data_2QA5 # _model_server_result.job_id qNKG1A6Nn_QFDpI71XjqOw _model_server_result.datetime_utc '2024-11-29 17:41:22' _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 2qa5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":316}' # _entry.id 2QA5 # _exptl.entry_id 2QA5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 128.37 _cell.angle_gamma 90 _cell.entry_id 2QA5 _cell.length_a 162.96 _cell.length_b 53.92 _cell.length_c 110.27 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QA5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 D 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 covale ? covale1 A C LEU 40 A LEU 40 1_555 A N MSE 41 A MSE 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C MSE 41 A MSE 41 1_555 A N VAL 42 A VAL 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C PHE 167 A PHE 167 1_555 A N MSE 168 A MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 168 A MSE 168 1_555 A N LYS 169 A LYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C THR 278 A THR 278 1_555 A N MSE 279 A MSE 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C MSE 279 A MSE 279 1_555 A N LEU 280 A LEU 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C HIS 283 A HIS 283 1_555 A N MSE 284 A MSE 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale8 A C MSE 284 A MSE 284 1_555 A N GLN 285 A GLN 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale9 B C LEU 40 B LEU 40 1_555 B N MSE 41 B MSE 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 B C MSE 41 B MSE 41 1_555 B N VAL 42 B VAL 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 B C PHE 167 B PHE 167 1_555 B N MSE 168 B MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale12 B C MSE 168 B MSE 168 1_555 B N LYS 169 B LYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 B C THR 278 B THR 278 1_555 B N MSE 279 B MSE 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale14 B C MSE 279 B MSE 279 1_555 B N LEU 280 B LEU 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale15 B C HIS 283 B HIS 283 1_555 B N MSE 284 B MSE 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale16 B C MSE 284 B MSE 284 1_555 B N GLN 285 B GLN 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? # _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 2QA5 _atom_sites.fract_transf_matrix[1][1] 0.006136 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004858 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018546 _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] 0.011567 _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 C 2 GDP A 1 316 1 GDP GDP . D 2 GDP B 1 316 2 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 . . . D 2 71.595 17.404 72.619 1 64.23 ? PB GDP 316 B 1 HETATM 2 O O1B GDP . . . D 2 70.446 17.467 73.58 1 63.18 ? O1B GDP 316 B 1 HETATM 3 O O2B GDP . . . D 2 71.59 18.62 71.744 1 63.92 ? O2B GDP 316 B 1 HETATM 4 O O3B GDP . . . D 2 72.863 17.298 73.421 1 64.14 ? O3B GDP 316 B 1 HETATM 5 O O3A GDP . . . D 2 71.478 16.153 71.635 1 65.01 ? O3A GDP 316 B 1 HETATM 6 P PA GDP . . . D 2 71.676 14.671 72.184 1 66.02 ? PA GDP 316 B 1 HETATM 7 O O1A GDP . . . D 2 72.844 14.043 71.495 1 65.86 ? O1A GDP 316 B 1 HETATM 8 O O2A GDP . . . D 2 71.87 14.697 73.677 1 66.4 ? O2A GDP 316 B 1 HETATM 9 O O5' GDP . . . D 2 70.287 13.934 71.865 1 66.73 ? O5' GDP 316 B 1 HETATM 10 C C5' GDP . . . D 2 69.946 13.421 70.591 1 68.29 ? C5' GDP 316 B 1 HETATM 11 C C4' GDP . . . D 2 69.493 11.974 70.766 1 70.48 ? C4' GDP 316 B 1 HETATM 12 O O4' GDP . . . D 2 68.698 11.574 69.65 1 71.2 ? O4' GDP 316 B 1 HETATM 13 C C3' GDP . . . D 2 70.678 11.023 70.798 1 71.33 ? C3' GDP 316 B 1 HETATM 14 O O3' GDP . . . D 2 70.79 10.387 72.071 1 71.97 ? O3' GDP 316 B 1 HETATM 15 C C2' GDP . . . D 2 70.382 10.012 69.718 1 72.02 ? C2' GDP 316 B 1 HETATM 16 O O2' GDP . . . D 2 69.662 8.928 70.313 1 72.7 ? O2' GDP 316 B 1 HETATM 17 C C1' GDP . . . D 2 69.447 10.736 68.773 1 73.23 ? C1' GDP 316 B 1 HETATM 18 N N9 GDP . . . D 2 70.174 11.594 67.785 1 73.82 ? N9 GDP 316 B 1 HETATM 19 C C8 GDP . . . D 2 71.054 12.563 68.094 1 74.25 ? C8 GDP 316 B 1 HETATM 20 N N7 GDP . . . D 2 71.554 13.188 67.012 1 74.24 ? N7 GDP 316 B 1 HETATM 21 C C5 GDP . . . D 2 70.983 12.618 65.956 1 73.86 ? C5 GDP 316 B 1 HETATM 22 C C6 GDP . . . D 2 71.085 12.819 64.504 1 74.04 ? C6 GDP 316 B 1 HETATM 23 O O6 GDP . . . D 2 71.839 13.685 64.025 1 74.35 ? O6 GDP 316 B 1 HETATM 24 N N1 GDP . . . D 2 70.349 12.045 63.719 1 74.13 ? N1 GDP 316 B 1 HETATM 25 C C2 GDP . . . D 2 69.532 11.111 64.213 1 74.18 ? C2 GDP 316 B 1 HETATM 26 N N2 GDP . . . D 2 68.833 10.387 63.316 1 73.99 ? N2 GDP 316 B 1 HETATM 27 N N3 GDP . . . D 2 69.389 10.855 65.542 1 74.23 ? N3 GDP 316 B 1 HETATM 28 C C4 GDP . . . D 2 70.077 11.574 66.454 1 73.84 ? C4 GDP 316 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #