data_6CVN # _model_server_result.job_id HOEVV3j-kQLOSvcI1vWwjA _model_server_result.datetime_utc '2024-11-19 07:23:58' _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 6cvn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 6CVN # _exptl.entry_id 6CVN _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 120-meric 120 'representative helical assembly' 1 ? tetrameric 4 'helical asymmetric unit' 2 ? tetrameric 4 'helical asymmetric unit, std helical frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 (1-30) A,B,C,D,E,F,G,H 2 16 A,B,C,D,E,F,G,H 3 H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'helical symmetry operation' ? ? 0.896873 -0.442289 0 0.442289 0.896873 0 0 0 1 155.44355 -96.66101 -130.5 3 'helical symmetry operation' ? ? 0.999962 -0.008727 0 0.008727 0.999962 0 0 0 1 2.49791 -2.47621 -121.8 4 'helical symmetry operation' ? ? 0.904455 0.426569 0 -0.426569 0.904455 0 0 0 1 -94.34181 148.80237 -113.1 5 'helical symmetry operation' ? ? 0.62932 0.777146 0 -0.777146 0.62932 0 0 0 1 -115.84291 327.13029 -104.4 6 'helical symmetry operation' ? ? 0.2292 0.973379 0 -0.973379 0.2292 0 0 0 1 -57.7352 497.09098 -95.7 7 'helical symmetry operation' ? ? -0.21644 0.976296 0 -0.976296 -0.21644 0 0 0 1 68.44093 624.92965 -87 8 'helical symmetry operation' ? ? -0.619094 0.785317 0 -0.785317 -0.619094 0 0 0 1 237.62645 685.2571 -78.3 9 'helical symmetry operation' ? ? -0.898794 0.438371 0 -0.438371 -0.898794 0 0 0 1 416.22053 666.09208 -69.6 10 'helical symmetry operation' ? ? -0.99999 0.004363 0 -0.004363 -0.99999 0 0 0 1 568.75374 571.24083 -60.9 11 'helical symmetry operation' ? ? -0.902585 -0.430511 0 0.430511 -0.902585 0 0 0 1 664.93247 419.54114 -52.2 12 'helical symmetry operation' ? ? -0.625923 -0.779884 0 0.779884 -0.625923 0 0 0 1 685.65527 241.12111 -43.5 13 'helical symmetry operation' ? ? -0.224951 -0.97437 0 0.97437 -0.224951 0 0 0 1 626.80652 71.41558 -34.8 14 'helical symmetry operation' ? ? 0.220697 -0.975342 0 0.975342 0.220697 0 0 0 1 500.07379 -55.87133 -26.1 15 'helical symmetry operation' ? ? 0.622515 -0.782608 0 0.782608 0.622515 0 0 0 1 330.62665 -115.46 -17.4 16 'helical symmetry operation' ? ? 0.900698 -0.434445 0 0.434445 0.900698 0 0 0 1 152.1179 -95.5159 -8.7 17 'helical symmetry operation' ? ? 0.900698 0.434445 0 -0.434445 0.900698 0 0 0 1 -95.5159 152.1179 8.7 18 'helical symmetry operation' ? ? 0.622515 0.782608 0 -0.782608 0.622515 0 0 0 1 -115.46 330.62665 17.4 19 'helical symmetry operation' ? ? 0.220697 0.975342 0 -0.975342 0.220697 0 0 0 1 -55.87133 500.07379 26.1 20 'helical symmetry operation' ? ? -0.224951 0.97437 0 -0.97437 -0.224951 0 0 0 1 71.41558 626.80652 34.8 21 'helical symmetry operation' ? ? -0.625923 0.779884 0 -0.779884 -0.625923 0 0 0 1 241.12111 685.65527 43.5 22 'helical symmetry operation' ? ? -0.902585 0.430511 0 -0.430511 -0.902585 0 0 0 1 419.54114 664.93247 52.2 23 'helical symmetry operation' ? ? -0.99999 -0.004363 0 0.004363 -0.99999 0 0 0 1 571.24083 568.75374 60.9 24 'helical symmetry operation' ? ? -0.898794 -0.438371 0 0.438371 -0.898794 0 0 0 1 666.09208 416.22053 69.6 25 'helical symmetry operation' ? ? -0.619094 -0.785317 0 0.785317 -0.619094 0 0 0 1 685.2571 237.62645 78.3 26 'helical symmetry operation' ? ? -0.21644 -0.976296 0 0.976296 -0.21644 0 0 0 1 624.92965 68.44093 87 27 'helical symmetry operation' ? ? 0.2292 -0.973379 0 0.973379 0.2292 0 0 0 1 497.09098 -57.7352 95.7 28 'helical symmetry operation' ? ? 0.62932 -0.777146 0 0.777146 0.62932 0 0 0 1 327.13029 -115.84291 104.4 29 'helical symmetry operation' ? ? 0.904455 -0.426569 0 0.426569 0.904455 0 0 0 1 148.80237 -94.34181 113.1 30 'helical symmetry operation' ? ? 0.999962 0.008727 0 -0.008727 0.999962 0 0 0 1 -2.47621 2.49791 121.8 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 H 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 . B GTP 501 1_555 G MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc2 F O1B GTP . B GTP 501 1_555 G MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? # _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 6CVN _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 4 GDP A 1 501 4 GDP GDP . F 5 GTP B 1 501 1 GTP GTP . G 6 MG B 1 502 2 MG MG . H 4 GDP C 1 501 3 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 . . . H 4 251.362 398.502 276.785 1 31.92 ? PB GDP 501 C 1 HETATM 2 O O1B GDP . . . H 4 250.557 399.521 276.014 1 31.67 ? O1B GDP 501 C 1 HETATM 3 O O2B GDP . . . H 4 251.036 397.129 276.249 1 31.87 ? O2B GDP 501 C 1 HETATM 4 O O3B GDP . . . H 4 250.99 398.596 278.245 1 31.5 ? O3B GDP 501 C 1 HETATM 5 O O3A GDP . . . H 4 252.928 398.814 276.562 1 30.8 ? O3A GDP 501 C 1 HETATM 6 P PA GDP . . . H 4 254.081 398.362 277.595 1 29.58 ? PA GDP 501 C 1 HETATM 7 O O1A GDP . . . H 4 254.782 397.123 277.091 1 29.43 ? O1A GDP 501 C 1 HETATM 8 O O2A GDP . . . H 4 253.538 398.129 278.985 1 29.61 ? O2A GDP 501 C 1 HETATM 9 O O5' GDP . . . H 4 255.097 399.611 277.601 1 29.32 ? O5' GDP 501 C 1 HETATM 10 C C5' GDP . . . H 4 256.491 399.407 277.384 1 29.02 ? C5' GDP 501 C 1 HETATM 11 C C4' GDP . . . H 4 257.293 399.964 278.55 1 28.53 ? C4' GDP 501 C 1 HETATM 12 O O4' GDP . . . H 4 257.198 399.045 279.639 1 27.91 ? O4' GDP 501 C 1 HETATM 13 C C3' GDP . . . H 4 258.761 400.092 278.188 1 28.19 ? C3' GDP 501 C 1 HETATM 14 O O3' GDP . . . H 4 259.252 401.372 278.594 1 27.97 ? O3' GDP 501 C 1 HETATM 15 C C2' GDP . . . H 4 259.474 399.009 278.971 1 27.95 ? C2' GDP 501 C 1 HETATM 16 O O2' GDP . . . H 4 260.685 399.513 279.54 1 28.49 ? O2' GDP 501 C 1 HETATM 17 C C1' GDP . . . H 4 258.493 398.608 280.06 1 27.52 ? C1' GDP 501 C 1 HETATM 18 N N9 GDP . . . H 4 258.495 397.136 280.23 1 26.58 ? N9 GDP 501 C 1 HETATM 19 C C8 GDP . . . H 4 258.051 396.236 279.333 1 26.5 ? C8 GDP 501 C 1 HETATM 20 N N7 GDP . . . H 4 258.189 394.971 279.805 1 26.3 ? N7 GDP 501 C 1 HETATM 21 C C5 GDP . . . H 4 258.727 395.051 281.036 1 25.88 ? C5 GDP 501 C 1 HETATM 22 C C6 GDP . . . H 4 259.135 394.099 282.097 1 25.55 ? C6 GDP 501 C 1 HETATM 23 O O6 GDP . . . H 4 259.005 392.866 281.95 1 25.51 ? O6 GDP 501 C 1 HETATM 24 N N1 GDP . . . H 4 259.652 394.599 283.226 1 25.51 ? N1 GDP 501 C 1 HETATM 25 C C2 GDP . . . H 4 259.809 395.92 283.424 1 25.69 ? C2 GDP 501 C 1 HETATM 26 N N2 GDP . . . H 4 260.341 396.341 284.597 1 25.89 ? N2 GDP 501 C 1 HETATM 27 N N3 GDP . . . H 4 259.46 396.849 282.498 1 25.7 ? N3 GDP 501 C 1 HETATM 28 C C4 GDP . . . H 4 258.926 396.481 281.31 1 25.92 ? C4 GDP 501 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #