data_9DFU # _model_server_result.job_id CGb77OLBDNGrRz44CFIcWA _model_server_result.datetime_utc '2025-02-23 09:49:45' _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 9dfu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 9DFU # _exptl.entry_id 9DFU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-TRIPHOSPHATE" _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 9DFU _cell.length_a 37.137 _cell.length_b 55.959 _cell.length_c 152.81 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DFU _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 ? _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,E,F _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 # 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 SG CYS 38 A CYS 45 1_555 C FE4 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc2 A SG CYS 42 A CYS 49 1_555 C FE1 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc3 A SG CYS 45 A CYS 52 1_555 C FE3 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 C FE2 SF4 . A SF4 402 1_555 D N SAM . A SAM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc5 C FE2 SF4 . A SF4 402 1_555 D OXT SAM . A SAM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id CTP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-TRIPHOSPHATE" _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 N1 C2 CTP sing 70 n n N1 C6 CTP sing 71 n n N1 C1' CTP sing 72 n n C2 N3 CTP sing 73 n n C2 O2 CTP doub 74 n n N3 C4 CTP doub 75 n n C4 C5 CTP sing 76 n n C4 N4 CTP sing 77 n n C5 C6 CTP doub 78 n n C5 H5 CTP sing 79 n n C6 H6 CTP sing 80 n n N4 HN41 CTP sing 81 n n N4 HN42 CTP sing 82 n n C1' C2' CTP sing 83 n n C1' O4' CTP sing 84 n n C1' H1' CTP sing 85 n n C2' O2' CTP sing 86 n n C2' C3' CTP sing 87 n n C2' H2' CTP sing 88 n n O2' HO2' CTP sing 89 n n C3' C4' CTP sing 90 n n C3' O3' CTP sing 91 n n C3' H3' CTP sing 92 n n C4' O4' CTP sing 93 n n C4' C5' CTP sing 94 n n C4' H4' CTP sing 95 n n O3' HO3' CTP sing 96 n n C5' O5' CTP sing 97 n n C5' "H5'1" CTP sing 98 n n C5' "H5'2" CTP sing 99 n n O5' PA CTP sing 100 n n PA O1A CTP doub 101 n n PA O2A CTP sing 102 n n PA O3A CTP sing 103 n n O2A HOA2 CTP sing 104 n n O3A PB CTP sing 105 n n PB O1B CTP doub 106 n n PB O2B CTP sing 107 n n PB O3B CTP sing 108 n n O2B HOB2 CTP sing 109 n n O3B PG CTP sing 110 n n PG O1G CTP doub 111 n n PG O2G CTP sing 112 n n PG O3G CTP sing 113 n n O2G HOG2 CTP sing 114 n n O3G HOG3 CTP sing 115 n n # _atom_sites.entry_id 9DFU _atom_sites.fract_transf_matrix[1][1] 0.026927 _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] 0.01787 _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] 0.006544 _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 CTP A 1 401 401 CTP CTP . C 3 SF4 A 1 402 402 SF4 SF4 . D 4 SAM A 1 403 403 SAM SAM . E 5 CL A 1 404 1 CL CL . F 6 HOH A 1 501 91 HOH HOH . F 6 HOH A 2 502 131 HOH HOH . F 6 HOH A 3 503 12 HOH HOH . F 6 HOH A 4 504 9 HOH HOH . F 6 HOH A 5 505 77 HOH HOH . F 6 HOH A 6 506 52 HOH HOH . F 6 HOH A 7 507 3 HOH HOH . F 6 HOH A 8 508 85 HOH HOH . F 6 HOH A 9 509 59 HOH HOH . F 6 HOH A 10 510 61 HOH HOH . F 6 HOH A 11 511 4 HOH HOH . F 6 HOH A 12 512 68 HOH HOH . F 6 HOH A 13 513 48 HOH HOH . F 6 HOH A 14 514 18 HOH HOH . F 6 HOH A 15 515 32 HOH HOH . F 6 HOH A 16 516 126 HOH HOH . F 6 HOH A 17 517 54 HOH HOH . F 6 HOH A 18 518 117 HOH HOH . F 6 HOH A 19 519 5 HOH HOH . F 6 HOH A 20 520 13 HOH HOH . F 6 HOH A 21 521 1 HOH HOH . F 6 HOH A 22 522 64 HOH HOH . F 6 HOH A 23 523 60 HOH HOH . F 6 HOH A 24 524 31 HOH HOH . F 6 HOH A 25 525 10 HOH HOH . F 6 HOH A 26 526 19 HOH HOH . F 6 HOH A 27 527 58 HOH HOH . F 6 HOH A 28 528 41 HOH HOH . F 6 HOH A 29 529 35 HOH HOH . F 6 HOH A 30 530 25 HOH HOH . F 6 HOH A 31 531 42 HOH HOH . F 6 HOH A 32 532 6 HOH HOH . F 6 HOH A 33 533 8 HOH HOH . F 6 HOH A 34 534 11 HOH HOH . F 6 HOH A 35 535 2 HOH HOH . F 6 HOH A 36 536 27 HOH HOH . F 6 HOH A 37 537 39 HOH HOH . F 6 HOH A 38 538 34 HOH HOH . F 6 HOH A 39 539 90 HOH HOH . F 6 HOH A 40 540 36 HOH HOH . F 6 HOH A 41 541 24 HOH HOH . F 6 HOH A 42 542 22 HOH HOH . F 6 HOH A 43 543 51 HOH HOH . F 6 HOH A 44 544 40 HOH HOH . F 6 HOH A 45 545 21 HOH HOH . F 6 HOH A 46 546 110 HOH HOH . F 6 HOH A 47 547 20 HOH HOH . F 6 HOH A 48 548 16 HOH HOH . F 6 HOH A 49 549 109 HOH HOH . F 6 HOH A 50 550 74 HOH HOH . F 6 HOH A 51 551 49 HOH HOH . F 6 HOH A 52 552 46 HOH HOH . F 6 HOH A 53 553 76 HOH HOH . F 6 HOH A 54 554 69 HOH HOH . F 6 HOH A 55 555 55 HOH HOH . F 6 HOH A 56 556 28 HOH HOH . F 6 HOH A 57 557 15 HOH HOH . F 6 HOH A 58 558 72 HOH HOH . F 6 HOH A 59 559 71 HOH HOH . F 6 HOH A 60 560 98 HOH HOH . F 6 HOH A 61 561 70 HOH HOH . F 6 HOH A 62 562 23 HOH HOH . F 6 HOH A 63 563 33 HOH HOH . F 6 HOH A 64 564 7 HOH HOH . F 6 HOH A 65 565 38 HOH HOH . F 6 HOH A 66 566 14 HOH HOH . F 6 HOH A 67 567 63 HOH HOH . F 6 HOH A 68 568 80 HOH HOH . F 6 HOH A 69 569 100 HOH HOH . F 6 HOH A 70 570 62 HOH HOH . F 6 HOH A 71 571 95 HOH HOH . F 6 HOH A 72 572 50 HOH HOH . F 6 HOH A 73 573 89 HOH HOH . F 6 HOH A 74 574 67 HOH HOH . F 6 HOH A 75 575 53 HOH HOH . F 6 HOH A 76 576 114 HOH HOH . F 6 HOH A 77 577 30 HOH HOH . F 6 HOH A 78 578 82 HOH HOH . F 6 HOH A 79 579 81 HOH HOH . F 6 HOH A 80 580 94 HOH HOH . F 6 HOH A 81 581 105 HOH HOH . F 6 HOH A 82 582 43 HOH HOH . F 6 HOH A 83 583 47 HOH HOH . F 6 HOH A 84 584 102 HOH HOH . F 6 HOH A 85 585 124 HOH HOH . F 6 HOH A 86 586 45 HOH HOH . F 6 HOH A 87 587 57 HOH HOH . F 6 HOH A 88 588 122 HOH HOH . F 6 HOH A 89 589 127 HOH HOH . F 6 HOH A 90 590 119 HOH HOH . F 6 HOH A 91 591 118 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 N N1 CTP . . . B 2 -12.071 -3.366 19.364 1 18.19 ? N1 CTP 401 A 1 HETATM 2 C C2 CTP . . . B 2 -13.126 -2.495 19.067 1 16.77 ? C2 CTP 401 A 1 HETATM 3 N N3 CTP . . . B 2 -12.883 -1.237 18.684 1 16.4 ? N3 CTP 401 A 1 HETATM 4 C C4 CTP . . . B 2 -11.62 -0.796 18.587 1 18.91 ? C4 CTP 401 A 1 HETATM 5 C C5 CTP . . . B 2 -10.567 -1.645 18.884 1 17.79 ? C5 CTP 401 A 1 HETATM 6 C C6 CTP . . . B 2 -10.817 -2.947 19.275 1 19.22 ? C6 CTP 401 A 1 HETATM 7 O O2 CTP . . . B 2 -14.293 -2.896 19.159 1 18.64 ? O2 CTP 401 A 1 HETATM 8 N N4 CTP . . . B 2 -11.375 0.473 18.202 1 14.46 ? N4 CTP 401 A 1 HETATM 9 C C1' CTP . . . B 2 -12.391 -4.725 19.789 1 20.39 ? C1' CTP 401 A 1 HETATM 10 C C2' CTP . . . B 2 -11.939 -5.768 18.794 1 18.25 ? C2' CTP 401 A 1 HETATM 11 O O2' CTP . . . B 2 -12.907 -5.887 17.768 1 20.55 ? O2' CTP 401 A 1 HETATM 12 C C3' CTP . . . B 2 -11.811 -7 19.657 1 17.6 ? C3' CTP 401 A 1 HETATM 13 C C4' CTP . . . B 2 -11.773 -6.504 21.088 1 23.02 ? C4' CTP 401 A 1 HETATM 14 O O4' CTP . . . B 2 -11.719 -5.083 20.992 1 22.48 ? O4' CTP 401 A 1 HETATM 15 O O3' CTP . . . B 2 -12.947 -7.832 19.532 1 16.99 ? O3' CTP 401 A 1 HETATM 16 C C5' CTP . . . B 2 -10.618 -7.101 21.898 1 20.32 ? C5' CTP 401 A 1 HETATM 17 O O5' CTP . . . B 2 -9.444 -7.29 21.125 1 22.27 ? O5' CTP 401 A 1 HETATM 18 P PA CTP . . . B 2 -8.678 -8.693 21.022 1 16.98 ? PA CTP 401 A 1 HETATM 19 O O1A CTP . . . B 2 -9.336 -9.727 21.86 1 14.38 ? O1A CTP 401 A 1 HETATM 20 O O2A CTP . . . B 2 -7.24 -8.407 21.265 1 24.68 ? O2A CTP 401 A 1 HETATM 21 O O3A CTP . . . B 2 -8.916 -9.007 19.463 1 20.26 ? O3A CTP 401 A 1 HETATM 22 P PB CTP . . . B 2 -8.206 -10.135 18.569 1 18.24 ? PB CTP 401 A 1 HETATM 23 O O1B CTP . . . B 2 -8.609 -11.486 19.075 1 18.82 ? O1B CTP 401 A 1 HETATM 24 O O2B CTP . . . B 2 -8.509 -9.796 17.151 1 18.6 ? O2B CTP 401 A 1 HETATM 25 O O3B CTP . . . B 2 -6.648 -9.895 18.832 1 21.65 ? O3B CTP 401 A 1 HETATM 26 P PG CTP . . . B 2 -5.498 -10.968 18.522 1 21.46 ? PG CTP 401 A 1 HETATM 27 O O1G CTP . . . B 2 -5.518 -11.877 19.705 1 24.98 ? O1G CTP 401 A 1 HETATM 28 O O2G CTP . . . B 2 -4.27 -10.125 18.436 1 23.84 ? O2G CTP 401 A 1 HETATM 29 O O3G CTP . . . B 2 -5.852 -11.61 17.224 1 20.97 ? O3G CTP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 701 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 29 #