data_7EPK # _model_server_result.job_id by5lcQxulG4aJhL4SO0NiA _model_server_result.datetime_utc '2025-01-12 01:50:26' _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 7epk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7EPK # _exptl.entry_id 7EPK _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 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 7EPK _cell.length_a 82.498 _cell.length_b 82.498 _cell.length_c 140.805 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EPK _symmetry.cell_setting ? _symmetry.Int_Tables_number 153 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 1 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 OG1 THR 110 A THR 110 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc2 B O3B GDP . A GDP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc3 C MG MG . A MG 502 1_555 D O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc4 C MG MG . A MG 502 1_555 D O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc5 C MG MG . A MG 502 1_555 D O HOH . A HOH 633 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 7EPK _atom_sites.fract_transf_matrix[1][1] 0.012122 _atom_sites.fract_transf_matrix[1][2] 0.006998 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013997 _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] 0.007102 _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 GDP A 1 501 501 GDP GDP . C 3 MG A 1 502 601 MG MG . D 4 HOH A 1 601 31 HOH HOH . D 4 HOH A 2 602 29 HOH HOH . D 4 HOH A 3 603 16 HOH HOH . D 4 HOH A 4 604 35 HOH HOH . D 4 HOH A 5 605 17 HOH HOH . D 4 HOH A 6 606 8 HOH HOH . D 4 HOH A 7 607 1 HOH HOH . D 4 HOH A 8 608 9 HOH HOH . D 4 HOH A 9 609 20 HOH HOH . D 4 HOH A 10 610 4 HOH HOH . D 4 HOH A 11 611 15 HOH HOH . D 4 HOH A 12 612 19 HOH HOH . D 4 HOH A 13 613 24 HOH HOH . D 4 HOH A 14 614 5 HOH HOH . D 4 HOH A 15 615 33 HOH HOH . D 4 HOH A 16 616 3 HOH HOH . D 4 HOH A 17 617 28 HOH HOH . D 4 HOH A 18 618 23 HOH HOH . D 4 HOH A 19 619 25 HOH HOH . D 4 HOH A 20 620 2 HOH HOH . D 4 HOH A 21 621 30 HOH HOH . D 4 HOH A 22 622 42 HOH HOH . D 4 HOH A 23 623 13 HOH HOH . D 4 HOH A 24 624 41 HOH HOH . D 4 HOH A 25 625 27 HOH HOH . D 4 HOH A 26 626 6 HOH HOH . D 4 HOH A 27 627 18 HOH HOH . D 4 HOH A 28 628 37 HOH HOH . D 4 HOH A 29 629 11 HOH HOH . D 4 HOH A 30 630 34 HOH HOH . D 4 HOH A 31 631 21 HOH HOH . D 4 HOH A 32 632 12 HOH HOH . D 4 HOH A 33 633 7 HOH HOH . D 4 HOH A 34 634 38 HOH HOH . D 4 HOH A 35 635 22 HOH HOH . D 4 HOH A 36 636 32 HOH HOH . D 4 HOH A 37 637 39 HOH HOH . D 4 HOH A 38 638 10 HOH HOH . D 4 HOH A 39 639 14 HOH HOH . D 4 HOH A 40 640 36 HOH HOH . D 4 HOH A 41 641 26 HOH HOH . D 4 HOH A 42 642 40 HOH HOH . D 4 HOH A 43 643 43 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 . . . B 2 -146.81 39.354 -0.635 1 77 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . B 2 -146.424 40.489 -1.558 1 73.14 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . B 2 -147.252 38.139 -1.428 1 93.84 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . B 2 -145.791 39.013 0.441 1 83.72 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . B 2 -148.104 39.793 0.214 1 65.95 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . B 2 -148.08 40.327 1.751 1 68.27 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . B 2 -147.198 41.568 1.736 1 68.89 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . B 2 -147.917 39.205 2.749 1 56.23 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . B 2 -149.572 40.829 2.045 1 73.13 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . B 2 -150.325 41.607 1.096 1 73.71 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . B 2 -151.657 41.939 1.746 1 71.54 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . B 2 -152.406 40.727 1.909 1 75.53 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . B 2 -151.46 42.508 3.148 1 69.98 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . B 2 -152.288 43.656 3.308 1 65.19 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . B 2 -151.84 41.382 4.099 1 74.7 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . B 2 -152.334 41.906 5.34 1 74.91 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . B 2 -152.88 40.61 3.27 1 83.21 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . B 2 -153.193 39.167 3.6 1 87.59 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . B 2 -152.375 38.098 3.526 1 94.61 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . B 2 -153.013 36.944 3.868 1 95.88 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . B 2 -154.276 37.27 4.14 1 88.66 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . B 2 -155.477 36.54 4.554 1 98.96 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . B 2 -155.432 35.312 4.741 1 100.68 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . B 2 -156.605 37.231 4.755 1 117.86 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . B 2 -156.67 38.567 4.581 1 118.86 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . B 2 -157.853 39.196 4.792 1 122.22 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . B 2 -155.597 39.306 4.196 1 110.83 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . B 2 -154.396 38.718 3.968 1 93.47 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #