data_3P27 # _model_server_result.job_id e3GqMfJiX-j4mXM3Hkk8Dg _model_server_result.datetime_utc '2024-10-13 09:14:13' _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 3p27 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":663}' # _entry.id 3P27 # _exptl.entry_id 3P27 _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 90 _cell.angle_gamma 90 _cell.entry_id 3P27 _cell.length_a 109.964 _cell.length_b 109.964 _cell.length_c 188.199 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3P27 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 49 A LEU 183 1_555 A N MSE 50 A MSE 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 50 A MSE 184 1_555 A N GLY 51 A GLY 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C ILE 85 A ILE 219 1_555 A N MSE 86 A MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 86 A MSE 220 1_555 A N ASP 87 A ASP 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C ILE 129 A ILE 263 1_555 A N MSE 130 A MSE 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C MSE 130 A MSE 264 1_555 A N GLY 131 A GLY 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C ASP 136 A ASP 270 1_555 A N MSE 137 A MSE 271 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 A C MSE 137 A MSE 271 1_555 A N ALA 138 A ALA 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale9 A C HIS 162 A HIS 296 1_555 A N MSE 163 A MSE 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale10 A C MSE 163 A MSE 297 1_555 A N LEU 164 A LEU 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 A C ALA 177 A ALA 311 1_555 A N MSE 178 A MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 A C MSE 178 A MSE 312 1_555 A N ASN 179 A ASN 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale13 A C LYS 180 A LYS 314 1_555 A N MSE 181 A MSE 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale14 A C MSE 181 A MSE 315 1_555 A N ASP 182 A ASP 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale15 A C LEU 243 A LEU 377 1_555 A N MSE 244 A MSE 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale16 A C MSE 244 A MSE 378 1_555 A N SER 245 A SER 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale17 A C ASP 380 A ASP 514 1_555 A N MSE 381 A MSE 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale18 A C MSE 381 A MSE 515 1_555 A N ASN 382 A ASN 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale19 B C LEU 49 B LEU 183 1_555 B N MSE 50 B MSE 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale20 B C MSE 50 B MSE 184 1_555 B N GLY 51 B GLY 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale21 B C ILE 85 B ILE 219 1_555 B N MSE 86 B MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale22 B C MSE 86 B MSE 220 1_555 B N ASP 87 B ASP 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale23 B C ILE 129 B ILE 263 1_555 B N MSE 130 B MSE 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale24 B C MSE 130 B MSE 264 1_555 B N GLY 131 B GLY 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale25 B C ASP 136 B ASP 270 1_555 B N MSE 137 B MSE 271 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale26 B C MSE 137 B MSE 271 1_555 B N ALA 138 B ALA 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale27 B C HIS 162 B HIS 296 1_555 B N MSE 163 B MSE 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale28 B C MSE 163 B MSE 297 1_555 B N LEU 164 B LEU 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale29 B C ALA 177 B ALA 311 1_555 B N MSE 178 B MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale30 B C MSE 178 B MSE 312 1_555 B N ASN 179 B ASN 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale31 B C LYS 180 B LYS 314 1_555 B N MSE 181 B MSE 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale32 B C MSE 181 B MSE 315 1_555 B N ASP 182 B ASP 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale33 B C LEU 243 B LEU 377 1_555 B N MSE 244 B MSE 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale34 B C MSE 244 B MSE 378 1_555 B N SER 245 B SER 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale35 B C ASP 380 B ASP 514 1_555 B N MSE 381 B MSE 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale36 B C MSE 381 B MSE 515 1_555 B N ASN 382 B ASN 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? # _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 ? # _atom_sites.entry_id 3P27 _atom_sites.fract_transf_matrix[1][1] 0.009094 _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] 0.009094 _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] 0.005314 _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 1 663 663 GDP GDP . D 2 GDP B 1 663 663 GDP GDP . E 3 HOH A 1 1 1 HOH HOH . E 3 HOH A 2 5 5 HOH HOH . E 3 HOH A 3 6 6 HOH HOH . E 3 HOH A 4 7 7 HOH HOH . E 3 HOH A 5 10 10 HOH HOH . E 3 HOH A 6 11 11 HOH HOH . E 3 HOH A 7 16 16 HOH HOH . E 3 HOH A 8 17 17 HOH HOH . E 3 HOH A 9 18 18 HOH HOH . E 3 HOH A 10 19 19 HOH HOH . E 3 HOH A 11 20 20 HOH HOH . E 3 HOH A 12 23 23 HOH HOH . E 3 HOH A 13 24 24 HOH HOH . E 3 HOH A 14 28 28 HOH HOH . E 3 HOH A 15 34 34 HOH HOH . E 3 HOH A 16 36 36 HOH HOH . E 3 HOH A 17 38 38 HOH HOH . E 3 HOH A 18 40 40 HOH HOH . E 3 HOH A 19 43 43 HOH HOH . E 3 HOH A 20 44 44 HOH HOH . E 3 HOH A 21 47 47 HOH HOH . E 3 HOH A 22 49 49 HOH HOH . E 3 HOH A 23 50 50 HOH HOH . E 3 HOH A 24 51 51 HOH HOH . E 3 HOH A 25 54 54 HOH HOH . E 3 HOH A 26 55 55 HOH HOH . E 3 HOH A 27 56 56 HOH HOH . E 3 HOH A 28 60 60 HOH HOH . E 3 HOH A 29 61 61 HOH HOH . E 3 HOH A 30 63 63 HOH HOH . E 3 HOH A 31 66 66 HOH HOH . F 3 HOH B 1 3 3 HOH HOH . F 3 HOH B 2 4 4 HOH HOH . F 3 HOH B 3 9 9 HOH HOH . F 3 HOH B 4 12 12 HOH HOH . F 3 HOH B 5 13 13 HOH HOH . F 3 HOH B 6 14 14 HOH HOH . F 3 HOH B 7 15 15 HOH HOH . F 3 HOH B 8 21 21 HOH HOH . F 3 HOH B 9 22 22 HOH HOH . F 3 HOH B 10 25 25 HOH HOH . F 3 HOH B 11 26 26 HOH HOH . F 3 HOH B 12 27 27 HOH HOH . F 3 HOH B 13 29 29 HOH HOH . F 3 HOH B 14 30 30 HOH HOH . F 3 HOH B 15 31 31 HOH HOH . F 3 HOH B 16 32 32 HOH HOH . F 3 HOH B 17 33 33 HOH HOH . F 3 HOH B 18 35 35 HOH HOH . F 3 HOH B 19 37 37 HOH HOH . F 3 HOH B 20 39 39 HOH HOH . F 3 HOH B 21 41 41 HOH HOH . F 3 HOH B 22 42 42 HOH HOH . F 3 HOH B 23 45 45 HOH HOH . F 3 HOH B 24 46 46 HOH HOH . F 3 HOH B 25 48 48 HOH HOH . F 3 HOH B 26 52 52 HOH HOH . F 3 HOH B 27 53 53 HOH HOH . F 3 HOH B 28 57 57 HOH HOH . F 3 HOH B 29 58 58 HOH HOH . F 3 HOH B 30 59 59 HOH HOH . F 3 HOH B 31 62 62 HOH HOH . F 3 HOH B 32 64 64 HOH HOH . F 3 HOH B 33 65 65 HOH HOH . # 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 . . . C 2 79.497 -12.703 67.494 1 90.64 ? PB GDP 663 A 1 HETATM 2 O O1B GDP . . . C 2 79.158 -12.22 66.096 1 71.05 ? O1B GDP 663 A 1 HETATM 3 O O2B GDP . . . C 2 78.466 -13.724 67.958 1 62.93 ? O2B GDP 663 A 1 HETATM 4 O O3B GDP . . . C 2 80.909 -13.255 67.518 1 78.86 ? O3B GDP 663 A 1 HETATM 5 O O3A GDP . . . C 2 79.396 -11.448 68.492 1 81.57 ? O3A GDP 663 A 1 HETATM 6 P PA GDP . . . C 2 80.274 -11.333 69.831 1 78.78 ? PA GDP 663 A 1 HETATM 7 O O1A GDP . . . C 2 79.419 -10.943 71.027 1 57.66 ? O1A GDP 663 A 1 HETATM 8 O O2A GDP . . . C 2 80.969 -12.645 70.129 1 81.29 ? O2A GDP 663 A 1 HETATM 9 O O5' GDP . . . C 2 81.355 -10.243 69.307 1 76.39 ? O5' GDP 663 A 1 HETATM 10 C C5' GDP . . . C 2 81.003 -8.969 68.766 1 72.07 ? C5' GDP 663 A 1 HETATM 11 C C4' GDP . . . C 2 81.915 -7.916 69.383 1 81.55 ? C4' GDP 663 A 1 HETATM 12 O O4' GDP . . . C 2 81.159 -6.712 69.572 1 78.51 ? O4' GDP 663 A 1 HETATM 13 C C3' GDP . . . C 2 82.343 -8.369 70.768 1 84.44 ? C3' GDP 663 A 1 HETATM 14 O O3' GDP . . . C 2 83.559 -7.72 71.173 1 75.65 ? O3' GDP 663 A 1 HETATM 15 C C2' GDP . . . C 2 81.156 -7.917 71.603 1 84.47 ? C2' GDP 663 A 1 HETATM 16 O O2' GDP . . . C 2 81.435 -7.87 73.012 1 76.97 ? O2' GDP 663 A 1 HETATM 17 C C1' GDP . . . C 2 80.814 -6.568 70.957 1 81.22 ? C1' GDP 663 A 1 HETATM 18 N N9 GDP . . . C 2 79.383 -6.188 71.151 1 77.99 ? N9 GDP 663 A 1 HETATM 19 C C8 GDP . . . C 2 78.32 -7.015 71.203 1 74.82 ? C8 GDP 663 A 1 HETATM 20 N N7 GDP . . . C 2 77.162 -6.327 71.406 1 77.76 ? N7 GDP 663 A 1 HETATM 21 C C5 GDP . . . C 2 77.482 -5.016 71.479 1 77.6 ? C5 GDP 663 A 1 HETATM 22 C C6 GDP . . . C 2 76.757 -3.735 71.675 1 72.59 ? C6 GDP 663 A 1 HETATM 23 O O6 GDP . . . C 2 75.523 -3.714 71.827 1 72.83 ? O6 GDP 663 A 1 HETATM 24 N N1 GDP . . . C 2 77.454 -2.594 71.693 1 74.13 ? N1 GDP 663 A 1 HETATM 25 C C2 GDP . . . C 2 78.793 -2.579 71.537 1 79.81 ? C2 GDP 663 A 1 HETATM 26 N N2 GDP . . . C 2 79.44 -1.391 71.559 1 79.01 ? N2 GDP 663 A 1 HETATM 27 N N3 GDP . . . C 2 79.525 -3.706 71.353 1 82.42 ? N3 GDP 663 A 1 HETATM 28 C C4 GDP . . . C 2 78.941 -4.932 71.314 1 83.87 ? C4 GDP 663 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #