data_6RF2 # _model_server_result.job_id FYAv0FNNFoV_h2O4j6AHiA _model_server_result.datetime_utc '2024-10-20 01:29:04' _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 6rf2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 6RF2 # _exptl.entry_id 6RF2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 90 _cell.entry_id 6RF2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RF2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,K,L,M _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 ? _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 ? 7 I N N ? 7 J 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 F O1G GTP . a GTP 501 1_555 G MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc2 F O2B GTP . a GTP 501 1_555 G MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc3 F O3A GTP . a GTP 501 1_555 G MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc4 F O2A GTP . a GTP 501 1_555 G MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc5 L O1G GTP . A GTP 502 1_555 M MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc6 L O2B GTP . A GTP 502 1_555 M MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc7 L O3A GTP . A GTP 502 1_555 M MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc8 L O2A GTP . A GTP 502 1_555 M MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 6RF2 _atom_sites.fract_transf_matrix[1][1] 0.007573 _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] 0.01199 _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] 0.007736 _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 F 4 GTP a 1 501 501 GTP GTP . G 5 MG a 1 502 502 MG MG . H 6 PO4 a 1 503 503 PO4 PO4 . I 7 GDP B 1 501 501 GDP GDP . J 7 GDP b 1 501 501 GDP GDP . K 6 PO4 A 1 501 501 PO4 PO4 . L 4 GTP A 1 502 502 GTP GTP . M 5 MG A 1 503 503 MG MG . # 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 . . . J 7 30.887 43.59 63.442 1 117.84 ? PB GDP 501 b 1 HETATM 2 O O1B GDP . . . J 7 30.635 43.047 62.094 1 117.84 ? O1B GDP 501 b 1 HETATM 3 O O2B GDP . . . J 7 30.814 45.11 63.496 1 117.84 ? O2B GDP 501 b 1 HETATM 4 O O3B GDP . . . J 7 29.944 43.021 64.49 1 117.84 ? O3B GDP 501 b 1 HETATM 5 O O3A GDP . . . J 7 32.352 43.213 63.934 1 117.84 ? O3A GDP 501 b 1 HETATM 6 P PA GDP . . . J 7 33.756 43.904 63.651 1 117.84 ? PA GDP 501 b 1 HETATM 7 O O1A GDP . . . J 7 33.554 45.129 62.855 1 117.84 ? O1A GDP 501 b 1 HETATM 8 O O2A GDP . . . J 7 34.38 44.253 64.993 1 117.84 ? O2A GDP 501 b 1 HETATM 9 O O5' GDP . . . J 7 34.666 42.828 62.942 1 117.84 ? O5' GDP 501 b 1 HETATM 10 C C5' GDP . . . J 7 36.031 42.533 63.292 1 117.84 ? C5' GDP 501 b 1 HETATM 11 C C4' GDP . . . J 7 36.844 42.461 62.026 1 117.84 ? C4' GDP 501 b 1 HETATM 12 O O4' GDP . . . J 7 36.866 43.759 61.388 1 117.84 ? O4' GDP 501 b 1 HETATM 13 C C3' GDP . . . J 7 38.306 42.053 62.218 1 117.84 ? C3' GDP 501 b 1 HETATM 14 O O3' GDP . . . J 7 38.722 41.161 61.191 1 117.84 ? O3' GDP 501 b 1 HETATM 15 C C2' GDP . . . J 7 39.045 43.389 62.145 1 117.84 ? C2' GDP 501 b 1 HETATM 16 O O2' GDP . . . J 7 40.378 43.234 61.674 1 117.84 ? O2' GDP 501 b 1 HETATM 17 C C1' GDP . . . J 7 38.204 44.117 61.108 1 117.84 ? C1' GDP 501 b 1 HETATM 18 N N9 GDP . . . J 7 38.32 45.58 61.166 1 117.84 ? N9 GDP 501 b 1 HETATM 19 C C8 GDP . . . J 7 37.729 46.431 62.059 1 117.84 ? C8 GDP 501 b 1 HETATM 20 N N7 GDP . . . J 7 37.991 47.695 61.822 1 117.84 ? N7 GDP 501 b 1 HETATM 21 C C5 GDP . . . J 7 38.807 47.669 60.703 1 117.84 ? C5 GDP 501 b 1 HETATM 22 C C6 GDP . . . J 7 39.402 48.724 59.951 1 117.84 ? C6 GDP 501 b 1 HETATM 23 O O6 GDP . . . J 7 39.311 49.93 60.165 1 117.84 ? O6 GDP 501 b 1 HETATM 24 N N1 GDP . . . J 7 40.138 48.255 58.883 1 117.84 ? N1 GDP 501 b 1 HETATM 25 C C2 GDP . . . J 7 40.299 46.937 58.558 1 117.84 ? C2 GDP 501 b 1 HETATM 26 N N2 GDP . . . J 7 41.042 46.663 57.486 1 117.84 ? N2 GDP 501 b 1 HETATM 27 N N3 GDP . . . J 7 39.75 45.942 59.25 1 117.84 ? N3 GDP 501 b 1 HETATM 28 C C4 GDP . . . J 7 39.023 46.373 60.295 1 117.84 ? C4 GDP 501 b 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 200 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 42 _model_server_stats.element_count 28 #