data_3JAS # _model_server_result.job_id bLUYyQK2BplLUbtxiPm9YA _model_server_result.datetime_utc '2025-01-31 10:45:23' _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 3jas # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":501}' # _entry.id 3JAS # _exptl.entry_id 3JAS _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 6 _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 3JAS _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JAS _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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 O N N ? 5 R N N ? 5 U N N ? 5 X N N ? 5 AA N N ? 5 DA 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 OD2 ASP 98 E ASP 98 1_555 N MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc2 M O1B GTP . E GTP 501 1_555 N MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc3 M O1G GTP . E GTP 501 1_555 N MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc4 C OD2 ASP 98 J ASP 98 1_555 Q MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc5 P O1B GTP . J GTP 501 1_555 Q MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc6 P O3G GTP . J GTP 501 1_555 Q MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc7 E OD2 ASP 98 C ASP 98 1_555 T MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc8 S O1B GTP . C GTP 501 1_555 T MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? metalc ? metalc9 S O1G GTP . C GTP 501 1_555 T MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc10 G OD2 ASP 98 L ASP 98 1_555 W MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? metalc ? metalc11 V O1B GTP . L GTP 501 1_555 W MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? metalc ? metalc12 V O3G GTP . L GTP 501 1_555 W MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc13 I OD2 ASP 98 A ASP 98 1_555 Z MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc14 Y O1B GTP . A GTP 501 1_555 Z MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc15 Y O1G GTP . A GTP 501 1_555 Z MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc16 K OD2 ASP 98 K ASP 98 1_555 CA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc17 BA O1B GTP . K GTP 501 1_555 CA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? metalc ? metalc18 BA O3G GTP . K GTP 501 1_555 CA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? # _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 3JAS _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 M 3 GTP E 1 501 501 GTP GTP . N 4 MG E 1 502 502 MG MG . O 5 GDP F 1 501 501 GDP GDP . P 3 GTP J 1 501 501 GTP GTP . Q 4 MG J 1 502 502 MG MG . R 5 GDP G 1 501 501 GDP GDP . S 3 GTP C 1 501 501 GTP GTP . T 4 MG C 1 502 502 MG MG . U 5 GDP D 1 501 501 GDP GDP . V 3 GTP L 1 501 501 GTP GTP . W 4 MG L 1 502 502 MG MG . X 5 GDP I 1 501 501 GDP GDP . Y 3 GTP A 1 501 501 GTP GTP . Z 4 MG A 1 502 502 MG MG . AA 5 GDP B 1 501 501 GDP GDP . BA 3 GTP K 1 501 501 GTP GTP . CA 4 MG K 1 502 502 MG MG . DA 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 . . . DA 5 335.59 457.823 226.686 1 56.73 ? PB GDP 501 H 1 HETATM 2 O O1B GDP . . . DA 5 335.021 458.887 225.779 1 57.21 ? O1B GDP 501 H 1 HETATM 3 O O2B GDP . . . DA 5 335.158 456.426 226.309 1 56.18 ? O2B GDP 501 H 1 HETATM 4 O O3B GDP . . . DA 5 335.498 458.17 228.154 1 56.28 ? O3B GDP 501 H 1 HETATM 5 O O3A GDP . . . DA 5 337.17 457.862 226.358 1 56.43 ? O3A GDP 501 H 1 HETATM 6 P PA GDP . . . DA 5 338.264 456.881 227.032 1 55.55 ? PA GDP 501 H 1 HETATM 7 O O1A GDP . . . DA 5 338.682 455.835 226.024 1 54.35 ? O1A GDP 501 H 1 HETATM 8 O O2A GDP . . . DA 5 337.793 456.428 228.394 1 55.36 ? O2A GDP 501 H 1 HETATM 9 O O5' GDP . . . DA 5 339.463 457.928 227.31 1 53.67 ? O5' GDP 501 H 1 HETATM 10 C C5' GDP . . . DA 5 340.807 457.809 226.837 1 52.23 ? C5' GDP 501 H 1 HETATM 11 C C4' GDP . . . DA 5 341.719 458.017 228.04 1 50.75 ? C4' GDP 501 H 1 HETATM 12 O O4' GDP . . . DA 5 341.457 456.969 228.971 1 48.61 ? O4' GDP 501 H 1 HETATM 13 C C3' GDP . . . DA 5 343.207 457.923 227.713 1 50.28 ? C3' GDP 501 H 1 HETATM 14 O O3' GDP . . . DA 5 343.932 458.85 228.531 1 50.11 ? O3' GDP 501 H 1 HETATM 15 C C2' GDP . . . DA 5 343.575 456.485 228.047 1 48.42 ? C2' GDP 501 H 1 HETATM 16 O O2' GDP . . . DA 5 344.942 456.352 228.446 1 48.52 ? O2' GDP 501 H 1 HETATM 17 C C1' GDP . . . DA 5 342.622 456.167 229.181 1 47.23 ? C1' GDP 501 H 1 HETATM 18 N N9 GDP . . . DA 5 342.241 454.739 229.197 1 44.5 ? N9 GDP 501 H 1 HETATM 19 C C8 GDP . . . DA 5 341.513 454.086 228.275 1 43.86 ? C8 GDP 501 H 1 HETATM 20 N N7 GDP . . . DA 5 341.325 452.791 228.644 1 42.69 ? N7 GDP 501 H 1 HETATM 21 C C5 GDP . . . DA 5 341.911 452.62 229.837 1 41.91 ? C5 GDP 501 H 1 HETATM 22 C C6 GDP . . . DA 5 342.089 451.511 230.8 1 41.41 ? C6 GDP 501 H 1 HETATM 23 O O6 GDP . . . DA 5 341.62 450.381 230.561 1 41.51 ? O6 GDP 501 H 1 HETATM 24 N N1 GDP . . . DA 5 342.773 451.752 231.93 1 41.58 ? N1 GDP 501 H 1 HETATM 25 C C2 GDP . . . DA 5 343.298 452.964 232.213 1 41.91 ? C2 GDP 501 H 1 HETATM 26 N N2 GDP . . . DA 5 343.981 453.142 233.371 1 41.9 ? N2 GDP 501 H 1 HETATM 27 N N3 GDP . . . DA 5 343.177 454.024 231.372 1 42.27 ? N3 GDP 501 H 1 HETATM 28 C C4 GDP . . . DA 5 342.509 453.91 230.198 1 42.82 ? C4 GDP 501 H 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 98 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #