data_4LYJ # _model_server_result.job_id EFvwHla-ROcMjwYSAuiDBA _model_server_result.datetime_utc '2024-11-22 12:40:26' _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 4lyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 4LYJ # _exptl.entry_id 4LYJ _exptl.method 'X-RAY DIFFRACTION' # _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 1 _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 4LYJ _cell.length_a 38.775 _cell.length_b 43.195 _cell.length_c 87.536 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 13 A CYS 12 1_555 C C17 21F . A 21F 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.831 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc2 A OH TYR 33 A TYR 32 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc3 B MG MG . A MG 201 1_555 D O1B GDP . A GDP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc4 B MG MG . A MG 201 1_555 E O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc5 B MG MG . A MG 201 1_555 E O HOH . A HOH 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? # _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 133 n n PB O2B GDP sing 134 n n PB O3B GDP sing 135 n n PB O3A GDP sing 136 n n O2B HOB2 GDP sing 137 n n O3B HOB3 GDP sing 138 n n O3A PA GDP sing 139 n n PA O1A GDP doub 140 n n PA O2A GDP sing 141 n n PA O5' GDP sing 142 n n O2A HOA2 GDP sing 143 n n O5' C5' GDP sing 144 n n C5' C4' GDP sing 145 n n C5' H5' GDP sing 146 n n C5' "H5''" GDP sing 147 n n C4' O4' GDP sing 148 n n C4' C3' GDP sing 149 n n C4' H4' GDP sing 150 n n O4' C1' GDP sing 151 n n C3' O3' GDP sing 152 n n C3' C2' GDP sing 153 n n C3' H3' GDP sing 154 n n O3' HO3' GDP sing 155 n n C2' O2' GDP sing 156 n n C2' C1' GDP sing 157 n n C2' H2' GDP sing 158 n n O2' HO2' GDP sing 159 n n C1' N9 GDP sing 160 n n C1' H1' GDP sing 161 n n N9 C8 GDP sing 162 n y N9 C4 GDP sing 163 n y C8 N7 GDP doub 164 n y C8 H8 GDP sing 165 n n N7 C5 GDP sing 166 n y C5 C6 GDP sing 167 n n C5 C4 GDP doub 168 n y C6 O6 GDP doub 169 n n C6 N1 GDP sing 170 n n N1 C2 GDP sing 171 n n N1 HN1 GDP sing 172 n n C2 N2 GDP sing 173 n n C2 N3 GDP doub 174 n n N2 HN21 GDP sing 175 n n N2 HN22 GDP sing 176 n n N3 C4 GDP sing 177 n n # _atom_sites.entry_id 4LYJ _atom_sites.fract_transf_matrix[1][1] 0.02579 _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] 0.023151 _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] 0.011424 _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 B 2 MG A 1 201 200 MG MG . C 3 21F A 1 202 210 21F LIG . D 4 GDP A 1 203 220 GDP GDP . E 5 HOH A 1 301 1 HOH HOH . E 5 HOH A 2 302 2 HOH HOH . E 5 HOH A 3 303 3 HOH HOH . E 5 HOH A 4 304 4 HOH HOH . E 5 HOH A 5 305 5 HOH HOH . E 5 HOH A 6 306 6 HOH HOH . E 5 HOH A 7 307 7 HOH HOH . E 5 HOH A 8 308 8 HOH HOH . E 5 HOH A 9 309 9 HOH HOH . E 5 HOH A 10 310 10 HOH HOH . E 5 HOH A 11 311 11 HOH HOH . E 5 HOH A 12 312 12 HOH HOH . E 5 HOH A 13 313 13 HOH HOH . E 5 HOH A 14 314 14 HOH HOH . E 5 HOH A 15 315 15 HOH HOH . E 5 HOH A 16 316 16 HOH HOH . E 5 HOH A 17 317 17 HOH HOH . E 5 HOH A 18 318 18 HOH HOH . E 5 HOH A 19 319 19 HOH HOH . E 5 HOH A 20 320 20 HOH HOH . E 5 HOH A 21 321 21 HOH HOH . E 5 HOH A 22 322 22 HOH HOH . E 5 HOH A 23 323 23 HOH HOH . E 5 HOH A 24 324 24 HOH HOH . E 5 HOH A 25 325 25 HOH HOH . E 5 HOH A 26 326 26 HOH HOH . E 5 HOH A 27 327 27 HOH HOH . E 5 HOH A 28 328 28 HOH HOH . E 5 HOH A 29 329 29 HOH HOH . E 5 HOH A 30 330 30 HOH HOH . E 5 HOH A 31 331 31 HOH HOH . E 5 HOH A 32 332 32 HOH HOH . E 5 HOH A 33 333 33 HOH HOH . E 5 HOH A 34 334 34 HOH HOH . E 5 HOH A 35 335 35 HOH HOH . E 5 HOH A 36 336 36 HOH HOH . E 5 HOH A 37 337 37 HOH HOH . E 5 HOH A 38 338 38 HOH HOH . E 5 HOH A 39 339 39 HOH HOH . E 5 HOH A 40 340 40 HOH HOH . E 5 HOH A 41 341 41 HOH HOH . E 5 HOH A 42 342 42 HOH HOH . E 5 HOH A 43 343 43 HOH HOH . E 5 HOH A 44 344 44 HOH HOH . E 5 HOH A 45 345 45 HOH HOH . E 5 HOH A 46 346 46 HOH HOH . E 5 HOH A 47 347 47 HOH HOH . E 5 HOH A 48 348 48 HOH HOH . E 5 HOH A 49 349 49 HOH HOH . E 5 HOH A 50 350 50 HOH HOH . E 5 HOH A 51 351 51 HOH HOH . E 5 HOH A 52 352 52 HOH HOH . E 5 HOH A 53 353 53 HOH HOH . E 5 HOH A 54 354 54 HOH HOH . E 5 HOH A 55 355 55 HOH HOH . E 5 HOH A 56 356 56 HOH HOH . E 5 HOH A 57 357 57 HOH HOH . E 5 HOH A 58 358 58 HOH HOH . E 5 HOH A 59 359 59 HOH HOH . E 5 HOH A 60 360 60 HOH HOH . E 5 HOH A 61 361 61 HOH HOH . E 5 HOH A 62 362 62 HOH HOH . E 5 HOH A 63 363 63 HOH HOH . E 5 HOH A 64 364 64 HOH HOH . E 5 HOH A 65 365 65 HOH HOH . E 5 HOH A 66 366 66 HOH HOH . E 5 HOH A 67 367 67 HOH HOH . E 5 HOH A 68 368 68 HOH HOH . E 5 HOH A 69 369 69 HOH HOH . E 5 HOH A 70 370 70 HOH HOH . E 5 HOH A 71 371 71 HOH HOH . E 5 HOH A 72 372 72 HOH HOH . E 5 HOH A 73 373 73 HOH HOH . E 5 HOH A 74 374 74 HOH HOH . E 5 HOH A 75 375 75 HOH HOH . E 5 HOH A 76 376 76 HOH HOH . E 5 HOH A 77 377 77 HOH HOH . E 5 HOH A 78 378 78 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 4 -2.849 5.105 9.338 1 15.49 ? PB GDP 203 A 1 HETATM 2 O O1B GDP . . . D 4 -3.981 6.024 8.982 1 14.35 ? O1B GDP 203 A 1 HETATM 3 O O2B GDP . . . D 4 -1.912 5.758 10.312 1 16.05 ? O2B GDP 203 A 1 HETATM 4 O O3B GDP . . . D 4 -3.38 3.838 9.969 1 14.1 ? O3B GDP 203 A 1 HETATM 5 O O3A GDP . . . D 4 -2.024 4.626 8.056 1 11.84 ? O3A GDP 203 A 1 HETATM 6 P PA GDP . . . D 4 -2.072 5.415 6.664 1 18 ? PA GDP 203 A 1 HETATM 7 O O1A GDP . . . D 4 -3.462 5.421 6.089 1 14.99 ? O1A GDP 203 A 1 HETATM 8 O O2A GDP . . . D 4 -1.51 6.801 6.869 1 16.4 ? O2A GDP 203 A 1 HETATM 9 O O5' GDP . . . D 4 -1.084 4.501 5.785 1 17.33 ? O5' GDP 203 A 1 HETATM 10 C C5' GDP . . . D 4 0.295 4.418 6.131 1 12.55 ? C5' GDP 203 A 1 HETATM 11 C C4' GDP . . . D 4 1.101 4.116 4.877 1 14.36 ? C4' GDP 203 A 1 HETATM 12 O O4' GDP . . . D 4 0.743 2.82 4.404 1 16.43 ? O4' GDP 203 A 1 HETATM 13 C C3' GDP . . . D 4 0.796 5.08 3.742 1 15.85 ? C3' GDP 203 A 1 HETATM 14 O O3' GDP . . . D 4 2.021 5.322 3.046 1 19.99 ? O3' GDP 203 A 1 HETATM 15 C C2' GDP . . . D 4 -0.115 4.317 2.813 1 16.75 ? C2' GDP 203 A 1 HETATM 16 O O2' GDP . . . D 4 0.069 4.712 1.449 1 15.93 ? O2' GDP 203 A 1 HETATM 17 C C1' GDP . . . D 4 0.335 2.889 3.041 1 12.35 ? C1' GDP 203 A 1 HETATM 18 N N9 GDP . . . D 4 -0.774 1.943 2.867 1 12.07 ? N9 GDP 203 A 1 HETATM 19 C C8 GDP . . . D 4 -1.96 1.964 3.512 1 15.96 ? C8 GDP 203 A 1 HETATM 20 N N7 GDP . . . D 4 -2.741 0.931 3.117 1 14.92 ? N7 GDP 203 A 1 HETATM 21 C C5 GDP . . . D 4 -2.03 0.224 2.211 1 13.93 ? C5 GDP 203 A 1 HETATM 22 C C6 GDP . . . D 4 -2.25 -0.99 1.398 1 14.81 ? C6 GDP 203 A 1 HETATM 23 O O6 GDP . . . D 4 -3.329 -1.627 1.46 1 13.51 ? O6 GDP 203 A 1 HETATM 24 N N1 GDP . . . D 4 -1.259 -1.378 0.589 1 14.92 ? N1 GDP 203 A 1 HETATM 25 C C2 GDP . . . D 4 -0.091 -0.714 0.489 1 19.3 ? C2 GDP 203 A 1 HETATM 26 N N2 GDP . . . D 4 0.849 -1.187 -0.364 1 19.61 ? N2 GDP 203 A 1 HETATM 27 N N3 GDP . . . D 4 0.191 0.407 1.203 1 16.66 ? N3 GDP 203 A 1 HETATM 28 C C4 GDP . . . D 4 -0.734 0.902 2.059 1 15.37 ? C4 GDP 203 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 397 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #