data_5L3V # _model_server_result.job_id wsZXrUgIYV5K_vcWB1ysyg _model_server_result.datetime_utc '2024-11-08 10:36:17' _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 5l3v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 5L3V # _exptl.entry_id 5L3V _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 5L3V _cell.length_a 92.168 _cell.length_b 92.168 _cell.length_c 148.24 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L3V _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # 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,D,E,H 1 1 B,F,G,I 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 F N N # _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 5L3V _atom_sites.fract_transf_matrix[1][1] 0.01085 _atom_sites.fract_transf_matrix[1][2] 0.006264 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012528 _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] 0.006746 _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 1 301 301 GDP GDP . D 3 SO4 A 1 302 2 SO4 SO4 . E 3 SO4 A 1 303 3 SO4 SO4 . F 2 GDP B 1 301 302 GDP GDP . G 3 SO4 B 1 302 1 SO4 SO4 . H 4 HOH A 1 401 57 HOH HOH . H 4 HOH A 2 402 107 HOH HOH . H 4 HOH A 3 403 50 HOH HOH . H 4 HOH A 4 404 6 HOH HOH . H 4 HOH A 5 405 83 HOH HOH . H 4 HOH A 6 406 109 HOH HOH . H 4 HOH A 7 407 35 HOH HOH . H 4 HOH A 8 408 101 HOH HOH . H 4 HOH A 9 409 84 HOH HOH . H 4 HOH A 10 410 25 HOH HOH . H 4 HOH A 11 411 95 HOH HOH . H 4 HOH A 12 412 52 HOH HOH . H 4 HOH A 13 413 157 HOH HOH . H 4 HOH A 14 414 37 HOH HOH . H 4 HOH A 15 415 49 HOH HOH . H 4 HOH A 16 416 173 HOH HOH . H 4 HOH A 17 417 8 HOH HOH . H 4 HOH A 18 418 5 HOH HOH . H 4 HOH A 19 419 114 HOH HOH . H 4 HOH A 20 420 24 HOH HOH . H 4 HOH A 21 421 106 HOH HOH . H 4 HOH A 22 422 131 HOH HOH . H 4 HOH A 23 423 44 HOH HOH . H 4 HOH A 24 424 1 HOH HOH . H 4 HOH A 25 425 4 HOH HOH . H 4 HOH A 26 426 7 HOH HOH . H 4 HOH A 27 427 29 HOH HOH . H 4 HOH A 28 428 41 HOH HOH . H 4 HOH A 29 429 18 HOH HOH . H 4 HOH A 30 430 78 HOH HOH . H 4 HOH A 31 431 69 HOH HOH . H 4 HOH A 32 432 90 HOH HOH . H 4 HOH A 33 433 174 HOH HOH . H 4 HOH A 34 434 19 HOH HOH . H 4 HOH A 35 435 31 HOH HOH . H 4 HOH A 36 436 11 HOH HOH . H 4 HOH A 37 437 10 HOH HOH . H 4 HOH A 38 438 54 HOH HOH . H 4 HOH A 39 439 32 HOH HOH . H 4 HOH A 40 440 158 HOH HOH . H 4 HOH A 41 441 76 HOH HOH . H 4 HOH A 42 442 33 HOH HOH . H 4 HOH A 43 443 116 HOH HOH . H 4 HOH A 44 444 155 HOH HOH . H 4 HOH A 45 445 38 HOH HOH . H 4 HOH A 46 446 82 HOH HOH . H 4 HOH A 47 447 125 HOH HOH . H 4 HOH A 48 448 156 HOH HOH . H 4 HOH A 49 449 133 HOH HOH . H 4 HOH A 50 450 128 HOH HOH . H 4 HOH A 51 451 40 HOH HOH . H 4 HOH A 52 452 61 HOH HOH . H 4 HOH A 53 453 34 HOH HOH . H 4 HOH A 54 454 175 HOH HOH . H 4 HOH A 55 455 124 HOH HOH . H 4 HOH A 56 456 74 HOH HOH . H 4 HOH A 57 457 103 HOH HOH . H 4 HOH A 58 458 171 HOH HOH . H 4 HOH A 59 459 161 HOH HOH . H 4 HOH A 60 460 130 HOH HOH . H 4 HOH A 61 461 28 HOH HOH . H 4 HOH A 62 462 2 HOH HOH . H 4 HOH A 63 463 60 HOH HOH . H 4 HOH A 64 464 12 HOH HOH . H 4 HOH A 65 465 147 HOH HOH . H 4 HOH A 66 466 140 HOH HOH . H 4 HOH A 67 467 145 HOH HOH . H 4 HOH A 68 468 75 HOH HOH . H 4 HOH A 69 469 88 HOH HOH . H 4 HOH A 70 470 63 HOH HOH . H 4 HOH A 71 471 166 HOH HOH . H 4 HOH A 72 472 58 HOH HOH . H 4 HOH A 73 473 159 HOH HOH . H 4 HOH A 74 474 51 HOH HOH . H 4 HOH A 75 475 77 HOH HOH . H 4 HOH A 76 476 89 HOH HOH . H 4 HOH A 77 477 13 HOH HOH . H 4 HOH A 78 478 152 HOH HOH . H 4 HOH A 79 479 30 HOH HOH . H 4 HOH A 80 480 70 HOH HOH . H 4 HOH A 81 481 178 HOH HOH . H 4 HOH A 82 482 15 HOH HOH . H 4 HOH A 83 483 85 HOH HOH . H 4 HOH A 84 484 110 HOH HOH . H 4 HOH A 85 485 59 HOH HOH . H 4 HOH A 86 486 97 HOH HOH . H 4 HOH A 87 487 26 HOH HOH . H 4 HOH A 88 488 142 HOH HOH . H 4 HOH A 89 489 167 HOH HOH . H 4 HOH A 90 490 172 HOH HOH . H 4 HOH A 91 491 104 HOH HOH . H 4 HOH A 92 492 143 HOH HOH . H 4 HOH A 93 493 151 HOH HOH . H 4 HOH A 94 494 64 HOH HOH . H 4 HOH A 95 495 122 HOH HOH . H 4 HOH A 96 496 73 HOH HOH . H 4 HOH A 97 497 102 HOH HOH . I 4 HOH B 1 401 162 HOH HOH . I 4 HOH B 2 402 139 HOH HOH . I 4 HOH B 3 403 120 HOH HOH . I 4 HOH B 4 404 48 HOH HOH . I 4 HOH B 5 405 115 HOH HOH . I 4 HOH B 6 406 132 HOH HOH . I 4 HOH B 7 407 87 HOH HOH . I 4 HOH B 8 408 113 HOH HOH . I 4 HOH B 9 409 66 HOH HOH . I 4 HOH B 10 410 117 HOH HOH . I 4 HOH B 11 411 39 HOH HOH . I 4 HOH B 12 412 68 HOH HOH . I 4 HOH B 13 413 123 HOH HOH . I 4 HOH B 14 414 9 HOH HOH . I 4 HOH B 15 415 65 HOH HOH . I 4 HOH B 16 416 176 HOH HOH . I 4 HOH B 17 417 153 HOH HOH . I 4 HOH B 18 418 23 HOH HOH . I 4 HOH B 19 419 146 HOH HOH . I 4 HOH B 20 420 27 HOH HOH . I 4 HOH B 21 421 43 HOH HOH . I 4 HOH B 22 422 168 HOH HOH . I 4 HOH B 23 423 36 HOH HOH . I 4 HOH B 24 424 17 HOH HOH . I 4 HOH B 25 425 141 HOH HOH . I 4 HOH B 26 426 148 HOH HOH . I 4 HOH B 27 427 100 HOH HOH . I 4 HOH B 28 428 137 HOH HOH . I 4 HOH B 29 429 86 HOH HOH . I 4 HOH B 30 430 79 HOH HOH . I 4 HOH B 31 431 71 HOH HOH . I 4 HOH B 32 432 14 HOH HOH . I 4 HOH B 33 433 45 HOH HOH . I 4 HOH B 34 434 105 HOH HOH . I 4 HOH B 35 435 129 HOH HOH . I 4 HOH B 36 436 177 HOH HOH . I 4 HOH B 37 437 154 HOH HOH . I 4 HOH B 38 438 121 HOH HOH . I 4 HOH B 39 439 94 HOH HOH . I 4 HOH B 40 440 56 HOH HOH . I 4 HOH B 41 441 55 HOH HOH . I 4 HOH B 42 442 149 HOH HOH . I 4 HOH B 43 443 20 HOH HOH . I 4 HOH B 44 444 81 HOH HOH . I 4 HOH B 45 445 126 HOH HOH . I 4 HOH B 46 446 62 HOH HOH . I 4 HOH B 47 447 80 HOH HOH . I 4 HOH B 48 448 135 HOH HOH . I 4 HOH B 49 449 21 HOH HOH . I 4 HOH B 50 450 144 HOH HOH . I 4 HOH B 51 451 96 HOH HOH . I 4 HOH B 52 452 47 HOH HOH . I 4 HOH B 53 453 92 HOH HOH . I 4 HOH B 54 454 119 HOH HOH . I 4 HOH B 55 455 108 HOH HOH . I 4 HOH B 56 456 16 HOH HOH . I 4 HOH B 57 457 169 HOH HOH . I 4 HOH B 58 458 170 HOH HOH . I 4 HOH B 59 459 99 HOH HOH . I 4 HOH B 60 460 160 HOH HOH . I 4 HOH B 61 461 3 HOH HOH . I 4 HOH B 62 462 111 HOH HOH . I 4 HOH B 63 463 93 HOH HOH . I 4 HOH B 64 464 165 HOH HOH . I 4 HOH B 65 465 136 HOH HOH . I 4 HOH B 66 466 22 HOH HOH . I 4 HOH B 67 467 118 HOH HOH . I 4 HOH B 68 468 53 HOH HOH . I 4 HOH B 69 469 98 HOH HOH . I 4 HOH B 70 470 112 HOH HOH . I 4 HOH B 71 471 91 HOH HOH . I 4 HOH B 72 472 164 HOH HOH . I 4 HOH B 73 473 72 HOH HOH . I 4 HOH B 74 474 127 HOH HOH . I 4 HOH B 75 475 42 HOH HOH . I 4 HOH B 76 476 46 HOH HOH . I 4 HOH B 77 477 138 HOH HOH . I 4 HOH B 78 478 134 HOH HOH . I 4 HOH B 79 479 163 HOH HOH . I 4 HOH B 80 480 150 HOH HOH . I 4 HOH B 81 481 67 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 . . . F 2 0.474 114.936 65.248 1 50.69 ? PB GDP 301 B 1 HETATM 2 O O1B GDP . . . F 2 1.163 113.941 64.354 1 57.51 ? O1B GDP 301 B 1 HETATM 3 O O2B GDP . . . F 2 0.395 116.283 64.544 1 60.35 ? O2B GDP 301 B 1 HETATM 4 O O3B GDP . . . F 2 -0.925 114.407 65.435 1 51.35 ? O3B GDP 301 B 1 HETATM 5 O O3A GDP . . . F 2 1.314 115.096 66.621 1 46.27 ? O3A GDP 301 B 1 HETATM 6 P PA GDP . . . F 2 1.629 116.434 67.52 1 52.07 ? PA GDP 301 B 1 HETATM 7 O O1A GDP . . . F 2 2.592 117.379 66.837 1 42.55 ? O1A GDP 301 B 1 HETATM 8 O O2A GDP . . . F 2 0.356 117.122 67.966 1 57.06 ? O2A GDP 301 B 1 HETATM 9 O O5' GDP . . . F 2 2.422 115.862 68.81 1 51.51 ? O5' GDP 301 B 1 HETATM 10 C C5' GDP . . . F 2 1.834 114.879 69.675 1 45.42 ? C5' GDP 301 B 1 HETATM 11 C C4' GDP . . . F 2 2.565 114.948 71.014 1 46.38 ? C4' GDP 301 B 1 HETATM 12 O O4' GDP . . . F 2 3.925 114.554 70.806 1 47.26 ? O4' GDP 301 B 1 HETATM 13 C C3' GDP . . . F 2 2.616 116.372 71.56 1 48.75 ? C3' GDP 301 B 1 HETATM 14 O O3' GDP . . . F 2 2.289 116.375 72.953 1 56.34 ? O3' GDP 301 B 1 HETATM 15 C C2' GDP . . . F 2 4.056 116.817 71.39 1 54.69 ? C2' GDP 301 B 1 HETATM 16 O O2' GDP . . . F 2 4.51 117.669 72.442 1 55.28 ? O2' GDP 301 B 1 HETATM 17 C C1' GDP . . . F 2 4.819 115.504 71.399 1 52.87 ? C1' GDP 301 B 1 HETATM 18 N N9 GDP . . . F 2 6.094 115.594 70.636 1 56.24 ? N9 GDP 301 B 1 HETATM 19 C C8 GDP . . . F 2 6.249 115.841 69.315 1 49.72 ? C8 GDP 301 B 1 HETATM 20 N N7 GDP . . . F 2 7.568 115.84 68.966 1 47.04 ? N7 GDP 301 B 1 HETATM 21 C C5 GDP . . . F 2 8.281 115.573 70.083 1 54 ? C5 GDP 301 B 1 HETATM 22 C C6 GDP . . . F 2 9.713 115.406 70.449 1 40.92 ? C6 GDP 301 B 1 HETATM 23 O O6 GDP . . . F 2 10.629 115.515 69.612 1 40.52 ? O6 GDP 301 B 1 HETATM 24 N N1 GDP . . . F 2 10.006 115.141 71.725 1 49.04 ? N1 GDP 301 B 1 HETATM 25 C C2 GDP . . . F 2 9.066 115.005 72.68 1 51.84 ? C2 GDP 301 B 1 HETATM 26 N N2 GDP . . . F 2 9.463 114.729 73.944 1 54.09 ? N2 GDP 301 B 1 HETATM 27 N N3 GDP . . . F 2 7.744 115.134 72.425 1 52.85 ? N3 GDP 301 B 1 HETATM 28 C C4 GDP . . . F 2 7.301 115.41 71.175 1 56.94 ? C4 GDP 301 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 28 #