data_7Y9I # _model_server_result.job_id xSc3QbEeDMG7o6w5pToneg _model_server_result.datetime_utc '2025-03-09 02:07:33' _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 7y9i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7Y9I # _exptl.entry_id 7Y9I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 603.16 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5',3'-TETRAPHOSPHATE" _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 7Y9I _cell.length_a 72.46 _cell.length_b 111.5 _cell.length_c 52.33 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Y9I _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 _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 _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 OG SER 38 A SER 38 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc2 B O3B G4P . A G4P 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? # _chem_comp.formula 'C10 H17 N5 O17 P4' _chem_comp.formula_weight 603.16 _chem_comp.id G4P _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5',3'-TETRAPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms 'guanosine tetraphosphate;ppGpp' # 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 PB O1B G4P doub 83 n n PB O2B G4P sing 84 n n PB O3B G4P sing 85 n n PB O3A G4P sing 86 n n O2B HOB2 G4P sing 87 n n O3B HOB3 G4P sing 88 n n O3A PA G4P sing 89 n n PA O1A G4P doub 90 n n PA O2A G4P sing 91 n n PA O5' G4P sing 92 n n O2A HOA2 G4P sing 93 n n O5' C5' G4P sing 94 n n C5' C4' G4P sing 95 n n C5' H5' G4P sing 96 n n C5' "H5''" G4P sing 97 n n C4' O4' G4P sing 98 n n C4' C3' G4P sing 99 n n C4' H4' G4P sing 100 n n O4' C1' G4P sing 101 n n C3' O3' G4P sing 102 n n C3' C2' G4P sing 103 n n C3' H3' G4P sing 104 n n O3' PC G4P sing 105 n n C2' O2' G4P sing 106 n n C2' C1' G4P sing 107 n n C2' H2' G4P sing 108 n n O2' HO2' G4P sing 109 n n C1' N9 G4P sing 110 n n C1' H1' G4P sing 111 n n N9 C8 G4P sing 112 n y N9 C4 G4P sing 113 n y C8 N7 G4P doub 114 n y C8 H8 G4P sing 115 n n N7 C5 G4P sing 116 n y C5 C6 G4P sing 117 n n C5 C4 G4P doub 118 n y C6 O6 G4P doub 119 n n C6 N1 G4P sing 120 n n N1 C2 G4P sing 121 n n N1 HN1 G4P sing 122 n n C2 N2 G4P sing 123 n n C2 N3 G4P doub 124 n n N2 HN21 G4P sing 125 n n N2 HN22 G4P sing 126 n n N3 C4 G4P sing 127 n n PC O1C G4P doub 128 n n PC O2C G4P sing 129 n n PC O3C G4P sing 130 n n O2C H2C G4P sing 131 n n O3C PD G4P sing 132 n n PD O1D G4P doub 133 n n PD O2D G4P sing 134 n n PD O3D G4P sing 135 n n O2D H2D G4P sing 136 n n O3D H3D G4P sing 137 n n # _atom_sites.entry_id 7Y9I _atom_sites.fract_transf_matrix[1][1] 0.013801 _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] 0.008969 _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] 0.019109 _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 G4P A 1 401 202 G4P G4P . C 3 MG A 1 402 203 MG MG . D 4 HOH A 1 501 40 HOH HOH . D 4 HOH A 2 502 6 HOH HOH . D 4 HOH A 3 503 56 HOH HOH . D 4 HOH A 4 504 23 HOH HOH . D 4 HOH A 5 505 58 HOH HOH . D 4 HOH A 6 506 33 HOH HOH . D 4 HOH A 7 507 35 HOH HOH . D 4 HOH A 8 508 43 HOH HOH . D 4 HOH A 9 509 44 HOH HOH . D 4 HOH A 10 510 14 HOH HOH . D 4 HOH A 11 511 54 HOH HOH . D 4 HOH A 12 512 37 HOH HOH . D 4 HOH A 13 513 29 HOH HOH . D 4 HOH A 14 514 52 HOH HOH . D 4 HOH A 15 515 18 HOH HOH . D 4 HOH A 16 516 60 HOH HOH . D 4 HOH A 17 517 31 HOH HOH . D 4 HOH A 18 518 21 HOH HOH . D 4 HOH A 19 519 36 HOH HOH . D 4 HOH A 20 520 46 HOH HOH . D 4 HOH A 21 521 5 HOH HOH . D 4 HOH A 22 522 24 HOH HOH . D 4 HOH A 23 523 11 HOH HOH . D 4 HOH A 24 524 34 HOH HOH . D 4 HOH A 25 525 47 HOH HOH . D 4 HOH A 26 526 2 HOH HOH . D 4 HOH A 27 527 9 HOH HOH . D 4 HOH A 28 528 28 HOH HOH . D 4 HOH A 29 529 1 HOH HOH . D 4 HOH A 30 530 19 HOH HOH . D 4 HOH A 31 531 7 HOH HOH . D 4 HOH A 32 532 10 HOH HOH . D 4 HOH A 33 533 49 HOH HOH . D 4 HOH A 34 534 15 HOH HOH . D 4 HOH A 35 535 50 HOH HOH . D 4 HOH A 36 536 48 HOH HOH . D 4 HOH A 37 537 53 HOH HOH . D 4 HOH A 38 538 39 HOH HOH . D 4 HOH A 39 539 16 HOH HOH . D 4 HOH A 40 540 57 HOH HOH . D 4 HOH A 41 541 4 HOH HOH . D 4 HOH A 42 542 45 HOH HOH . D 4 HOH A 43 543 55 HOH HOH . D 4 HOH A 44 544 25 HOH HOH . D 4 HOH A 45 545 12 HOH HOH . D 4 HOH A 46 546 38 HOH HOH . D 4 HOH A 47 547 22 HOH HOH . D 4 HOH A 48 548 20 HOH HOH . D 4 HOH A 49 549 51 HOH HOH . D 4 HOH A 50 550 3 HOH HOH . D 4 HOH A 51 551 59 HOH HOH . D 4 HOH A 52 552 26 HOH HOH . D 4 HOH A 53 553 8 HOH HOH . D 4 HOH A 54 554 27 HOH HOH . D 4 HOH A 55 555 61 HOH HOH . D 4 HOH A 56 556 17 HOH HOH . D 4 HOH A 57 557 42 HOH HOH . D 4 HOH A 58 558 30 HOH HOH . D 4 HOH A 59 559 32 HOH HOH . D 4 HOH A 60 560 13 HOH HOH . D 4 HOH A 61 561 41 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 P PB G4P . . . B 2 18.846 -45.719 -32.052 1 44.81 0 PB G4P 401 A 1 HETATM 2 O O1B G4P . . . B 2 19.512 -47.072 -31.814 1 44.03 0 O1B G4P 401 A 1 HETATM 3 O O2B G4P . . . B 2 17.674 -45.552 -31.086 1 40.32 -1 O2B G4P 401 A 1 HETATM 4 O O3B G4P . . . B 2 19.825 -44.554 -32.043 1 44.13 0 O3B G4P 401 A 1 HETATM 5 O O3A G4P . . . B 2 18.083 -45.701 -33.463 1 44.41 0 O3A G4P 401 A 1 HETATM 6 P PA G4P . . . B 2 18.437 -44.825 -34.767 1 46.96 0 PA G4P 401 A 1 HETATM 7 O O1A G4P . . . B 2 19.946 -44.94 -34.916 1 49.28 -1 O1A G4P 401 A 1 HETATM 8 O O2A G4P . . . B 2 17.732 -43.502 -34.804 1 47.54 0 O2A G4P 401 A 1 HETATM 9 O O5' G4P . . . B 2 17.757 -45.673 -35.95 1 50.31 0 O5' G4P 401 A 1 HETATM 10 C C5' G4P . . . B 2 18.258 -46.999 -36.125 1 52.04 0 C5' G4P 401 A 1 HETATM 11 C C4' G4P . . . B 2 17.266 -47.863 -36.882 1 55.15 0 C4' G4P 401 A 1 HETATM 12 O O4' G4P . . . B 2 16.103 -48.135 -36.091 1 53.17 0 O4' G4P 401 A 1 HETATM 13 C C3' G4P . . . B 2 16.811 -47.269 -38.203 1 58.38 0 C3' G4P 401 A 1 HETATM 14 O O3' G4P . . . B 2 17.719 -47.6 -39.271 1 65.84 0 O3' G4P 401 A 1 HETATM 15 C C2' G4P . . . B 2 15.444 -47.908 -38.327 1 59.27 0 C2' G4P 401 A 1 HETATM 16 O O2' G4P . . . B 2 15.472 -49.275 -38.738 1 64.77 0 O2' G4P 401 A 1 HETATM 17 C C1' G4P . . . B 2 14.949 -47.988 -36.916 1 56.15 0 C1' G4P 401 A 1 HETATM 18 N N9 G4P . . . B 2 14.206 -46.758 -36.598 1 59.87 0 N9 G4P 401 A 1 HETATM 19 C C8 G4P . . . B 2 14.635 -45.684 -35.878 1 59.06 0 C8 G4P 401 A 1 HETATM 20 N N7 G4P . . . B 2 13.657 -44.758 -35.797 1 55.21 0 N7 G4P 401 A 1 HETATM 21 C C5 G4P . . . B 2 12.599 -45.224 -36.471 1 52.76 0 C5 G4P 401 A 1 HETATM 22 C C6 G4P . . . B 2 11.245 -44.745 -36.77 1 52.3 0 C6 G4P 401 A 1 HETATM 23 O O6 G4P . . . B 2 10.898 -43.646 -36.318 1 49.28 0 O6 G4P 401 A 1 HETATM 24 N N1 G4P . . . B 2 10.432 -45.529 -37.517 1 57.39 0 N1 G4P 401 A 1 HETATM 25 C C2 G4P . . . B 2 10.864 -46.739 -37.97 1 58.67 0 C2 G4P 401 A 1 HETATM 26 N N2 G4P . . . B 2 10.054 -47.517 -38.703 1 53.46 0 N2 G4P 401 A 1 HETATM 27 N N3 G4P . . . B 2 12.103 -47.245 -37.729 1 54.33 0 N3 G4P 401 A 1 HETATM 28 C C4 G4P . . . B 2 12.974 -46.541 -37.002 1 54.15 0 C4 G4P 401 A 1 HETATM 29 P PC G4P . . . B 2 17.914 -46.702 -40.608 1 80.23 0 PC G4P 401 A 1 HETATM 30 O O1C G4P . . . B 2 19.073 -47.244 -41.429 1 92.47 -1 O1C G4P 401 A 1 HETATM 31 O O2C G4P . . . B 2 17.977 -45.237 -40.255 1 77.38 0 O2C G4P 401 A 1 HETATM 32 O O3C G4P . . . B 2 16.523 -47.075 -41.332 1 91.18 0 O3C G4P 401 A 1 HETATM 33 P PD G4P . . . B 2 16.336 -48.441 -42.191 1 106.81 0 PD G4P 401 A 1 HETATM 34 O O1D G4P . . . B 2 14.907 -48.884 -41.938 1 93.99 0 O1D G4P 401 A 1 HETATM 35 O O2D G4P . . . B 2 16.672 -47.895 -43.57 1 102.98 -1 O2D G4P 401 A 1 HETATM 36 O O3D G4P . . . B 2 17.321 -49.467 -41.676 1 97.77 0 O3D G4P 401 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 36 #