data_5C1S # _model_server_result.job_id u6X1xb6ODtnC7Y9cHljlmg _model_server_result.datetime_utc '2024-10-20 05:33:18' _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 5c1s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5C1S # _exptl.entry_id 5C1S _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 120 _cell.entry_id 5C1S _cell.length_a 63.679 _cell.length_b 63.679 _cell.length_c 324.674 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C1S _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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 disulf ? disulf1 B SG CYS 81 B CYS 39 1_555 B SG CYS 205 B CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A C VAL 133 A VAL 91 1_555 A N MSE 134 A MSE 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MSE 134 A MSE 92 1_555 A N TYR 135 A TYR 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C THR 148 A THR 106 1_555 A N MSE 149 A MSE 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 149 A MSE 107 1_555 A N TRP 150 A TRP 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C ARG 224 A ARG 182 1_555 A N MSE 225 A MSE 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C MSE 225 A MSE 183 1_555 A N LEU 226 A LEU 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 A C LEU 226 A LEU 184 1_555 A N MSE 227 A MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 227 A MSE 185 1_555 A N VAL 228 A VAL 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 A C PHE 252 A PHE 210 1_555 A N MSE 253 A MSE 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 A C MSE 253 A MSE 211 1_555 A N ASN 254 A ASN 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 A C ILE 270 A ILE 228 1_555 A N MSE 271 A MSE 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale12 A C MSE 271 A MSE 229 1_555 A N ILE 272 A ILE 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale13 A C THR 342 A THR 300 1_555 A N MSE 343 A MSE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 A C MSE 343 A MSE 301 1_555 A N GLY 344 A GLY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 A C GLU 359 A GLU 317 1_555 A N MSE 360 A MSE 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 A C MSE 360 A MSE 318 1_555 A N SER 361 A SER 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale17 B C VAL 133 B VAL 91 1_555 B N MSE 134 B MSE 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale18 B C MSE 134 B MSE 92 1_555 B N TYR 135 B TYR 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale19 B C THR 148 B THR 106 1_555 B N MSE 149 B MSE 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale20 B C MSE 149 B MSE 107 1_555 B N TRP 150 B TRP 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale21 B C ARG 224 B ARG 182 1_555 B N MSE 225 B MSE 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale22 B C MSE 225 B MSE 183 1_555 B N LEU 226 B LEU 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale23 B C LEU 226 B LEU 184 1_555 B N MSE 227 B MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale24 B C MSE 227 B MSE 185 1_555 B N VAL 228 B VAL 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale25 B NH2 ARG 240 B ARG 198 1_555 B O TRP 352 B TRP 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale26 B O GLY 249 B GLY 207 1_555 B N ASP 251 B ASP 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale27 B C PHE 252 B PHE 210 1_555 B N MSE 253 B MSE 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale28 B C MSE 253 B MSE 211 1_555 B N ASN 254 B ASN 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale29 B C GLU 261 B GLU 219 1_555 B N MSE 262 B MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale30 B C MSE 262 B MSE 220 1_555 B N GLU 263 B GLU 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale31 B C ILE 270 B ILE 228 1_555 B N MSE 271 B MSE 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale32 B C MSE 271 B MSE 229 1_555 B N ILE 272 B ILE 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale33 B C THR 342 B THR 300 1_555 B N MSE 343 B MSE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale34 B C MSE 343 B MSE 301 1_555 B N GLY 344 B GLY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale35 B C GLU 359 B GLU 317 1_555 B N MSE 360 B MSE 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale36 B C MSE 360 B MSE 318 1_555 B N SER 361 B SER 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? # _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 5C1S _atom_sites.fract_transf_matrix[1][1] 0.015704 _atom_sites.fract_transf_matrix[1][2] 0.009067 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018133 _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] 0.00308 _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 1 401 401 GDP GDP . D 2 GDP B 1 401 401 GDP GDP . E 3 HOH A 1 501 501 HOH HOH . E 3 HOH A 2 502 502 HOH HOH . E 3 HOH A 3 503 503 HOH HOH . E 3 HOH A 4 504 504 HOH HOH . E 3 HOH A 5 505 505 HOH HOH . E 3 HOH A 6 506 506 HOH HOH . E 3 HOH A 7 507 507 HOH HOH . E 3 HOH A 8 508 508 HOH HOH . E 3 HOH A 9 509 509 HOH HOH . E 3 HOH A 10 510 511 HOH HOH . E 3 HOH A 11 511 512 HOH HOH . E 3 HOH A 12 512 513 HOH HOH . E 3 HOH A 13 513 514 HOH HOH . E 3 HOH A 14 514 515 HOH HOH . E 3 HOH A 15 515 516 HOH HOH . E 3 HOH A 16 516 517 HOH HOH . E 3 HOH A 17 517 518 HOH HOH . E 3 HOH A 18 518 519 HOH HOH . E 3 HOH A 19 519 520 HOH HOH . E 3 HOH A 20 520 521 HOH HOH . E 3 HOH A 21 521 522 HOH HOH . E 3 HOH A 22 522 523 HOH HOH . E 3 HOH A 23 523 524 HOH HOH . E 3 HOH A 24 524 525 HOH HOH . E 3 HOH A 25 525 527 HOH HOH . E 3 HOH A 26 526 528 HOH HOH . E 3 HOH A 27 527 529 HOH HOH . E 3 HOH A 28 528 530 HOH HOH . E 3 HOH A 29 529 531 HOH HOH . F 3 HOH B 1 501 501 HOH HOH . F 3 HOH B 2 502 502 HOH HOH . F 3 HOH B 3 503 503 HOH HOH . F 3 HOH B 4 504 504 HOH HOH . F 3 HOH B 5 505 505 HOH HOH . F 3 HOH B 6 506 506 HOH HOH . F 3 HOH B 7 507 507 HOH HOH . F 3 HOH B 8 508 508 HOH HOH . F 3 HOH B 9 509 509 HOH HOH . F 3 HOH B 10 510 510 HOH HOH . F 3 HOH B 11 511 511 HOH HOH . F 3 HOH B 12 512 512 HOH HOH . F 3 HOH B 13 513 513 HOH HOH . F 3 HOH B 14 514 514 HOH HOH . F 3 HOH B 15 515 515 HOH HOH . F 3 HOH B 16 516 517 HOH HOH . F 3 HOH B 17 517 518 HOH HOH . F 3 HOH B 18 518 519 HOH HOH . F 3 HOH B 19 519 520 HOH HOH . F 3 HOH B 20 520 521 HOH HOH . F 3 HOH B 21 521 522 HOH HOH . F 3 HOH B 22 522 523 HOH HOH . F 3 HOH B 23 523 524 HOH HOH . F 3 HOH B 24 524 525 HOH HOH . F 3 HOH B 25 525 526 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 . . . D 2 -24.282 62.774 -16.561 1 128.52 ? PB GDP 401 B 1 HETATM 2 O O1B GDP . . . D 2 -24.299 61.921 -15.319 1 127.37 ? O1B GDP 401 B 1 HETATM 3 O O2B GDP . . . D 2 -25.68 63.268 -16.862 1 136.31 ? O2B GDP 401 B 1 HETATM 4 O O3B GDP . . . D 2 -23.357 63.952 -16.36 1 121.21 ? O3B GDP 401 B 1 HETATM 5 O O3A GDP . . . D 2 -23.745 61.871 -17.775 1 122.69 ? O3A GDP 401 B 1 HETATM 6 P PA GDP . . . D 2 -22.315 61.148 -17.642 1 118.27 ? PA GDP 401 B 1 HETATM 7 O O1A GDP . . . D 2 -21.439 61.841 -16.623 1 119.91 ? O1A GDP 401 B 1 HETATM 8 O O2A GDP . . . D 2 -22.468 59.678 -17.316 1 117.83 ? O2A GDP 401 B 1 HETATM 9 O O5' GDP . . . D 2 -21.749 61.355 -19.132 1 128.84 ? O5' GDP 401 B 1 HETATM 10 C C5' GDP . . . D 2 -22.35 62.354 -19.954 1 129.99 ? C5' GDP 401 B 1 HETATM 11 C C4' GDP . . . D 2 -21.413 62.634 -21.115 1 138.27 ? C4' GDP 401 B 1 HETATM 12 O O4' GDP . . . D 2 -20.251 61.827 -20.926 1 141.79 ? O4' GDP 401 B 1 HETATM 13 C C3' GDP . . . D 2 -22.041 62.244 -22.438 1 154.28 ? C3' GDP 401 B 1 HETATM 14 O O3' GDP . . . D 2 -21.872 63.308 -23.377 1 156.62 ? O3' GDP 401 B 1 HETATM 15 C C2' GDP . . . D 2 -21.294 61.01 -22.902 1 158.97 ? C2' GDP 401 B 1 HETATM 16 O O2' GDP . . . D 2 -20.901 61.149 -24.27 1 149.26 ? O2' GDP 401 B 1 HETATM 17 C C1' GDP . . . D 2 -20.067 60.908 -22.006 1 148.85 ? C1' GDP 401 B 1 HETATM 18 N N9 GDP . . . D 2 -19.925 59.535 -21.459 1 132.11 ? N9 GDP 401 B 1 HETATM 19 C C8 GDP . . . D 2 -20.855 58.861 -20.757 1 129.4 ? C8 GDP 401 B 1 HETATM 20 N N7 GDP . . . D 2 -20.402 57.632 -20.398 1 124.07 ? N7 GDP 401 B 1 HETATM 21 C C5 GDP . . . D 2 -19.145 57.512 -20.869 1 118.81 ? C5 GDP 401 B 1 HETATM 22 C C6 GDP . . . D 2 -18.086 56.477 -20.847 1 107.83 ? C6 GDP 401 B 1 HETATM 23 O O6 GDP . . . D 2 -18.273 55.381 -20.278 1 90.01 ? O6 GDP 401 B 1 HETATM 24 N N1 GDP . . . D 2 -16.926 56.753 -21.456 1 114.98 ? N1 GDP 401 B 1 HETATM 25 C C2 GDP . . . D 2 -16.696 57.924 -22.078 1 117.78 ? C2 GDP 401 B 1 HETATM 26 N N2 GDP . . . D 2 -15.493 58.124 -22.669 1 104.61 ? N2 GDP 401 B 1 HETATM 27 N N3 GDP . . . D 2 -17.62 58.915 -22.136 1 127.72 ? N3 GDP 401 B 1 HETATM 28 C C4 GDP . . . D 2 -18.837 58.77 -21.562 1 129.28 ? C4 GDP 401 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 28 #