data_2XRP # _model_server_result.job_id k4T9NZ-SLSXT2WkmaRizRQ _model_server_result.datetime_utc '2024-11-28 06:40:33' _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 2xrp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":600}' # _entry.id 2XRP # _exptl.entry_id 2XRP _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 4 _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 2XRP _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XRP _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,N,O,P,Q _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 J N N ? 4 L N N ? 4 N N N ? 4 P N N # _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 2XRP _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 J 4 GDP A 1 600 600 GDP GDP . K 5 GTP B 1 500 500 GTP GTP . L 4 GDP C 1 600 600 GDP GDP . M 5 GTP D 1 500 500 GTP GTP . N 4 GDP E 1 600 600 GDP GDP . O 5 GTP F 1 500 500 GTP GTP . P 4 GDP G 1 600 600 GDP GDP . Q 5 GTP H 1 500 500 GTP GTP . # 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 4 91.272 45.881 139.385 1 22 ? PB GDP 600 A 1 HETATM 2 O O1B GDP . . . J 4 90.567 46.434 138.213 1 23 ? O1B GDP 600 A 1 HETATM 3 O O2B GDP . . . J 4 92.58 46.331 139.585 1 23 ? O2B GDP 600 A 1 HETATM 4 O O3B GDP . . . J 4 90.305 46.05 140.692 1 25 ? O3B GDP 600 A 1 HETATM 5 O O3A GDP . . . J 4 91.424 44.337 139.113 1 19 ? O3A GDP 600 A 1 HETATM 6 P PA GDP . . . J 4 92.797 43.387 139.043 1 20 ? PA GDP 600 A 1 HETATM 7 O O1A GDP . . . J 4 93.616 43.801 137.87 1 23 ? O1A GDP 600 A 1 HETATM 8 O O2A GDP . . . J 4 93.476 43.524 140.396 1 0 ? O2A GDP 600 A 1 HETATM 9 O O5' GDP . . . J 4 92.178 41.991 138.747 1 16 ? O5' GDP 600 A 1 HETATM 10 C C5' GDP . . . J 4 92.88 40.76 139.097 1 7 ? C5' GDP 600 A 1 HETATM 11 C C4' GDP . . . J 4 93.136 39.864 137.982 1 2 ? C4' GDP 600 A 1 HETATM 12 O O4' GDP . . . J 4 94.049 40.541 137.032 1 0 ? O4' GDP 600 A 1 HETATM 13 C C3' GDP . . . J 4 93.96 38.573 138.334 1 3 ? C3' GDP 600 A 1 HETATM 14 O O3' GDP . . . J 4 93.383 37.493 137.514 1 2 ? O3' GDP 600 A 1 HETATM 15 C C2' GDP . . . J 4 95.432 38.777 137.904 1 2 ? C2' GDP 600 A 1 HETATM 16 O O2' GDP . . . J 4 96.193 37.642 137.454 1 0 ? O2' GDP 600 A 1 HETATM 17 C C1' GDP . . . J 4 95.32 39.799 136.775 1 0 ? C1' GDP 600 A 1 HETATM 18 N N9 GDP . . . J 4 96.407 40.777 136.729 1 5 ? N9 GDP 600 A 1 HETATM 19 C C8 GDP . . . J 4 96.491 41.828 137.8 1 9 ? C8 GDP 600 A 1 HETATM 20 N N7 GDP . . . J 4 97.636 42.424 137.243 1 10 ? N7 GDP 600 A 1 HETATM 21 C C5 GDP . . . J 4 98.184 41.936 136.135 1 10 ? C5 GDP 600 A 1 HETATM 22 C C6 GDP . . . J 4 99.228 42.063 135.194 1 13 ? C6 GDP 600 A 1 HETATM 23 O O6 GDP . . . J 4 100.08 43.082 135.39 1 11 ? O6 GDP 600 A 1 HETATM 24 N N1 GDP . . . J 4 99.396 41.26 134.119 1 10 ? N1 GDP 600 A 1 HETATM 25 C C2 GDP . . . J 4 98.431 40.147 133.914 1 5 ? C2 GDP 600 A 1 HETATM 26 N N2 GDP . . . J 4 98.797 39.492 132.834 1 6 ? N2 GDP 600 A 1 HETATM 27 N N3 GDP . . . J 4 97.482 39.965 134.735 1 4 ? N3 GDP 600 A 1 HETATM 28 C C4 GDP . . . J 4 97.334 40.813 135.771 1 7 ? C4 GDP 600 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #