data_5WZY # _model_server_result.job_id FjtV85IoNFhC_LcxoZZb2Q _model_server_result.datetime_utc '2024-11-04 22:55:29' _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 5wzy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":510}' # _entry.id 5WZY # _exptl.entry_id 5WZY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 5 _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 120 _cell.entry_id 5WZY _cell.length_a 129.242 _cell.length_b 129.242 _cell.length_c 251.825 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WZY _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 64.621 -111.926855 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 129.242 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 2 6 3 MAN BMA C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 501 NAG 2 n B NAG 2 B 2 NAG A 502 NAG 2 n B BMA 3 B 3 BMA A 503 BMA 2 n B MAN 4 B 4 MAN A 505 MAN 2 n B MAN 5 B 5 MAN A 506 MAN 2 n B MAN 6 B 6 MAN A 504 MAN # 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 disulf ? disulf1 A SG CYS 94 A CYS 119 1_555 A SG CYS 143 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf2 A SG CYS 104 A CYS 129 1_555 A SG CYS 127 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 110 A CYS 135 1_555 A SG CYS 137 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 A SG CYS 195 A CYS 220 1_555 A SG CYS 205 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf5 A SG CYS 239 A CYS 264 1_555 A SG CYS 248 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? covale ? covale1 A ND2 ASN 88 A ASN 113 1_555 C C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 A ND2 ASN 188 A ASN 213 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale5 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale6 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 B O3 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? # _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 ? # _atom_sites.entry_id 5WZY _atom_sites.fract_transf_matrix[1][1] 0.007737 _atom_sites.fract_transf_matrix[1][2] 0.004467 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008934 _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] 0.003971 _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 C 3 NAG A 1 507 507 NAG NAG . D 4 GOL A 1 508 509 GOL GOL . E 4 GOL A 1 509 510 GOL GOL . F 5 CTP A 1 510 1 CTP CTP . G 6 HOH A 1 601 29 HOH HOH . G 6 HOH A 2 602 39 HOH HOH . G 6 HOH A 3 603 56 HOH HOH . G 6 HOH A 4 604 69 HOH HOH . G 6 HOH A 5 605 16 HOH HOH . G 6 HOH A 6 606 3 HOH HOH . G 6 HOH A 7 607 38 HOH HOH . G 6 HOH A 8 608 41 HOH HOH . G 6 HOH A 9 609 59 HOH HOH . G 6 HOH A 10 610 71 HOH HOH . G 6 HOH A 11 611 9 HOH HOH . G 6 HOH A 12 612 70 HOH HOH . G 6 HOH A 13 613 62 HOH HOH . G 6 HOH A 14 614 26 HOH HOH . G 6 HOH A 15 615 45 HOH HOH . G 6 HOH A 16 616 7 HOH HOH . G 6 HOH A 17 617 60 HOH HOH . G 6 HOH A 18 618 53 HOH HOH . G 6 HOH A 19 619 65 HOH HOH . G 6 HOH A 20 620 18 HOH HOH . G 6 HOH A 21 621 28 HOH HOH . G 6 HOH A 22 622 57 HOH HOH . G 6 HOH A 23 623 21 HOH HOH . G 6 HOH A 24 624 52 HOH HOH . G 6 HOH A 25 625 63 HOH HOH . G 6 HOH A 26 626 12 HOH HOH . G 6 HOH A 27 627 4 HOH HOH . G 6 HOH A 28 628 27 HOH HOH . G 6 HOH A 29 629 5 HOH HOH . G 6 HOH A 30 630 35 HOH HOH . G 6 HOH A 31 631 33 HOH HOH . G 6 HOH A 32 632 11 HOH HOH . G 6 HOH A 33 633 58 HOH HOH . G 6 HOH A 34 634 23 HOH HOH . G 6 HOH A 35 635 6 HOH HOH . G 6 HOH A 36 636 32 HOH HOH . G 6 HOH A 37 637 14 HOH HOH . G 6 HOH A 38 638 64 HOH HOH . G 6 HOH A 39 639 25 HOH HOH . G 6 HOH A 40 640 13 HOH HOH . G 6 HOH A 41 641 68 HOH HOH . G 6 HOH A 42 642 43 HOH HOH . G 6 HOH A 43 643 49 HOH HOH . G 6 HOH A 44 644 54 HOH HOH . G 6 HOH A 45 645 55 HOH HOH . G 6 HOH A 46 646 36 HOH HOH . G 6 HOH A 47 647 34 HOH HOH . G 6 HOH A 48 648 48 HOH HOH . G 6 HOH A 49 649 22 HOH HOH . G 6 HOH A 50 650 8 HOH HOH . G 6 HOH A 51 651 30 HOH HOH . G 6 HOH A 52 652 20 HOH HOH . G 6 HOH A 53 653 17 HOH HOH . G 6 HOH A 54 654 2 HOH HOH . G 6 HOH A 55 655 67 HOH HOH . G 6 HOH A 56 656 37 HOH HOH . G 6 HOH A 57 657 66 HOH HOH . G 6 HOH A 58 658 10 HOH HOH . G 6 HOH A 59 659 15 HOH HOH . G 6 HOH A 60 660 42 HOH HOH . G 6 HOH A 61 661 72 HOH HOH . G 6 HOH A 62 662 61 HOH HOH . G 6 HOH A 63 663 19 HOH HOH . G 6 HOH A 64 664 46 HOH HOH . G 6 HOH A 65 665 40 HOH HOH . G 6 HOH A 66 666 47 HOH HOH . G 6 HOH A 67 667 51 HOH HOH . G 6 HOH A 68 668 50 HOH HOH . G 6 HOH A 69 669 31 HOH HOH . G 6 HOH A 70 670 1 HOH HOH . G 6 HOH A 71 671 24 HOH HOH . G 6 HOH A 72 672 44 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 . . . F 5 43.071 -41.548 -9.204 1 58.8 ? N1 CTP 510 A 1 HETATM 2 C C2 CTP . . . F 5 42.845 -42.89 -8.988 1 58.95 ? C2 CTP 510 A 1 HETATM 3 N N3 CTP . . . F 5 43.845 -43.813 -9.229 1 64.09 ? N3 CTP 510 A 1 HETATM 4 C C4 CTP . . . F 5 45.144 -43.355 -9.409 1 55.5 ? C4 CTP 510 A 1 HETATM 5 C C5 CTP . . . F 5 45.381 -41.998 -9.555 1 53.22 ? C5 CTP 510 A 1 HETATM 6 C C6 CTP . . . F 5 44.3 -41.129 -9.632 1 55.14 ? C6 CTP 510 A 1 HETATM 7 O O2 CTP . . . F 5 41.75 -43.25 -8.588 1 60.97 ? O2 CTP 510 A 1 HETATM 8 N N4 CTP . . . F 5 46.161 -44.201 -9.439 1 50.32 ? N4 CTP 510 A 1 HETATM 9 C C1' CTP . . . F 5 41.909 -40.658 -9.322 1 54.63 ? C1' CTP 510 A 1 HETATM 10 C C2' CTP . . . F 5 41.899 -39.584 -8.254 1 53.96 ? C2' CTP 510 A 1 HETATM 11 O O2' CTP . . . F 5 41.457 -40.018 -6.998 1 55.81 ? O2' CTP 510 A 1 HETATM 12 C C3' CTP . . . F 5 40.922 -38.607 -8.858 1 63.47 ? C3' CTP 510 A 1 HETATM 13 C C4' CTP . . . F 5 41.215 -38.734 -10.343 1 58.17 ? C4' CTP 510 A 1 HETATM 14 O O4' CTP . . . F 5 41.962 -39.919 -10.519 1 53.84 ? O4' CTP 510 A 1 HETATM 15 O O3' CTP . . . F 5 39.583 -38.974 -8.556 1 64.97 ? O3' CTP 510 A 1 HETATM 16 C C5' CTP . . . F 5 41.965 -37.492 -10.828 1 59.8 ? C5' CTP 510 A 1 HETATM 17 O O5' CTP . . . F 5 43.365 -37.535 -10.634 1 60.6 ? O5' CTP 510 A 1 HETATM 18 P PA CTP . . . F 5 44.101 -36.373 -9.797 1 57.17 ? PA CTP 510 A 1 HETATM 19 O O1A CTP . . . F 5 43.759 -35.052 -10.425 1 49.74 ? O1A CTP 510 A 1 HETATM 20 O O2A CTP . . . F 5 45.596 -36.595 -9.737 1 53.49 ? O2A CTP 510 A 1 HETATM 21 O O3A CTP . . . F 5 43.408 -36.636 -8.368 1 53.9 ? O3A CTP 510 A 1 HETATM 22 P PB CTP . . . F 5 43.422 -35.663 -7.099 1 59.56 ? PB CTP 510 A 1 HETATM 23 O O1B CTP . . . F 5 42.429 -34.534 -7.244 1 64.75 ? O1B CTP 510 A 1 HETATM 24 O O2B CTP . . . F 5 44.785 -35.107 -6.805 1 65.79 ? O2B CTP 510 A 1 HETATM 25 O O3B CTP . . . F 5 42.875 -36.625 -5.943 1 59.54 ? O3B CTP 510 A 1 HETATM 26 P PG CTP . . . F 5 43.697 -37.81 -5.241 1 56.21 ? PG CTP 510 A 1 HETATM 27 O O1G CTP . . . F 5 44.817 -38.32 -6.095 1 55.76 ? O1G CTP 510 A 1 HETATM 28 O O2G CTP . . . F 5 42.767 -38.97 -4.972 1 60.59 ? O2G CTP 510 A 1 HETATM 29 O O3G CTP . . . F 5 44.225 -37.255 -3.949 1 60.32 ? O3G CTP 510 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #