data_2E87 # _model_server_result.job_id TbDFz9q_T35V3ZzOdSPjZg _model_server_result.datetime_utc '2025-02-27 01:49:57' _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 2e87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":400}' # _entry.id 2E87 # _exptl.entry_id 2E87 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 2E87 _cell.length_a 47.253 _cell.length_b 99.191 _cell.length_c 126.135 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2E87 _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,F,G _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 3 _struct_asym.id F _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 C MSE 1 A MSE 1 1_555 A N ARG 2 A ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C ARG 7 A ARG 7 1_555 A N MSE 8 A MSE 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C MSE 8 A MSE 8 1_555 A N PRO 9 A PRO 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C ALA 94 A ALA 94 1_555 A N MSE 95 A MSE 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C MSE 95 A MSE 95 1_555 A N ALA 96 A ALA 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 2E87 _atom_sites.fract_transf_matrix[1][1] 0.021163 _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] 0.010082 _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] 0.007928 _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 SO4 A 1 401 401 SO4 SO4 . C 2 SO4 A 1 402 402 SO4 SO4 . D 2 SO4 A 1 403 403 SO4 SO4 . E 2 SO4 A 1 404 404 SO4 SO4 . F 3 GDP A 1 400 400 GDP GDP . G 4 HOH A 1 405 1 HOH TIP . G 4 HOH A 2 406 2 HOH TIP . G 4 HOH A 3 407 3 HOH TIP . G 4 HOH A 4 408 4 HOH TIP . G 4 HOH A 5 409 5 HOH TIP . G 4 HOH A 6 410 6 HOH TIP . G 4 HOH A 7 411 7 HOH TIP . G 4 HOH A 8 412 8 HOH TIP . G 4 HOH A 9 413 9 HOH TIP . G 4 HOH A 10 414 10 HOH TIP . G 4 HOH A 11 415 11 HOH TIP . G 4 HOH A 12 416 12 HOH TIP . G 4 HOH A 13 417 13 HOH TIP . G 4 HOH A 14 418 14 HOH TIP . G 4 HOH A 15 419 15 HOH TIP . G 4 HOH A 16 420 16 HOH TIP . G 4 HOH A 17 421 17 HOH TIP . G 4 HOH A 18 422 18 HOH TIP . G 4 HOH A 19 423 19 HOH TIP . G 4 HOH A 20 424 20 HOH TIP . G 4 HOH A 21 425 21 HOH TIP . G 4 HOH A 22 426 22 HOH TIP . G 4 HOH A 23 427 23 HOH TIP . G 4 HOH A 24 428 24 HOH TIP . G 4 HOH A 25 429 25 HOH TIP . G 4 HOH A 26 430 26 HOH TIP . G 4 HOH A 27 431 27 HOH TIP . G 4 HOH A 28 432 28 HOH TIP . G 4 HOH A 29 433 29 HOH TIP . G 4 HOH A 30 434 30 HOH TIP . G 4 HOH A 31 435 31 HOH TIP . G 4 HOH A 32 436 32 HOH TIP . G 4 HOH A 33 437 33 HOH TIP . G 4 HOH A 34 438 34 HOH TIP . G 4 HOH A 35 439 35 HOH TIP . G 4 HOH A 36 440 36 HOH TIP . G 4 HOH A 37 441 37 HOH TIP . G 4 HOH A 38 442 38 HOH TIP . G 4 HOH A 39 443 39 HOH TIP . G 4 HOH A 40 444 40 HOH TIP . G 4 HOH A 41 445 41 HOH TIP . G 4 HOH A 42 446 42 HOH TIP . G 4 HOH A 43 447 43 HOH TIP . G 4 HOH A 44 448 44 HOH TIP . G 4 HOH A 45 449 45 HOH TIP . G 4 HOH A 46 450 46 HOH TIP . G 4 HOH A 47 451 47 HOH TIP . G 4 HOH A 48 452 48 HOH TIP . G 4 HOH A 49 453 49 HOH TIP . G 4 HOH A 50 454 50 HOH TIP . G 4 HOH A 51 455 51 HOH TIP . G 4 HOH A 52 456 52 HOH TIP . # 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 . . . F 3 34.95 60.291 27.616 1 34.29 ? PB GDP 400 A 1 HETATM 2 O O1B GDP . . . F 3 33.647 61.054 27.761 1 35.5 ? O1B GDP 400 A 1 HETATM 3 O O2B GDP . . . F 3 35.111 59.153 28.756 1 38.01 ? O2B GDP 400 A 1 HETATM 4 O O3B GDP . . . F 3 35.426 59.952 26.2 1 40.28 ? O3B GDP 400 A 1 HETATM 5 O O3A GDP . . . F 3 36.02 61.373 28.092 1 38.1 ? O3A GDP 400 A 1 HETATM 6 P PA GDP . . . F 3 37.036 62.267 27.207 1 49.44 ? PA GDP 400 A 1 HETATM 7 O O1A GDP . . . F 3 37.98 61.413 26.435 1 35.94 ? O1A GDP 400 A 1 HETATM 8 O O2A GDP . . . F 3 36.171 63.208 26.212 1 43.14 ? O2A GDP 400 A 1 HETATM 9 O O5' GDP . . . F 3 37.871 63.159 28.252 1 49.6 ? O5' GDP 400 A 1 HETATM 10 C C5' GDP . . . F 3 36.952 64.009 28.965 1 49.26 ? C5' GDP 400 A 1 HETATM 11 C C4' GDP . . . F 3 37.675 65.289 29.424 1 50.05 ? C4' GDP 400 A 1 HETATM 12 O O4' GDP . . . F 3 38.841 64.926 30.256 1 45.67 ? O4' GDP 400 A 1 HETATM 13 C C3' GDP . . . F 3 38.281 66.126 28.296 1 50.55 ? C3' GDP 400 A 1 HETATM 14 O O3' GDP . . . F 3 38.207 67.544 28.127 1 52.83 ? O3' GDP 400 A 1 HETATM 15 C C2' GDP . . . F 3 39.67 65.484 28.111 1 50.41 ? C2' GDP 400 A 1 HETATM 16 O O2' GDP . . . F 3 40.541 66.489 27.555 1 51.86 ? O2' GDP 400 A 1 HETATM 17 C C1' GDP . . . F 3 40.068 65.388 29.569 1 51.49 ? C1' GDP 400 A 1 HETATM 18 N N9 GDP . . . F 3 41.141 64.411 29.806 1 55.3 ? N9 GDP 400 A 1 HETATM 19 C C8 GDP . . . F 3 41.31 63.192 29.202 1 58.1 ? C8 GDP 400 A 1 HETATM 20 N N7 GDP . . . F 3 42.379 62.601 29.668 1 57.03 ? N7 GDP 400 A 1 HETATM 21 C C5 GDP . . . F 3 42.96 63.397 30.599 1 55.6 ? C5 GDP 400 A 1 HETATM 22 C C6 GDP . . . F 3 44.129 63.295 31.434 1 53.62 ? C6 GDP 400 A 1 HETATM 23 O O6 GDP . . . F 3 44.854 62.306 31.387 1 48.85 ? O6 GDP 400 A 1 HETATM 24 N N1 GDP . . . F 3 44.411 64.336 32.289 1 57.49 ? N1 GDP 400 A 1 HETATM 25 C C2 GDP . . . F 3 43.59 65.458 32.344 1 57.6 ? C2 GDP 400 A 1 HETATM 26 N N2 GDP . . . F 3 43.896 66.478 33.203 1 61.75 ? N2 GDP 400 A 1 HETATM 27 N N3 GDP . . . F 3 42.515 65.563 31.575 1 56.93 ? N3 GDP 400 A 1 HETATM 28 C C4 GDP . . . F 3 42.166 64.57 30.701 1 58.5 ? C4 GDP 400 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #