data_5MFU # _model_server_result.job_id 4C387iB-MOEFn5AF4ZvZQA _model_server_result.datetime_utc '2024-11-25 23:18:30' _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 5mfu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 5MFU # _exptl.entry_id 5MFU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 5MFU _cell.length_a 64.78 _cell.length_b 64.78 _cell.length_c 135.787 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MFU _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N 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 OE2 GLU 35 A GLU 39 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc2 A OD1 ASN 94 A ASN 98 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 A OE1 GLU 126 A GLU 130 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc4 A OD2 ASP 156 A ASP 160 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc5 A OD2 ASP 156 A ASP 160 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc6 B MN MN . A MN 501 1_555 D OP1 G . A G 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc7 B MN MN . A MN 501 1_555 F O HOH . A HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc8 C NA NA . A NA 502 1_555 D OP2 G . A G 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc9 C NA NA . A NA 502 1_555 E O2' G . A G 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc10 C NA NA . A NA 502 1_555 F O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc11 C NA NA . A NA 502 1_555 F O HOH . A HOH 666 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id G _chem_comp.mon_nstd_flag y _chem_comp.name "GUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type 'rna linking' _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 OP3 P G sing 83 n n OP3 HOP3 G sing 84 n n P OP1 G doub 85 n n P OP2 G sing 86 n n P O5' G sing 87 n n OP2 HOP2 G sing 88 n n O5' C5' G sing 89 n n C5' C4' G sing 90 n n C5' H5' G sing 91 n n C5' "H5''" G sing 92 n n C4' O4' G sing 93 n n C4' C3' G sing 94 n n C4' H4' G sing 95 n n O4' C1' G sing 96 n n C3' O3' G sing 97 n n C3' C2' G sing 98 n n C3' H3' G sing 99 n n O3' HO3' G sing 100 n n C2' O2' G sing 101 n n C2' C1' G sing 102 n n C2' H2' G sing 103 n n O2' HO2' G sing 104 n n C1' N9 G sing 105 n n C1' H1' G sing 106 n n N9 C8 G sing 107 n y N9 C4 G sing 108 n y C8 N7 G doub 109 n y C8 H8 G sing 110 n n N7 C5 G sing 111 n y C5 C6 G sing 112 n n C5 C4 G doub 113 n y C6 O6 G doub 114 n n C6 N1 G sing 115 n n N1 C2 G sing 116 n n N1 H1 G sing 117 n n C2 N2 G sing 118 n n C2 N3 G doub 119 n n N2 H21 G sing 120 n n N2 H22 G sing 121 n n N3 C4 G sing 122 n n # _atom_sites.entry_id 5MFU _atom_sites.fract_transf_matrix[1][1] 0.015437 _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] 0.015437 _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] 0.007364 _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 MN A 1 501 501 MN Mn . C 3 NA A 1 502 502 NA NA . D 4 G A 1 503 601 G G . E 4 G A 1 504 602 G G . F 5 HOH A 1 601 1237 HOH HOH . F 5 HOH A 2 602 1217 HOH HOH . F 5 HOH A 3 603 998 HOH HOH . F 5 HOH A 4 604 1000 HOH HOH . F 5 HOH A 5 605 1100 HOH HOH . F 5 HOH A 6 606 1215 HOH HOH . F 5 HOH A 7 607 66 HOH HOH . F 5 HOH A 8 608 26 HOH HOH . F 5 HOH A 9 609 1222 HOH HOH . F 5 HOH A 10 610 1223 HOH HOH . F 5 HOH A 11 611 123 HOH HOH . F 5 HOH A 12 612 16 HOH HOH . F 5 HOH A 13 613 1018 HOH HOH . F 5 HOH A 14 614 1101 HOH HOH . F 5 HOH A 15 615 101 HOH HOH . F 5 HOH A 16 616 103 HOH HOH . F 5 HOH A 17 617 49 HOH HOH . F 5 HOH A 18 618 3 HOH HOH . F 5 HOH A 19 619 36 HOH HOH . F 5 HOH A 20 620 1220 HOH HOH . F 5 HOH A 21 621 1209 HOH HOH . F 5 HOH A 22 622 670 HOH HOH . F 5 HOH A 23 623 1022 HOH HOH . F 5 HOH A 24 624 65 HOH HOH . F 5 HOH A 25 625 5 HOH HOH . F 5 HOH A 26 626 1208 HOH HOH . F 5 HOH A 27 627 688 HOH HOH . F 5 HOH A 28 628 1204 HOH HOH . F 5 HOH A 29 629 17 HOH HOH . F 5 HOH A 30 630 1074 HOH HOH . F 5 HOH A 31 631 61 HOH HOH . F 5 HOH A 32 632 45 HOH HOH . F 5 HOH A 33 633 1008 HOH HOH . F 5 HOH A 34 634 1206 HOH HOH . F 5 HOH A 35 635 1034 HOH HOH . F 5 HOH A 36 636 634 HOH HOH . F 5 HOH A 37 637 994 HOH HOH . F 5 HOH A 38 638 1150 HOH HOH . F 5 HOH A 39 639 675 HOH HOH . F 5 HOH A 40 640 1043 HOH HOH . F 5 HOH A 41 641 35 HOH HOH . F 5 HOH A 42 642 29 HOH HOH . F 5 HOH A 43 643 647 HOH HOH . F 5 HOH A 44 644 717 HOH HOH . F 5 HOH A 45 645 43 HOH HOH . F 5 HOH A 46 646 50 HOH HOH . F 5 HOH A 47 647 34 HOH HOH . F 5 HOH A 48 648 20 HOH HOH . F 5 HOH A 49 649 107 HOH HOH . F 5 HOH A 50 650 705 HOH HOH . F 5 HOH A 51 651 111 HOH HOH . F 5 HOH A 52 652 55 HOH HOH . F 5 HOH A 53 653 561 HOH HOH . F 5 HOH A 54 654 198 HOH HOH . F 5 HOH A 55 655 345 HOH HOH . F 5 HOH A 56 656 654 HOH HOH . F 5 HOH A 57 657 347 HOH HOH . F 5 HOH A 58 658 13 HOH HOH . F 5 HOH A 59 659 645 HOH HOH . F 5 HOH A 60 660 576 HOH HOH . F 5 HOH A 61 661 27 HOH HOH . F 5 HOH A 62 662 11 HOH HOH . F 5 HOH A 63 663 1210 HOH HOH . F 5 HOH A 64 664 1027 HOH HOH . F 5 HOH A 65 665 563 HOH HOH . F 5 HOH A 66 666 1232 HOH HOH . F 5 HOH A 67 667 633 HOH HOH . F 5 HOH A 68 668 1012 HOH HOH . F 5 HOH A 69 669 63 HOH HOH . F 5 HOH A 70 670 19 HOH HOH . F 5 HOH A 71 671 1075 HOH HOH . F 5 HOH A 72 672 108 HOH HOH . F 5 HOH A 73 673 48 HOH HOH . F 5 HOH A 74 674 39 HOH HOH . F 5 HOH A 75 675 1094 HOH HOH . F 5 HOH A 76 676 62 HOH HOH . F 5 HOH A 77 677 1039 HOH HOH . F 5 HOH A 78 678 18 HOH HOH . F 5 HOH A 79 679 559 HOH HOH . F 5 HOH A 80 680 1004 HOH HOH . F 5 HOH A 81 681 659 HOH HOH . F 5 HOH A 82 682 993 HOH HOH . F 5 HOH A 83 683 40 HOH HOH . F 5 HOH A 84 684 1236 HOH HOH . F 5 HOH A 85 685 1068 HOH HOH . F 5 HOH A 86 686 1205 HOH HOH . F 5 HOH A 87 687 78 HOH HOH . F 5 HOH A 88 688 85 HOH HOH . F 5 HOH A 89 689 1109 HOH HOH . F 5 HOH A 90 690 344 HOH HOH . F 5 HOH A 91 691 56 HOH HOH . F 5 HOH A 92 692 1235 HOH HOH . F 5 HOH A 93 693 1119 HOH HOH . F 5 HOH A 94 694 115 HOH HOH . F 5 HOH A 95 695 652 HOH HOH . F 5 HOH A 96 696 558 HOH HOH . F 5 HOH A 97 697 1218 HOH HOH . F 5 HOH A 98 698 1214 HOH HOH . F 5 HOH A 99 699 1071 HOH HOH . F 5 HOH A 100 700 22 HOH HOH . F 5 HOH A 101 701 1221 HOH HOH . F 5 HOH A 102 702 1021 HOH HOH . F 5 HOH A 103 703 1229 HOH HOH . F 5 HOH A 104 704 1098 HOH HOH . F 5 HOH A 105 705 667 HOH HOH . F 5 HOH A 106 706 1122 HOH HOH . F 5 HOH A 107 707 1111 HOH HOH . F 5 HOH A 108 708 1233 HOH HOH . F 5 HOH A 109 709 1179 HOH HOH . F 5 HOH A 110 710 999 HOH HOH . F 5 HOH A 111 711 1017 HOH HOH . F 5 HOH A 112 712 1013 HOH HOH . F 5 HOH A 113 713 348 HOH HOH . F 5 HOH A 114 714 830 HOH HOH . F 5 HOH A 115 715 1193 HOH HOH . F 5 HOH A 116 716 973 HOH HOH . F 5 HOH A 117 717 959 HOH HOH . F 5 HOH A 118 718 73 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 OP3 G . . . D 4 -9.021 22.526 29.902 1 59.34 ? OP3 G 503 A 1 HETATM 2 P P G . . . D 4 -10.311 23.246 30.014 1 69.73 ? P G 503 A 1 HETATM 3 O OP1 G . . . D 4 -10.296 24.456 29.131 1 60.15 ? OP1 G 503 A 1 HETATM 4 O OP2 G . . . D 4 -11.395 22.218 29.876 1 57.49 ? OP2 G 503 A 1 HETATM 5 O O5' G . . . D 4 -10.298 23.745 31.524 1 61.84 ? O5' G 503 A 1 HETATM 6 C C5' G . . . D 4 -9.913 25.079 31.904 1 47.74 ? C5' G 503 A 1 HETATM 7 C C4' G . . . D 4 -10.617 25.396 33.2 1 44.35 ? C4' G 503 A 1 HETATM 8 O O4' G . . . D 4 -9.788 25.004 34.332 1 39.04 ? O4' G 503 A 1 HETATM 9 C C3' G . . . D 4 -10.958 26.855 33.426 1 36.75 ? C3' G 503 A 1 HETATM 10 O O3' G . . . D 4 -12.18 26.995 34.14 1 35.74 ? O3' G 503 A 1 HETATM 11 C C2' G . . . D 4 -9.797 27.331 34.264 1 33.52 ? C2' G 503 A 1 HETATM 12 O O2' G . . . D 4 -10.157 28.491 34.945 1 35.06 ? O2' G 503 A 1 HETATM 13 C C1' G . . . D 4 -9.573 26.119 35.167 1 34.81 ? C1' G 503 A 1 HETATM 14 N N9 G . . . D 4 -8.205 26.043 35.655 1 30.9 ? N9 G 503 A 1 HETATM 15 C C8 G . . . D 4 -7.08 26.34 34.932 1 31.43 ? C8 G 503 A 1 HETATM 16 N N7 G . . . D 4 -5.978 26.166 35.604 1 32.27 ? N7 G 503 A 1 HETATM 17 C C5 G . . . D 4 -6.398 25.673 36.827 1 28.86 ? C5 G 503 A 1 HETATM 18 C C6 G . . . D 4 -5.647 25.311 37.974 1 25.62 ? C6 G 503 A 1 HETATM 19 O O6 G . . . D 4 -4.419 25.336 38.132 1 23.53 ? O6 G 503 A 1 HETATM 20 N N1 G . . . D 4 -6.469 24.866 38.999 1 25.56 ? N1 G 503 A 1 HETATM 21 C C2 G . . . D 4 -7.846 24.84 38.956 1 30.87 ? C2 G 503 A 1 HETATM 22 N N2 G . . . D 4 -8.466 24.426 40.073 1 31.96 ? N2 G 503 A 1 HETATM 23 N N3 G . . . D 4 -8.559 25.185 37.893 1 27.24 ? N3 G 503 A 1 HETATM 24 C C4 G . . . D 4 -7.775 25.606 36.879 1 28.43 ? C4 G 503 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #