data_2FE4 # _model_server_result.job_id T0TVUzxVElUOWM7rccbZDA _model_server_result.datetime_utc '2024-12-02 20:47:59' _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 2fe4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 2FE4 # _exptl.entry_id 2FE4 _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 2FE4 _cell.length_a 36.036 _cell.length_b 61.125 _cell.length_c 66.634 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2FE4 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 metalc ? metalc1 A OG1 THR 16 A THR 27 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc2 A OG1 THR 34 A THR 45 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc3 D O3B GDP . A GDP 201 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc4 B MG MG . A MG 202 1_555 C O3 NO3 . A NO3 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc5 B MG MG . A MG 202 1_555 E O HOH . A HOH 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc6 B MG MG . A MG 202 1_555 E O HOH . A HOH 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 2FE4 _atom_sites.fract_transf_matrix[1][1] 0.02775 _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] 0.01636 _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] 0.015007 _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 1 202 202 MG MG . C 3 NO3 A 1 203 203 NO3 NO3 . D 4 GDP A 1 201 201 GDP GDP . E 5 HOH A 1 204 1 HOH HOH . E 5 HOH A 2 205 2 HOH HOH . E 5 HOH A 3 206 3 HOH HOH . E 5 HOH A 4 207 4 HOH HOH . E 5 HOH A 5 208 5 HOH HOH . E 5 HOH A 6 209 6 HOH HOH . E 5 HOH A 7 210 7 HOH HOH . E 5 HOH A 8 211 8 HOH HOH . E 5 HOH A 9 212 9 HOH HOH . E 5 HOH A 10 213 10 HOH HOH . E 5 HOH A 11 214 11 HOH HOH . E 5 HOH A 12 215 12 HOH HOH . E 5 HOH A 13 216 13 HOH HOH . E 5 HOH A 14 217 14 HOH HOH . E 5 HOH A 15 218 15 HOH HOH . E 5 HOH A 16 219 16 HOH HOH . E 5 HOH A 17 220 17 HOH HOH . E 5 HOH A 18 221 18 HOH HOH . E 5 HOH A 19 222 19 HOH HOH . E 5 HOH A 20 223 20 HOH HOH . E 5 HOH A 21 224 21 HOH HOH . E 5 HOH A 22 225 22 HOH HOH . E 5 HOH A 23 226 23 HOH HOH . E 5 HOH A 24 227 24 HOH HOH . E 5 HOH A 25 228 25 HOH HOH . E 5 HOH A 26 229 26 HOH HOH . E 5 HOH A 27 230 27 HOH HOH . E 5 HOH A 28 231 28 HOH HOH . E 5 HOH A 29 232 29 HOH HOH . E 5 HOH A 30 233 30 HOH HOH . E 5 HOH A 31 234 31 HOH HOH . E 5 HOH A 32 235 32 HOH HOH . E 5 HOH A 33 236 33 HOH HOH . E 5 HOH A 34 237 34 HOH HOH . E 5 HOH A 35 238 35 HOH HOH . E 5 HOH A 36 239 36 HOH HOH . E 5 HOH A 37 240 37 HOH HOH . E 5 HOH A 38 241 38 HOH HOH . E 5 HOH A 39 242 39 HOH HOH . E 5 HOH A 40 243 40 HOH HOH . E 5 HOH A 41 244 41 HOH HOH . E 5 HOH A 42 245 42 HOH HOH . E 5 HOH A 43 246 43 HOH HOH . E 5 HOH A 44 247 44 HOH HOH . E 5 HOH A 45 248 45 HOH HOH . E 5 HOH A 46 249 46 HOH HOH . E 5 HOH A 47 250 47 HOH HOH . E 5 HOH A 48 251 48 HOH HOH . E 5 HOH A 49 252 49 HOH HOH . E 5 HOH A 50 253 50 HOH HOH . E 5 HOH A 51 254 51 HOH HOH . E 5 HOH A 52 255 52 HOH HOH . E 5 HOH A 53 256 53 HOH HOH . E 5 HOH A 54 257 54 HOH HOH . E 5 HOH A 55 258 55 HOH HOH . E 5 HOH A 56 259 56 HOH HOH . E 5 HOH A 57 260 57 HOH HOH . E 5 HOH A 58 261 58 HOH HOH . E 5 HOH A 59 262 59 HOH HOH . E 5 HOH A 60 263 60 HOH HOH . E 5 HOH A 61 264 61 HOH HOH . E 5 HOH A 62 265 62 HOH HOH . E 5 HOH A 63 266 63 HOH HOH . E 5 HOH A 64 267 64 HOH HOH . E 5 HOH A 65 268 65 HOH HOH . E 5 HOH A 66 269 66 HOH HOH . E 5 HOH A 67 270 67 HOH HOH . E 5 HOH A 68 271 68 HOH HOH . E 5 HOH A 69 272 69 HOH HOH . E 5 HOH A 70 273 70 HOH HOH . E 5 HOH A 71 274 71 HOH HOH . E 5 HOH A 72 275 72 HOH HOH . E 5 HOH A 73 276 73 HOH HOH . E 5 HOH A 74 277 74 HOH HOH . E 5 HOH A 75 278 75 HOH HOH . E 5 HOH A 76 279 76 HOH HOH . E 5 HOH A 77 280 77 HOH HOH . E 5 HOH A 78 281 78 HOH HOH . E 5 HOH A 79 282 79 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 13.801 32.149 29.131 1 14.67 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . D 4 12.883 33.197 29.516 1 13.01 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . D 4 13.244 31.201 28.167 1 19.31 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . D 4 15.065 32.656 28.556 1 11.03 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . D 4 14.13 31.343 30.463 1 13.38 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . D 4 15.373 31.419 31.473 1 9.8 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . D 4 15.447 32.763 32.004 1 11.51 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . D 4 16.577 30.976 30.719 1 13.47 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . D 4 14.917 30.32 32.505 1 12.97 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . D 4 13.761 30.536 33.34 1 13.79 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . D 4 13.904 29.854 34.7 1 9.95 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . D 4 14.017 28.41 34.459 1 9.42 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . D 4 15.173 30.258 35.459 1 9.7 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . D 4 14.764 30.423 36.822 1 11.74 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . D 4 16.156 29.098 35.194 1 10.65 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . D 4 17.137 28.944 36.258 1 12.05 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . D 4 15.254 27.876 35.003 1 11.61 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . D 4 15.822 26.872 34.021 1 10.13 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . D 4 16.325 27.044 32.726 1 8.74 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . D 4 16.746 25.956 32.132 1 8.07 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . D 4 16.515 24.995 33.081 1 5.13 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . D 4 16.731 23.571 33.083 1 2 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . D 4 17.217 22.897 32.193 1 5.74 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . D 4 16.348 22.911 34.278 1 2 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . D 4 15.762 23.558 35.418 1 3.53 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . D 4 15.437 22.838 36.478 1 4.97 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . D 4 15.552 24.897 35.43 1 3.68 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . D 4 15.924 25.554 34.254 1 8.64 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 455 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #