data_8VA2 # _model_server_result.job_id TyPmRsscVr7iR1k-GsSacQ _model_server_result.datetime_utc '2024-11-23 13:09:43' _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 8va2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 8VA2 # _exptl.entry_id 8VA2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 8VA2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VA2 _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 ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 ? _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 ? 5 I N N ? 5 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 E O2G GTP . a GTP 501 1_555 F MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc2 E O3G GTP . a GTP 501 1_555 F MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc3 E O3B GTP . a GTP 501 1_555 F MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc4 E O2B GTP . a GTP 501 1_555 F MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.888 ? metalc ? metalc5 G O2G GTP . b GTP 501 1_555 H MG MG . b MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc6 G O3G GTP . b GTP 501 1_555 H MG MG . b MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc7 G O3B GTP . b GTP 501 1_555 H MG MG . b MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc8 G O1B GTP . b GTP 501 1_555 H MG MG . b MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc9 G O2B GTP . b GTP 501 1_555 H MG MG . b MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? # _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 8VA2 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 E 3 GTP a 1 501 501 GTP GTP . F 4 MG a 1 502 502 MG MG . G 3 GTP b 1 501 501 GTP GTP . H 4 MG b 1 502 502 MG MG . I 5 GDP g 1 501 501 GDP GDP . J 5 GDP h 1 501 501 GDP GDP . # 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 . . . I 5 186.044 329.73 193.385 1 107.86 ? PB GDP 501 g 1 HETATM 2 O O1B GDP . . . I 5 186.744 329.211 192.145 1 107.86 ? O1B GDP 501 g 1 HETATM 3 O O2B GDP . . . I 5 185.061 330.84 193.088 1 107.86 ? O2B GDP 501 g 1 HETATM 4 O O3B GDP . . . I 5 185.651 328.702 194.427 1 107.86 ? O3B GDP 501 g 1 HETATM 5 O O3A GDP . . . I 5 187.274 330.46 194.349 1 107.86 ? O3A GDP 501 g 1 HETATM 6 P PA GDP . . . I 5 187.513 330.984 195.775 1 107.86 ? PA GDP 501 g 1 HETATM 7 O O1A GDP . . . I 5 186.295 331.649 196.329 1 107.86 ? O1A GDP 501 g 1 HETATM 8 O O2A GDP . . . I 5 188.482 330.346 196.738 1 107.86 ? O2A GDP 501 g 1 HETATM 9 O O5' GDP . . . I 5 188.429 332.388 195.345 1 107.86 ? O5' GDP 501 g 1 HETATM 10 C C5' GDP . . . I 5 189.789 332.395 195.421 1 107.86 ? C5' GDP 501 g 1 HETATM 11 C C4' GDP . . . I 5 190.041 333.035 196.799 1 107.86 ? C4' GDP 501 g 1 HETATM 12 O O4' GDP . . . I 5 190.362 331.988 197.716 1 107.86 ? O4' GDP 501 g 1 HETATM 13 C C3' GDP . . . I 5 191.299 333.961 196.787 1 107.86 ? C3' GDP 501 g 1 HETATM 14 O O3' GDP . . . I 5 191.179 334.849 197.836 1 107.86 ? O3' GDP 501 g 1 HETATM 15 C C2' GDP . . . I 5 192.431 332.95 197.047 1 107.86 ? C2' GDP 501 g 1 HETATM 16 O O2' GDP . . . I 5 193.469 333.629 197.673 1 107.86 ? O2' GDP 501 g 1 HETATM 17 C C1' GDP . . . I 5 191.689 332.085 198.078 1 107.86 ? C1' GDP 501 g 1 HETATM 18 N N9 GDP . . . I 5 192.265 330.744 198.052 1 107.86 ? N9 GDP 501 g 1 HETATM 19 C C8 GDP . . . I 5 191.986 329.604 197.272 1 107.86 ? C8 GDP 501 g 1 HETATM 20 N N7 GDP . . . I 5 192.788 328.576 197.614 1 107.86 ? N7 GDP 501 g 1 HETATM 21 C C5 GDP . . . I 5 193.596 329.07 198.637 1 107.86 ? C5 GDP 501 g 1 HETATM 22 C C6 GDP . . . I 5 194.613 328.408 199.358 1 107.86 ? C6 GDP 501 g 1 HETATM 23 O O6 GDP . . . I 5 195.066 327.274 199.303 1 107.86 ? O6 GDP 501 g 1 HETATM 24 N N1 GDP . . . I 5 195.209 329.26 200.332 1 107.86 ? N1 GDP 501 g 1 HETATM 25 C C2 GDP . . . I 5 194.809 330.587 200.517 1 107.86 ? C2 GDP 501 g 1 HETATM 26 N N2 GDP . . . I 5 195.487 331.287 201.502 1 107.86 ? N2 GDP 501 g 1 HETATM 27 N N3 GDP . . . I 5 193.854 331.242 199.855 1 107.86 ? N3 GDP 501 g 1 HETATM 28 C C4 GDP . . . I 5 193.277 330.411 198.911 1 107.86 ? C4 GDP 501 g 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #