data_7OQX # _model_server_result.job_id 3KJL3dhfw4WDJG2igMYy1Q _model_server_result.datetime_utc '2025-01-14 22:51:18' _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 7oqx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7OQX # _exptl.entry_id 7OQX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 481.184 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine" _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 7OQX _cell.length_a 69.8 _cell.length_b 69.8 _cell.length_c 290.85 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OQX _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall 'P 4nw 2abw' _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,D,E,F,G,H,I,J,K,L,M,N,O _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 H18 N3 O13 P3' _chem_comp.formula_weight 481.184 _chem_comp.id 2TM _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CMPcPP # 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 N4 C4 2TM sing 1 n n N3 C4 2TM doub 2 n n N3 C2 2TM sing 3 n n O2 C2 2TM doub 4 n n C4 C5 2TM sing 5 n n C2 N1 2TM sing 6 n n C5 C6 2TM doub 7 n n N1 C6 2TM sing 8 n n N1 C1' 2TM sing 9 n n O2' C2' 2TM sing 10 n n C2' C1' 2TM sing 11 n n C2' C3' 2TM sing 12 n n C1' O4' 2TM sing 13 n n C3' O3' 2TM sing 14 n n C3' C4' 2TM sing 15 n n O4' C4' 2TM sing 16 n n C4' C5' 2TM sing 17 n n C5' O5' 2TM sing 18 n n O5' PA 2TM sing 19 n n O1A PA 2TM doub 20 n n PA O2A 2TM sing 21 n n PA C1 2TM sing 22 n n O2B PB 2TM doub 23 n n C1 PB 2TM sing 24 n n PB O3B 2TM sing 25 n n PB O1B 2TM sing 26 n n O3B PG 2TM sing 27 n n PG O1G 2TM doub 28 n n PG O2G 2TM sing 29 n n PG O3G 2TM sing 30 n n C5' H1 2TM sing 31 n n C5' H2 2TM sing 32 n n C4' H3 2TM sing 33 n n C3' H4 2TM sing 34 n n O3' H5 2TM sing 35 n n C2' H6 2TM sing 36 n n O2' H7 2TM sing 37 n n C1' H8 2TM sing 38 n n C5 H9 2TM sing 39 n n C6 H10 2TM sing 40 n n O3G H11 2TM sing 41 n n O2G H12 2TM sing 42 n n O1B H13 2TM sing 43 n n O2A H14 2TM sing 44 n n N4 H15 2TM sing 45 n n N4 H16 2TM sing 46 n n C1 H17 2TM sing 47 n n C1 H18 2TM sing 48 n n # _atom_sites.entry_id 7OQX _atom_sites.fract_transf_matrix[1][1] 0.014327 _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] 0.014327 _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] 0.003438 _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 2TM A 1 401 1 2TM 2TM . C 3 PO4 A 1 402 2 PO4 PO4 . D 3 PO4 A 1 403 3 PO4 PO4 . E 4 ACT A 1 404 4 ACT ACT . F 4 ACT A 1 405 5 ACT ACT . G 4 ACT A 1 406 6 ACT ACT . H 4 ACT A 1 407 7 ACT ACT . I 4 ACT A 1 408 8 ACT ACT . J 4 ACT A 1 409 9 ACT ACT . K 4 ACT A 1 410 10 ACT ACT . L 4 ACT A 1 411 11 ACT ACT . M 4 ACT A 1 412 12 ACT ACT . N 5 GOL A 1 413 13 GOL GOL . O 6 HOH A 1 501 74 HOH HOH . O 6 HOH A 2 502 80 HOH HOH . O 6 HOH A 3 503 106 HOH HOH . O 6 HOH A 4 504 75 HOH HOH . O 6 HOH A 5 505 58 HOH HOH . O 6 HOH A 6 506 109 HOH HOH . O 6 HOH A 7 507 33 HOH HOH . O 6 HOH A 8 508 53 HOH HOH . O 6 HOH A 9 509 63 HOH HOH . O 6 HOH A 10 510 60 HOH HOH . O 6 HOH A 11 511 71 HOH HOH . O 6 HOH A 12 512 30 HOH HOH . O 6 HOH A 13 513 27 HOH HOH . O 6 HOH A 14 514 99 HOH HOH . O 6 HOH A 15 515 29 HOH HOH . O 6 HOH A 16 516 90 HOH HOH . O 6 HOH A 17 517 45 HOH HOH . O 6 HOH A 18 518 26 HOH HOH . O 6 HOH A 19 519 66 HOH HOH . O 6 HOH A 20 520 88 HOH HOH . O 6 HOH A 21 521 16 HOH HOH . O 6 HOH A 22 522 20 HOH HOH . O 6 HOH A 23 523 95 HOH HOH . O 6 HOH A 24 524 24 HOH HOH . O 6 HOH A 25 525 42 HOH HOH . O 6 HOH A 26 526 48 HOH HOH . O 6 HOH A 27 527 15 HOH HOH . O 6 HOH A 28 528 23 HOH HOH . O 6 HOH A 29 529 78 HOH HOH . O 6 HOH A 30 530 62 HOH HOH . O 6 HOH A 31 531 110 HOH HOH . O 6 HOH A 32 532 17 HOH HOH . O 6 HOH A 33 533 41 HOH HOH . O 6 HOH A 34 534 21 HOH HOH . O 6 HOH A 35 535 67 HOH HOH . O 6 HOH A 36 536 65 HOH HOH . O 6 HOH A 37 537 70 HOH HOH . O 6 HOH A 38 538 61 HOH HOH . O 6 HOH A 39 539 47 HOH HOH . O 6 HOH A 40 540 55 HOH HOH . O 6 HOH A 41 541 18 HOH HOH . O 6 HOH A 42 542 94 HOH HOH . O 6 HOH A 43 543 19 HOH HOH . O 6 HOH A 44 544 34 HOH HOH . O 6 HOH A 45 545 102 HOH HOH . O 6 HOH A 46 546 98 HOH HOH . O 6 HOH A 47 547 14 HOH HOH . O 6 HOH A 48 548 108 HOH HOH . O 6 HOH A 49 549 79 HOH HOH . O 6 HOH A 50 550 31 HOH HOH . O 6 HOH A 51 551 73 HOH HOH . O 6 HOH A 52 552 32 HOH HOH . O 6 HOH A 53 553 97 HOH HOH . O 6 HOH A 54 554 103 HOH HOH . O 6 HOH A 55 555 101 HOH HOH . O 6 HOH A 56 556 39 HOH HOH . O 6 HOH A 57 557 89 HOH HOH . O 6 HOH A 58 558 100 HOH HOH . O 6 HOH A 59 559 44 HOH HOH . O 6 HOH A 60 560 104 HOH HOH . O 6 HOH A 61 561 76 HOH HOH . O 6 HOH A 62 562 107 HOH HOH . O 6 HOH A 63 563 28 HOH HOH . O 6 HOH A 64 564 36 HOH HOH . O 6 HOH A 65 565 77 HOH HOH . O 6 HOH A 66 566 59 HOH HOH . O 6 HOH A 67 567 68 HOH HOH . O 6 HOH A 68 568 84 HOH HOH . O 6 HOH A 69 569 87 HOH HOH . O 6 HOH A 70 570 82 HOH HOH . O 6 HOH A 71 571 93 HOH HOH . O 6 HOH A 72 572 56 HOH HOH . O 6 HOH A 73 573 25 HOH HOH . O 6 HOH A 74 574 49 HOH HOH . O 6 HOH A 75 575 46 HOH HOH . O 6 HOH A 76 576 105 HOH HOH . O 6 HOH A 77 577 69 HOH HOH . O 6 HOH A 78 578 40 HOH HOH . O 6 HOH A 79 579 72 HOH HOH . O 6 HOH A 80 580 85 HOH HOH . O 6 HOH A 81 581 38 HOH HOH . O 6 HOH A 82 582 86 HOH HOH . O 6 HOH A 83 583 50 HOH HOH . O 6 HOH A 84 584 37 HOH HOH . O 6 HOH A 85 585 57 HOH HOH . O 6 HOH A 86 586 43 HOH HOH . O 6 HOH A 87 587 92 HOH HOH . O 6 HOH A 88 588 64 HOH HOH . O 6 HOH A 89 589 96 HOH HOH . O 6 HOH A 90 590 52 HOH HOH . O 6 HOH A 91 591 111 HOH HOH . O 6 HOH A 92 592 81 HOH HOH . O 6 HOH A 93 593 22 HOH HOH . O 6 HOH A 94 594 51 HOH HOH . O 6 HOH A 95 595 91 HOH HOH . O 6 HOH A 96 596 112 HOH HOH . O 6 HOH A 97 597 83 HOH HOH . O 6 HOH A 98 598 35 HOH HOH . O 6 HOH A 99 599 54 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' 2TM . A . B 2 39.61 51.506 48.308 0.3 59.65 ? O5' 2TM 401 A 1 HETATM 2 O O5' 2TM . B . B 2 39.005 52.106 49.072 0.65 57.26 ? O5' 2TM 401 A 1 HETATM 3 C C5' 2TM . A . B 2 38.671 52.506 48.711 0.3 56.19 ? C5' 2TM 401 A 1 HETATM 4 C C5' 2TM . B . B 2 38.199 53.214 48.721 0.65 54.63 ? C5' 2TM 401 A 1 HETATM 5 C C4' 2TM . A . B 2 39.137 53.889 48.259 0.3 55.82 ? C4' 2TM 401 A 1 HETATM 6 C C4' 2TM . B . B 2 39.105 54.325 48.23 0.65 56.32 ? C4' 2TM 401 A 1 HETATM 7 O O4' 2TM . A . B 2 39.771 54.582 49.344 0.3 53.71 ? O4' 2TM 401 A 1 HETATM 8 O O4' 2TM . B . B 2 39.841 54.882 49.321 0.65 53.18 ? O4' 2TM 401 A 1 HETATM 9 C C3' 2TM . A . B 2 40.172 53.789 47.156 0.3 51.95 ? C3' 2TM 401 A 1 HETATM 10 C C3' 2TM . B . B 2 40.123 53.82 47.236 0.65 52.02 ? C3' 2TM 401 A 1 HETATM 11 O O3' 2TM . A . B 2 39.586 54.141 45.909 0.3 51.29 ? O3' 2TM 401 A 1 HETATM 12 O O3' 2TM . B . B 2 39.615 53.957 45.914 0.65 51.39 ? O3' 2TM 401 A 1 HETATM 13 C C2' 2TM . A . B 2 41.282 54.746 47.522 0.3 51.84 ? C2' 2TM 401 A 1 HETATM 14 C C2' 2TM . B . B 2 41.316 54.719 47.478 0.65 52.34 ? C2' 2TM 401 A 1 HETATM 15 O O2' 2TM . A . B 2 41.156 55.924 46.725 0.3 48.85 ? O2' 2TM 401 A 1 HETATM 16 O O2' 2TM . B . B 2 41.183 55.869 46.643 0.65 48.94 ? O2' 2TM 401 A 1 HETATM 17 C C1' 2TM . A . B 2 41.055 55.109 48.983 0.3 51.65 ? C1' 2TM 401 A 1 HETATM 18 C C1' 2TM . B . B 2 41.174 55.197 48.917 0.65 51.58 ? C1' 2TM 401 A 1 HETATM 19 C C5 2TM . A . B 2 42.757 52.857 51.384 0.3 55.19 ? C5 2TM 401 A 1 HETATM 20 C C5 2TM . B . B 2 42.704 52.852 51.348 0.65 55.31 ? C5 2TM 401 A 1 HETATM 21 C C6 2TM . A . B 2 41.801 53.441 50.577 0.3 52.07 ? C6 2TM 401 A 1 HETATM 22 C C6 2TM . B . B 2 41.788 53.468 50.517 0.65 52.02 ? C6 2TM 401 A 1 HETATM 23 N N1 2TM . A . B 2 42.096 54.508 49.83 0.3 52.56 ? N1 2TM 401 A 1 HETATM 24 N N1 2TM . B . B 2 42.143 54.534 49.797 0.65 52.7 ? N1 2TM 401 A 1 HETATM 25 C C2 2TM . A . B 2 43.406 55.038 49.887 0.3 49.89 ? C2 2TM 401 A 1 HETATM 26 C C2 2TM . B . B 2 43.457 55.029 49.904 0.65 49.91 ? C2 2TM 401 A 1 HETATM 27 N N3 2TM . A . B 2 44.337 54.466 50.675 0.3 47.87 ? N3 2TM 401 A 1 HETATM 28 N N3 2TM . B . B 2 44.35 54.428 50.711 0.65 47.77 ? N3 2TM 401 A 1 HETATM 29 C C4 2TM . A . B 2 44.034 53.387 51.42 0.3 54.15 ? C4 2TM 401 A 1 HETATM 30 C C4 2TM . B . B 2 43.994 53.348 51.431 0.65 54.49 ? C4 2TM 401 A 1 HETATM 31 O O3G 2TM . A . B 2 36.592 48.067 45.7 0.3 69.72 ? O3G 2TM 401 A 1 HETATM 32 O O3G 2TM . B . B 2 38.135 46.746 44.676 0.65 66.48 ? O3G 2TM 401 A 1 HETATM 33 P PG 2TM . A . B 2 37.667 47.02 45.573 0.3 70.63 ? PG 2TM 401 A 1 HETATM 34 P PG 2TM . B . B 2 37.675 47.572 45.843 0.65 73.02 ? PG 2TM 401 A 1 HETATM 35 O O1G 2TM . A . B 2 38.857 47.555 44.83 0.3 63.15 ? O1G 2TM 401 A 1 HETATM 36 O O1G 2TM . B . B 2 37.22 48.926 45.36 0.65 70.02 ? O1G 2TM 401 A 1 HETATM 37 O O2G 2TM . A . B 2 37.114 45.826 44.837 0.3 70.54 ? O2G 2TM 401 A 1 HETATM 38 O O2G 2TM . B . B 2 36.55 46.87 46.559 0.65 73.86 ? O2G 2TM 401 A 1 HETATM 39 O O3B 2TM . A . B 2 38.154 46.524 47.018 0.3 61.56 ? O3B 2TM 401 A 1 HETATM 40 O O3B 2TM . B . B 2 38.909 47.719 46.855 0.65 62.87 ? O3B 2TM 401 A 1 HETATM 41 P PB 2TM . A . B 2 38.399 47.489 48.28 0.3 65.47 ? PB 2TM 401 A 1 HETATM 42 P PB 2TM . B . B 2 39.243 49.048 47.697 0.65 62.67 ? PB 2TM 401 A 1 HETATM 43 O O1B 2TM . A . B 2 37.098 48.1 48.739 0.3 64.75 ? O1B 2TM 401 A 1 HETATM 44 O O1B 2TM . B . B 2 40.351 48.623 48.6 0.65 57.57 ? O1B 2TM 401 A 1 HETATM 45 O O2B 2TM . A . B 2 38.878 46.569 49.37 0.3 59.69 ? O2B 2TM 401 A 1 HETATM 46 O O2B 2TM . B . B 2 39.717 50.146 46.781 0.65 60.63 ? O2B 2TM 401 A 1 HETATM 47 P PA 2TM . A . B 2 39.177 50.319 47.305 0.3 63.18 ? PA 2TM 401 A 1 HETATM 48 P PA 2TM . B . B 2 38.348 50.898 49.883 0.65 50.76 ? PA 2TM 401 A 1 HETATM 49 O O1A 2TM . A . B 2 39.86 50.56 45.984 0.3 57.53 ? O1A 2TM 401 A 1 HETATM 50 O O1A 2TM . B . B 2 37.138 51.426 50.602 0.65 50.85 ? O1A 2TM 401 A 1 HETATM 51 O O2A 2TM . A . B 2 37.689 50.438 47.105 0.3 61.76 ? O2A 2TM 401 A 1 HETATM 52 O O2A 2TM . B . B 2 39.362 50.431 50.89 0.65 46.86 ? O2A 2TM 401 A 1 HETATM 53 N N4 2TM . A . B 2 44.965 52.813 52.209 0.3 52.76 ? N4 2TM 401 A 1 HETATM 54 N N4 2TM . B . B 2 44.885 52.743 52.243 0.65 52.87 ? N4 2TM 401 A 1 HETATM 55 O O2 2TM . A . B 2 43.727 56.038 49.222 0.3 44.94 ? O2 2TM 401 A 1 HETATM 56 O O2 2TM . B . B 2 43.804 56.026 49.253 0.65 44.74 ? O2 2TM 401 A 1 HETATM 57 C C1 2TM . A . B 2 39.699 48.719 47.975 0.3 59.65 ? C1 2TM 401 A 1 HETATM 58 C C1 2TM . B . B 2 37.852 49.588 48.728 0.65 58.23 ? C1 2TM 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 58 #