data_7E5A # _model_server_result.job_id gjtAg0QC44VbhTsknkGqCw _model_server_result.datetime_utc '2025-03-05 02:34:58' _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 7e5a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 7E5A # _exptl.entry_id 7E5A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 7E5A _cell.length_a 114.26 _cell.length_b 114.26 _cell.length_c 168.49 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7E5A _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 F 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 OG SER 53 A SER 52 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc2 A OG1 THR 76 A THR 75 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc3 C O2B GDP . A GDP 501 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc4 C O1A GDP . A GDP 501 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc5 B OG SER 53 B SER 52 1_555 H MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc6 B OG1 THR 76 B THR 75 1_555 H MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc7 F O2B GDP . B GDP 501 1_555 H MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _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 PB O1B GDP doub 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 7E5A _atom_sites.fract_transf_matrix[1][1] 0.008752 _atom_sites.fract_transf_matrix[1][2] 0.005053 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010106 _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] 0.005935 _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 2 GDP A 1 501 593 GDP GDP . D 3 AF3 A 1 502 594 AF3 AF3 . E 4 MG A 1 503 595 MG MG . F 2 GDP B 1 501 593 GDP GDP . G 3 AF3 B 1 502 594 AF3 AF3 . H 4 MG B 1 503 595 MG MG . I 5 HOH A 1 601 269 HOH HOH . I 5 HOH A 2 602 26 HOH HOH . I 5 HOH A 3 603 98 HOH HOH . I 5 HOH A 4 604 108 HOH HOH . I 5 HOH A 5 605 155 HOH HOH . I 5 HOH A 6 606 141 HOH HOH . I 5 HOH A 7 607 8 HOH HOH . I 5 HOH A 8 608 3 HOH HOH . I 5 HOH A 9 609 263 HOH HOH . I 5 HOH A 10 610 83 HOH HOH . I 5 HOH A 11 611 35 HOH HOH . I 5 HOH A 12 612 88 HOH HOH . I 5 HOH A 13 613 256 HOH HOH . I 5 HOH A 14 614 30 HOH HOH . I 5 HOH A 15 615 143 HOH HOH . I 5 HOH A 16 616 58 HOH HOH . I 5 HOH A 17 617 15 HOH HOH . I 5 HOH A 18 618 252 HOH HOH . I 5 HOH A 19 619 251 HOH HOH . I 5 HOH A 20 620 250 HOH HOH . I 5 HOH A 21 621 152 HOH HOH . I 5 HOH A 22 622 34 HOH HOH . I 5 HOH A 23 623 179 HOH HOH . I 5 HOH A 24 624 17 HOH HOH . I 5 HOH A 25 625 122 HOH HOH . I 5 HOH A 26 626 145 HOH HOH . I 5 HOH A 27 627 203 HOH HOH . I 5 HOH A 28 628 65 HOH HOH . I 5 HOH A 29 629 74 HOH HOH . I 5 HOH A 30 630 165 HOH HOH . I 5 HOH A 31 631 50 HOH HOH . I 5 HOH A 32 632 87 HOH HOH . I 5 HOH A 33 633 156 HOH HOH . I 5 HOH A 34 634 21 HOH HOH . I 5 HOH A 35 635 61 HOH HOH . I 5 HOH A 36 636 261 HOH HOH . I 5 HOH A 37 637 54 HOH HOH . I 5 HOH A 38 638 16 HOH HOH . I 5 HOH A 39 639 244 HOH HOH . I 5 HOH A 40 640 116 HOH HOH . I 5 HOH A 41 641 245 HOH HOH . I 5 HOH A 42 642 161 HOH HOH . I 5 HOH A 43 643 5 HOH HOH . I 5 HOH A 44 644 33 HOH HOH . I 5 HOH A 45 645 120 HOH HOH . I 5 HOH A 46 646 195 HOH HOH . I 5 HOH A 47 647 37 HOH HOH . I 5 HOH A 48 648 235 HOH HOH . I 5 HOH A 49 649 168 HOH HOH . I 5 HOH A 50 650 29 HOH HOH . I 5 HOH A 51 651 262 HOH HOH . I 5 HOH A 52 652 63 HOH HOH . I 5 HOH A 53 653 23 HOH HOH . I 5 HOH A 54 654 206 HOH HOH . I 5 HOH A 55 655 265 HOH HOH . I 5 HOH A 56 656 243 HOH HOH . I 5 HOH A 57 657 148 HOH HOH . I 5 HOH A 58 658 2 HOH HOH . I 5 HOH A 59 659 267 HOH HOH . I 5 HOH A 60 660 266 HOH HOH . I 5 HOH A 61 661 247 HOH HOH . I 5 HOH A 62 662 224 HOH HOH . I 5 HOH A 63 663 246 HOH HOH . J 5 HOH B 1 601 241 HOH HOH . J 5 HOH B 2 602 258 HOH HOH . J 5 HOH B 3 603 24 HOH HOH . J 5 HOH B 4 604 112 HOH HOH . J 5 HOH B 5 605 259 HOH HOH . J 5 HOH B 6 606 60 HOH HOH . J 5 HOH B 7 607 22 HOH HOH . J 5 HOH B 8 608 48 HOH HOH . J 5 HOH B 9 609 248 HOH HOH . J 5 HOH B 10 610 102 HOH HOH . J 5 HOH B 11 611 92 HOH HOH . J 5 HOH B 12 612 257 HOH HOH . J 5 HOH B 13 613 7 HOH HOH . J 5 HOH B 14 614 39 HOH HOH . J 5 HOH B 15 615 268 HOH HOH . J 5 HOH B 16 616 139 HOH HOH . J 5 HOH B 17 617 249 HOH HOH . J 5 HOH B 18 618 81 HOH HOH . J 5 HOH B 19 619 101 HOH HOH . J 5 HOH B 20 620 11 HOH HOH . J 5 HOH B 21 621 55 HOH HOH . J 5 HOH B 22 622 59 HOH HOH . J 5 HOH B 23 623 223 HOH HOH . J 5 HOH B 24 624 150 HOH HOH . J 5 HOH B 25 625 70 HOH HOH . J 5 HOH B 26 626 43 HOH HOH . J 5 HOH B 27 627 169 HOH HOH . J 5 HOH B 28 628 10 HOH HOH . J 5 HOH B 29 629 32 HOH HOH . J 5 HOH B 30 630 9 HOH HOH . J 5 HOH B 31 631 270 HOH HOH . J 5 HOH B 32 632 95 HOH HOH . J 5 HOH B 33 633 78 HOH HOH . J 5 HOH B 34 634 1 HOH HOH . J 5 HOH B 35 635 147 HOH HOH . J 5 HOH B 36 636 107 HOH HOH . J 5 HOH B 37 637 126 HOH HOH . J 5 HOH B 38 638 138 HOH HOH . J 5 HOH B 39 639 77 HOH HOH . J 5 HOH B 40 640 45 HOH HOH . J 5 HOH B 41 641 234 HOH HOH . J 5 HOH B 42 642 115 HOH HOH . J 5 HOH B 43 643 170 HOH HOH . J 5 HOH B 44 644 264 HOH HOH . J 5 HOH B 45 645 238 HOH HOH . J 5 HOH B 46 646 133 HOH HOH . J 5 HOH B 47 647 36 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 GDP . . . F 2 56.964 -3.286 -1.274 1 46.69 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . F 2 55.99 -2.364 -1.965 1 48.95 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . F 2 58.342 -3.132 -1.881 1 49.11 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . F 2 57.017 -2.982 0.2 1 40.64 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . F 2 56.445 -4.799 -1.422 1 64.91 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . F 2 57.443 -6.056 -1.45 1 56.37 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . F 2 58.262 -6.106 -2.719 1 49.01 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . F 2 58.332 -6.081 -0.23 1 51.95 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . F 2 56.366 -7.243 -1.409 1 56.5 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . F 2 55.609 -7.457 -0.221 1 52.67 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . F 2 55.006 -8.851 -0.286 1 53.59 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . F 2 54.052 -8.912 -1.346 1 44.05 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . F 2 56.072 -9.886 -0.602 1 53.2 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . F 2 55.916 -10.992 0.288 1 48.92 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . F 2 55.797 -10.32 -2.027 1 48.31 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . F 2 56.107 -11.701 -2.217 1 49.65 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . F 2 54.316 -10.034 -2.193 1 47.25 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . F 2 53.983 -9.639 -3.577 1 45.66 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . F 2 54.821 -9.32 -4.582 1 42.71 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . F 2 54.121 -8.995 -5.703 1 47 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . F 2 52.806 -9.087 -5.403 1 40.85 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . F 2 51.518 -8.882 -6.104 1 45.28 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . F 2 51.481 -8.525 -7.301 1 57.04 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . F 2 50.389 -9.09 -5.416 1 50.87 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . F 2 50.387 -9.474 -4.125 1 46.15 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . F 2 49.204 -9.66 -3.499 1 45.27 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . F 2 51.523 -9.683 -3.422 1 44.28 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . F 2 52.731 -9.507 -4.001 1 42.28 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #