data_6PGO # _model_server_result.job_id xOyflAgyUAZPzYf6YUEEbw _model_server_result.datetime_utc '2024-11-04 20:17:47' _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 6pgo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 6PGO # _exptl.entry_id 6PGO _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 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 90 _cell.entry_id 6PGO _cell.length_a 79.565 _cell.length_b 106.329 _cell.length_c 33.736 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PGO _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,I 1 1 B,F,G,H,J 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 ? 3 D N N ? 3 G N 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 26 A CYS 12 1_555 E C01 OJ1 . A OJ1 303 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.804 ? covale ? covale2 A SG CYS 26 A CYS 12 1_555 E C01 OJ1 . A OJ1 303 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.802 ? metalc ? metalc1 A OG SER 31 A SER 17 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? covale ? covale3 B SG CYS 26 B CYS 12 1_555 H C01 OJ1 . B OJ1 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? metalc ? metalc2 B OG SER 31 B SER 17 1_555 F MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc3 C MG MG . A MG 301 1_555 I O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc4 C MG MG . A MG 301 1_555 D O1B GDP . A GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc5 C MG MG . A MG 301 1_555 I O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc6 C MG MG . A MG 301 1_555 I O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc7 C MG MG . A MG 301 1_555 I O HOH . A HOH 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc8 F MG MG . B MG 301 1_555 J O HOH . B HOH 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc9 F MG MG . B MG 301 1_555 J O HOH . B HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 F MG MG . B MG 301 1_555 J O HOH . B HOH 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc11 F MG MG . B MG 301 1_555 J O HOH . B HOH 468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc12 F MG MG . B MG 301 1_555 G O2B GDP . B GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? # _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 ? # _atom_sites.entry_id 6PGO _atom_sites.fract_transf_matrix[1][1] 0.012568 _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] 0.009405 _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] 0.029642 _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 MG A 1 301 301 MG MG . D 3 GDP A 1 302 501 GDP GDP . E 4 OJ1 A 1 303 701 OJ1 UNL . F 2 MG B 1 301 301 MG MG . G 3 GDP B 1 302 501 GDP GDP . H 4 OJ1 B 1 303 701 OJ1 UNL . I 5 HOH A 1 401 100 HOH HOH . I 5 HOH A 2 402 98 HOH HOH . I 5 HOH A 3 403 153 HOH HOH . I 5 HOH A 4 404 52 HOH HOH . I 5 HOH A 5 405 403 HOH HOH . I 5 HOH A 6 406 103 HOH HOH . I 5 HOH A 7 407 112 HOH HOH . I 5 HOH A 8 408 401 HOH HOH . I 5 HOH A 9 409 402 HOH HOH . I 5 HOH A 10 410 152 HOH HOH . I 5 HOH A 11 411 6 HOH HOH . I 5 HOH A 12 412 127 HOH HOH . I 5 HOH A 13 413 38 HOH HOH . I 5 HOH A 14 414 99 HOH HOH . I 5 HOH A 15 415 60 HOH HOH . I 5 HOH A 16 416 10 HOH HOH . I 5 HOH A 17 417 3 HOH HOH . I 5 HOH A 18 418 16 HOH HOH . I 5 HOH A 19 419 104 HOH HOH . I 5 HOH A 20 420 118 HOH HOH . I 5 HOH A 21 421 111 HOH HOH . I 5 HOH A 22 422 126 HOH HOH . I 5 HOH A 23 423 115 HOH HOH . I 5 HOH A 24 424 8 HOH HOH . I 5 HOH A 25 425 55 HOH HOH . I 5 HOH A 26 426 26 HOH HOH . I 5 HOH A 27 427 5 HOH HOH . I 5 HOH A 28 428 17 HOH HOH . I 5 HOH A 29 429 11 HOH HOH . I 5 HOH A 30 430 120 HOH HOH . I 5 HOH A 31 431 41 HOH HOH . I 5 HOH A 32 432 95 HOH HOH . I 5 HOH A 33 433 106 HOH HOH . I 5 HOH A 34 434 123 HOH HOH . I 5 HOH A 35 435 51 HOH HOH . I 5 HOH A 36 436 404 HOH HOH . I 5 HOH A 37 437 45 HOH HOH . I 5 HOH A 38 438 46 HOH HOH . I 5 HOH A 39 439 114 HOH HOH . I 5 HOH A 40 440 36 HOH HOH . I 5 HOH A 41 441 29 HOH HOH . I 5 HOH A 42 442 1 HOH HOH . I 5 HOH A 43 443 31 HOH HOH . I 5 HOH A 44 444 129 HOH HOH . I 5 HOH A 45 445 44 HOH HOH . I 5 HOH A 46 446 14 HOH HOH . I 5 HOH A 47 447 90 HOH HOH . I 5 HOH A 48 448 144 HOH HOH . I 5 HOH A 49 449 130 HOH HOH . I 5 HOH A 50 450 23 HOH HOH . I 5 HOH A 51 451 101 HOH HOH . I 5 HOH A 52 452 18 HOH HOH . I 5 HOH A 53 453 109 HOH HOH . I 5 HOH A 54 454 49 HOH HOH . I 5 HOH A 55 455 50 HOH HOH . I 5 HOH A 56 456 4 HOH HOH . I 5 HOH A 57 457 7 HOH HOH . I 5 HOH A 58 458 42 HOH HOH . I 5 HOH A 59 459 39 HOH HOH . I 5 HOH A 60 460 27 HOH HOH . I 5 HOH A 61 461 12 HOH HOH . I 5 HOH A 62 462 47 HOH HOH . I 5 HOH A 63 463 113 HOH HOH . I 5 HOH A 64 464 34 HOH HOH . I 5 HOH A 65 465 25 HOH HOH . I 5 HOH A 66 466 131 HOH HOH . I 5 HOH A 67 467 124 HOH HOH . I 5 HOH A 68 468 56 HOH HOH . I 5 HOH A 69 469 30 HOH HOH . I 5 HOH A 70 470 2 HOH HOH . I 5 HOH A 71 471 151 HOH HOH . I 5 HOH A 72 472 119 HOH HOH . I 5 HOH A 73 473 154 HOH HOH . I 5 HOH A 74 474 108 HOH HOH . I 5 HOH A 75 475 132 HOH HOH . I 5 HOH A 76 476 105 HOH HOH . I 5 HOH A 77 477 24 HOH HOH . I 5 HOH A 78 478 125 HOH HOH . I 5 HOH A 79 479 133 HOH HOH . I 5 HOH A 80 480 143 HOH HOH . I 5 HOH A 81 481 150 HOH HOH . I 5 HOH A 82 482 58 HOH HOH . I 5 HOH A 83 483 97 HOH HOH . I 5 HOH A 84 484 54 HOH HOH . I 5 HOH A 85 485 128 HOH HOH . J 5 HOH B 1 401 65 HOH HOH . J 5 HOH B 2 402 135 HOH HOH . J 5 HOH B 3 403 72 HOH HOH . J 5 HOH B 4 404 96 HOH HOH . J 5 HOH B 5 405 78 HOH HOH . J 5 HOH B 6 406 91 HOH HOH . J 5 HOH B 7 407 21 HOH HOH . J 5 HOH B 8 408 94 HOH HOH . J 5 HOH B 9 409 83 HOH HOH . J 5 HOH B 10 410 73 HOH HOH . J 5 HOH B 11 411 92 HOH HOH . J 5 HOH B 12 412 33 HOH HOH . J 5 HOH B 13 413 59 HOH HOH . J 5 HOH B 14 414 136 HOH HOH . J 5 HOH B 15 415 68 HOH HOH . J 5 HOH B 16 416 89 HOH HOH . J 5 HOH B 17 417 140 HOH HOH . J 5 HOH B 18 418 71 HOH HOH . J 5 HOH B 19 419 19 HOH HOH . J 5 HOH B 20 420 74 HOH HOH . J 5 HOH B 21 421 122 HOH HOH . J 5 HOH B 22 422 40 HOH HOH . J 5 HOH B 23 423 63 HOH HOH . J 5 HOH B 24 424 148 HOH HOH . J 5 HOH B 25 425 61 HOH HOH . J 5 HOH B 26 426 67 HOH HOH . J 5 HOH B 27 427 13 HOH HOH . J 5 HOH B 28 428 80 HOH HOH . J 5 HOH B 29 429 15 HOH HOH . J 5 HOH B 30 430 85 HOH HOH . J 5 HOH B 31 431 138 HOH HOH . J 5 HOH B 32 432 86 HOH HOH . J 5 HOH B 33 433 147 HOH HOH . J 5 HOH B 34 434 142 HOH HOH . J 5 HOH B 35 435 43 HOH HOH . J 5 HOH B 36 436 84 HOH HOH . J 5 HOH B 37 437 155 HOH HOH . J 5 HOH B 38 438 404 HOH HOH . J 5 HOH B 39 439 403 HOH HOH . J 5 HOH B 40 440 139 HOH HOH . J 5 HOH B 41 441 57 HOH HOH . J 5 HOH B 42 442 53 HOH HOH . J 5 HOH B 43 443 66 HOH HOH . J 5 HOH B 44 444 401 HOH HOH . J 5 HOH B 45 445 149 HOH HOH . J 5 HOH B 46 446 69 HOH HOH . J 5 HOH B 47 447 93 HOH HOH . J 5 HOH B 48 448 77 HOH HOH . J 5 HOH B 49 449 48 HOH HOH . J 5 HOH B 50 450 70 HOH HOH . J 5 HOH B 51 451 22 HOH HOH . J 5 HOH B 52 452 102 HOH HOH . J 5 HOH B 53 453 9 HOH HOH . J 5 HOH B 54 454 87 HOH HOH . J 5 HOH B 55 455 79 HOH HOH . J 5 HOH B 56 456 20 HOH HOH . J 5 HOH B 57 457 28 HOH HOH . J 5 HOH B 58 458 37 HOH HOH . J 5 HOH B 59 459 75 HOH HOH . J 5 HOH B 60 460 146 HOH HOH . J 5 HOH B 61 461 88 HOH HOH . J 5 HOH B 62 462 35 HOH HOH . J 5 HOH B 63 463 145 HOH HOH . J 5 HOH B 64 464 76 HOH HOH . J 5 HOH B 65 465 134 HOH HOH . J 5 HOH B 66 466 62 HOH HOH . J 5 HOH B 67 467 137 HOH HOH . J 5 HOH B 68 468 402 HOH HOH . J 5 HOH B 69 469 107 HOH HOH . J 5 HOH B 70 470 117 HOH HOH . J 5 HOH B 71 471 141 HOH HOH . J 5 HOH B 72 472 110 HOH HOH . J 5 HOH B 73 473 64 HOH HOH . J 5 HOH B 74 474 116 HOH HOH . J 5 HOH B 75 475 121 HOH HOH . J 5 HOH B 76 476 81 HOH HOH . J 5 HOH B 77 477 82 HOH HOH . J 5 HOH B 78 478 32 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 3 8.03 -2.217 35.07 1 15.24 ? PB GDP 302 A 1 HETATM 2 O O1B GDP . . . D 3 8.804 -3.381 34.541 1 15.49 ? O1B GDP 302 A 1 HETATM 3 O O2B GDP . . . D 3 8.905 -1.038 35.443 1 15.37 ? O2B GDP 302 A 1 HETATM 4 O O3B GDP . . . D 3 7.025 -2.549 36.131 1 16.67 ? O3B GDP 302 A 1 HETATM 5 O O3A GDP . . . D 3 7.232 -1.65 33.788 1 15.93 ? O3A GDP 302 A 1 HETATM 6 P PA GDP . . . D 3 6.723 -2.451 32.481 1 16.24 ? PA GDP 302 A 1 HETATM 7 O O1A GDP . . . D 3 7.827 -2.689 31.493 1 16.19 ? O1A GDP 302 A 1 HETATM 8 O O2A GDP . . . D 3 5.915 -3.635 32.956 1 16.99 ? O2A GDP 302 A 1 HETATM 9 O O5' GDP . . . D 3 5.723 -1.366 31.855 1 16.93 ? O5' GDP 302 A 1 HETATM 10 C C5' GDP . . . D 3 4.6 -0.892 32.589 1 17.56 ? C5' GDP 302 A 1 HETATM 11 C C4' GDP . . . D 3 3.485 -0.486 31.641 1 18.33 ? C4' GDP 302 A 1 HETATM 12 O O4' GDP . . . D 3 3.895 0.632 30.852 1 17.69 ? O4' GDP 302 A 1 HETATM 13 C C3' GDP . . . D 3 3.144 -1.58 30.652 1 18.83 ? C3' GDP 302 A 1 HETATM 14 O O3' GDP . . . D 3 1.733 -1.521 30.415 1 19.91 ? O3' GDP 302 A 1 HETATM 15 C C2' GDP . . . D 3 3.948 -1.232 29.411 1 18.32 ? C2' GDP 302 A 1 HETATM 16 O O2' GDP . . . D 3 3.37 -1.712 28.196 1 20.7 ? O2' GDP 302 A 1 HETATM 17 C C1' GDP . . . D 3 3.917 0.274 29.47 1 17.42 ? C1' GDP 302 A 1 HETATM 18 N N9 GDP . . . D 3 5.093 0.949 28.908 1 16.27 ? N9 GDP 302 A 1 HETATM 19 C C8 GDP . . . D 3 6.383 0.704 29.194 1 15.56 ? C8 GDP 302 A 1 HETATM 20 N N7 GDP . . . D 3 7.178 1.563 28.519 1 15.1 ? N7 GDP 302 A 1 HETATM 21 C C5 GDP . . . D 3 6.371 2.375 27.814 1 15.26 ? C5 GDP 302 A 1 HETATM 22 C C6 GDP . . . D 3 6.544 3.503 26.891 1 15.5 ? C6 GDP 302 A 1 HETATM 23 O O6 GDP . . . D 3 7.679 3.923 26.613 1 15.69 ? O6 GDP 302 A 1 HETATM 24 N N1 GDP . . . D 3 5.447 4.077 26.386 1 15.24 ? N1 GDP 302 A 1 HETATM 25 C C2 GDP . . . D 3 4.191 3.651 26.657 1 15.74 ? C2 GDP 302 A 1 HETATM 26 N N2 GDP . . . D 3 3.137 4.288 26.086 1 15.25 ? N2 GDP 302 A 1 HETATM 27 N N3 GDP . . . D 3 3.952 2.614 27.5 1 15.48 ? N3 GDP 302 A 1 HETATM 28 C C4 GDP . . . D 3 4.994 1.968 28.079 1 15.51 ? C4 GDP 302 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #