 53 483 483 HOH WAT . D 4 HOH A 54 484 484 HOH WAT . D 4 HOH A 55 485 485 HOH WAT . D 4 HOH A 56 486 486 HOH WAT . D 4 HOH A 57 488 488 HOH WAT . D 4 HOH A 58 489 489 HOH WAT . D 4 HOH A 59 490 490 HOH WAT . D 4 HOH A 60 491 491 HOH WAT . D 4 HOH A 61 492 492 HOH WAT . D 4 HOH A 62 497 497 HOH WAT . D 4 HOH A 63 498 498 HOH WAT . D 4 HOH A 64 500 500 HOH WAT . D 4 HOH A 65 502 502 HOH WAT . D 4 HOH A 66 504 504 HOH WAT . D 4 HOH A 67 505 505 HOH WAT . D 4 HOH A 68 506 506 HOH WAT . D 4 HOH A 69 509 509 HOH WAT . D 4 HOH A 70 511 511 HOH WAT . D 4 HOH A 71 516 516 HOH WAT . D 4 HOH A 72 517 517 HOH WAT . D 4 HOH A 73 518 518 HOH WAT . D 4 HOH A 74 520 520 HOH WAT . D 4 HOH A 75 521 521 HOH WAT . D 4 HOH A 76 522 522 HOH WAT . D 4 HOH A 77 523 523 HOH WAT . D 4 HOH A 78 525 525 HOH WAT . D 4 HOH A 79 526 526 HOH WAT . D 4 HOH A 80 528 528 HOH WAT . D 4 HOH A 81 535 535 HOH WAT . D 4 HOH A 82 536 536 HOH WAT . D 4 HOH A 83 537 537 HOH WAT . D 4 HOH A 84 538 538 HOH WAT . D 4 HOH A 85 541 541 HOH WAT . D 4 HOH A 86 542 542 HOH WAT . D 4 HOH A 87 543 543 HOH WAT . D 4 HOH A 88 544 544 HOH WAT . D 4 HOH A 89 545 545 HOH WAT . D 4 HOH A 90 547 547 HOH WAT . D 4 HOH A 91 548 548 HOH WAT . D 4 HOH A 92 549 549 HOH WAT . D 4 HOH A 93 550 550 HOH WAT . D 4 HOH A 94 552 552 HOH WAT . D 4 HOH A 95 554 554 HOH WAT . D 4 HOH A 96 555 555 HOH WAT . D 4 HOH A 97 556 556 HOH WAT . D 4 HOH A 98 557 557 HOH WAT . D 4 HOH A 99 558 558 HOH WAT . D 4 HOH A 100 559 559 HOH WAT . D 4 HOH A 101 560 560 HOH WAT . D 4 HOH A 102 561 561 HOH WAT . D 4 HOH A 103 562 562 HOH WAT . D 4 HOH A 104 563 563 HOH WAT . D 4 HOH A 105 564 564 HOH WAT . D 4 HOH A 106 565 565 HOH WAT . D 4 HOH A 107 566 566 HOH WAT . D 4 HOH A 108 567 567 HOH WAT . D 4 HOH A 109 569 569 HOH WAT . D 4 HOH A 110 571 571 HOH WAT . D 4 HOH A 111 572 572 HOH WAT . D 4 HOH A 112 573 573 HOH WAT . D 4 HOH A 113 574 574 HOH WAT . D 4 HOH A 114 576 576 HOH WAT . D 4 HOH A 115 577 577 HOH WAT . D 4 HOH A 116 578 578 HOH WAT . D 4 HOH A 117 579 579 HOH WAT . D 4 HOH A 118 580 580 HOH WAT . D 4 HOH A 119 581 581 HOH WAT . D 4 HOH A 120 582 582 HOH WAT . D 4 HOH A 121 583 583 HOH WAT . D 4 HOH A 122 584 584 HOH WAT . D 4 HOH A 123 585 585 HOH WAT . D 4 HOH A 124 586 586 HOH WAT . D 4 HOH A 125 587 587 HOH WAT . D 4 HOH A 126 588 588 HOH WAT . D 4 HOH A 127 589 589 HOH WAT . D 4 HOH A 128 590 590 HOH WAT . D 4 HOH A 129 591 591 HOH WAT . D 4 HOH A 130 593 593 HOH WAT . D 4 HOH A 131 594 594 HOH WAT . D 4 HOH A 132 595 595 HOH WAT . D 4 HOH A 133 596 596 HOH WAT . D 4 HOH A 134 597 597 HOH WAT . D 4 HOH A 135 598 598 HOH WAT . D 4 HOH A 136 599 599 HOH WAT . D 4 HOH A 137 600 600 HOH WAT . D 4 HOH A 138 603 603 HOH WAT . D 4 HOH A 139 604 604 HOH WAT . D 4 HOH A 140 606 606 HOH WAT . D 4 HOH A 141 607 607 HOH WAT . D 4 HOH A 142 609 609 HOH WAT . D 4 HOH A 143 610 610 HOH WAT . D 4 HOH A 144 611 611 HOH WAT . D 4 HOH A 145 612 612 HOH WAT . D 4 HOH A 146 614 614 HOH WAT . D 4 HOH A 147 615 615 HOH WAT . D 4 HOH A 148 616 616 HOH WAT . D 4 HOH A 149 618 618 HOH WAT . D 4 HOH A 150 619 619 HOH WAT . D 4 HOH A 151 622 622 HOH WAT . D 4 HOH A 152 623 623 HOH WAT . D 4 HOH A 153 624 624 HOH WAT . D 4 HOH A 154 626 626 HOH WAT . D 4 HOH A 155 627 627 HOH WAT . D 4 HOH A 156 630 630 HOH WAT . D 4 HOH A 157 631 631 HOH WAT . D 4 HOH A 158 632 632 HOH WAT . # 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 N N3 RBZ . . . B 2 56.382 41.525 14.125 1 14.77 ? N3 RBZ 990 A 1 HETATM 2 N N1 RBZ . . . B 2 56.769 40.908 11.984 1 21.71 ? N1 RBZ 990 A 1 HETATM 3 C C2 RBZ . . . B 2 56.005 40.762 13.085 1 25.83 ? C2 RBZ 990 A 1 HETATM 4 C C7A RBZ . . . B 2 57.761 41.837 12.406 1 15.59 ? C7A RBZ 990 A 1 HETATM 5 C C3A RBZ . . . B 2 57.506 42.224 13.71 1 13.78 ? C3A RBZ 990 A 1 HETATM 6 C C4 RBZ . . . B 2 58.313 43.172 14.353 1 9.92 ? C4 RBZ 990 A 1 HETATM 7 C C5 RBZ . . . B 2 59.414 43.698 13.694 1 17.41 ? C5 RBZ 990 A 1 HETATM 8 C C6 RBZ . . . B 2 59.7 43.289 12.373 1 6.61 ? C6 RBZ 990 A 1 HETATM 9 C C7 RBZ . . . B 2 58.881 42.36 11.736 1 16.42 ? C7 RBZ 990 A 1 HETATM 10 C C8 RBZ . . . B 2 60.303 44.738 14.385 1 15.55 ? C8 RBZ 990 A 1 HETATM 11 C C9 RBZ . . . B 2 60.894 43.88 11.641 1 18.71 ? C9 RBZ 990 A 1 HETATM 12 P P RBZ . . . B 2 59.61 39.398 6.086 1 12.56 ? P RBZ 990 A 1 HETATM 13 O O1P RBZ . . . B 2 59.273 38.12 5.392 1 13.89 ? O1P RBZ 990 A 1 HETATM 14 O O2P RBZ . . . B 2 59.806 40.563 5.196 1 9.27 ? O2P RBZ 990 A 1 HETATM 15 O O3P RBZ . . . B 2 60.61 39.194 7.147 1 10.77 ? O3P RBZ 990 A 1 HETATM 16 O O5' RBZ . . . B 2 58.363 39.735 7.053 1 12.71 ? O5' RBZ 990 A 1 HETATM 17 C C5' RBZ . . . B 2 57.817 38.741 7.972 1 5.26 ? C5' RBZ 990 A 1 HETATM 18 C C4' RBZ . . . B 2 58.231 39.083 9.388 1 10.7 ? C4' RBZ 990 A 1 HETATM 19 O O4' RBZ . . . B 2 57.729 40.396 9.796 1 22.68 ? O4' RBZ 990 A 1 HETATM 20 C C3' RBZ . . . B 2 57.731 38.153 10.461 1 9.36 ? C3' RBZ 990 A 1 HETATM 21 O O3' RBZ . . . B 2 58.461 38.264 11.675 1 15.71 ? O3' RBZ 990 A 1 HETATM 22 C C2' RBZ . . . B 2 56.342 38.769 10.649 1 29.44 ? C2' RBZ 990 A 1 HETATM 23 O O2' RBZ . . . B 2 55.85 38.333 11.93 1 14.54 ? O2' RBZ 990 A 1 HETATM 24 C C1' RBZ . . . B 2 56.608 40.27 10.648 1 22.54 ? C1' RBZ 990 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 217 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 24 #