data_4DSU # _model_server_result.job_id xHTNsytDF4UuBxhHeS1Tsw _model_server_result.datetime_utc '2024-11-27 21:23:49' _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 4dsu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4DSU # _exptl.entry_id 4DSU _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 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 120 _cell.entry_id 4DSU _cell.length_a 79.553 _cell.length_b 79.553 _cell.length_c 78.055 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DSU _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 2 _struct_asym.id B _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 metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? # _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 99 n n PB O2B GDP sing 100 n n PB O3B GDP sing 101 n n PB O3A GDP sing 102 n n O2B HOB2 GDP sing 103 n n O3B HOB3 GDP sing 104 n n O3A PA GDP sing 105 n n PA O1A GDP doub 106 n n PA O2A GDP sing 107 n n PA O5' GDP sing 108 n n O2A HOA2 GDP sing 109 n n O5' C5' GDP sing 110 n n C5' C4' GDP sing 111 n n C5' H5' GDP sing 112 n n C5' "H5''" GDP sing 113 n n C4' O4' GDP sing 114 n n C4' C3' GDP sing 115 n n C4' H4' GDP sing 116 n n O4' C1' GDP sing 117 n n C3' O3' GDP sing 118 n n C3' C2' GDP sing 119 n n C3' H3' GDP sing 120 n n O3' HO3' GDP sing 121 n n C2' O2' GDP sing 122 n n C2' C1' GDP sing 123 n n C2' H2' GDP sing 124 n n O2' HO2' GDP sing 125 n n C1' N9 GDP sing 126 n n C1' H1' GDP sing 127 n n N9 C8 GDP sing 128 n y N9 C4 GDP sing 129 n y C8 N7 GDP doub 130 n y C8 H8 GDP sing 131 n n N7 C5 GDP sing 132 n y C5 C6 GDP sing 133 n n C5 C4 GDP doub 134 n y C6 O6 GDP doub 135 n n C6 N1 GDP sing 136 n n N1 C2 GDP sing 137 n n N1 HN1 GDP sing 138 n n C2 N2 GDP sing 139 n n C2 N3 GDP doub 140 n n N2 HN21 GDP sing 141 n n N2 HN22 GDP sing 142 n n N3 C4 GDP sing 143 n n # _atom_sites.entry_id 4DSU _atom_sites.fract_transf_matrix[1][1] 0.01257 _atom_sites.fract_transf_matrix[1][2] 0.007257 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014515 _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] 0.012811 _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 GDP A 1 201 1 GDP GDP . C 3 MG A 1 202 1 MG MG . D 4 BZI A 1 203 1 BZI BZI . 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 18 HOH HOH . E 5 HOH A 18 318 19 HOH HOH . E 5 HOH A 19 319 20 HOH HOH . E 5 HOH A 20 320 21 HOH HOH . E 5 HOH A 21 321 22 HOH HOH . E 5 HOH A 22 322 24 HOH HOH . E 5 HOH A 23 323 25 HOH HOH . E 5 HOH A 24 324 26 HOH HOH . E 5 HOH A 25 325 28 HOH HOH . E 5 HOH A 26 326 29 HOH HOH . E 5 HOH A 27 327 30 HOH HOH . E 5 HOH A 28 328 31 HOH HOH . E 5 HOH A 29 329 32 HOH HOH . E 5 HOH A 30 330 33 HOH HOH . E 5 HOH A 31 331 34 HOH HOH . E 5 HOH A 32 332 35 HOH HOH . E 5 HOH A 33 333 36 HOH HOH . E 5 HOH A 34 334 37 HOH HOH . E 5 HOH A 35 335 38 HOH HOH . E 5 HOH A 36 336 39 HOH HOH . E 5 HOH A 37 337 40 HOH HOH . E 5 HOH A 38 338 41 HOH HOH . E 5 HOH A 39 339 42 HOH HOH . E 5 HOH A 40 340 43 HOH HOH . E 5 HOH A 41 341 44 HOH HOH . E 5 HOH A 42 342 45 HOH HOH . E 5 HOH A 43 343 46 HOH HOH . E 5 HOH A 44 344 47 HOH HOH . E 5 HOH A 45 345 48 HOH HOH . E 5 HOH A 46 346 49 HOH HOH . E 5 HOH A 47 347 50 HOH HOH . E 5 HOH A 48 348 51 HOH HOH . E 5 HOH A 49 349 52 HOH HOH . E 5 HOH A 50 350 53 HOH HOH . E 5 HOH A 51 351 54 HOH HOH . E 5 HOH A 52 352 55 HOH HOH . E 5 HOH A 53 353 56 HOH HOH . E 5 HOH A 54 354 57 HOH HOH . E 5 HOH A 55 355 58 HOH HOH . E 5 HOH A 56 356 59 HOH HOH . E 5 HOH A 57 357 60 HOH HOH . E 5 HOH A 58 358 61 HOH HOH . E 5 HOH A 59 359 62 HOH HOH . E 5 HOH A 60 360 63 HOH HOH . E 5 HOH A 61 361 64 HOH HOH . E 5 HOH A 62 362 65 HOH HOH . E 5 HOH A 63 363 66 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 . . . B 2 15.501 -0.157 5.923 1 27.86 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 14.426 -0.41 6.952 1 29.52 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 15.06 0.882 4.917 1 27.41 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 16.784 0.306 6.556 1 25.94 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 15.76 -1.513 5.102 1 29.22 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 16.91 -2.594 5.41 1 29.11 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 16.918 -3.107 6.826 1 31.85 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 18.268 -2.087 5.001 1 30.53 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 16.45 -3.753 4.399 1 29.66 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 15.213 -4.43 4.634 1 30.1 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 15.279 -5.816 4.007 1 30.24 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 15.44 -5.64 2.603 1 28.76 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 16.492 -6.602 4.495 1 32.38 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 16.153 -7.994 4.555 1 34.52 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 17.513 -6.385 3.4 1 31.11 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 18.456 -7.454 3.282 1 33.05 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 16.632 -6.286 2.167 1 29.18 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 17.248 -5.442 1.126 1 25.58 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 17.751 -4.199 1.281 1 26.41 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 18.209 -3.727 0.092 1 23.77 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 17.978 -4.688 -0.833 1 25.04 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 18.198 -4.846 -2.279 1 25.97 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 18.737 -3.925 -2.93 1 26.47 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 17.796 -5.988 -2.861 1 25.72 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 17.211 -6.991 -2.169 1 25.98 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 16.836 -8.118 -2.819 1 27.62 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 16.968 -6.912 -0.84 1 25.17 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 17.336 -5.806 -0.145 1 25.16 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #