data_8GZX # _model_server_result.job_id 7xifWUW8izljllgcJHu5zw _model_server_result.datetime_utc '2025-04-03 22:59:51' _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 8gzx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8GZX # _exptl.entry_id 8GZX _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 8GZX _cell.length_a 45.105 _cell.length_b 63.301 _cell.length_c 123.049 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GZX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 8GZX _atom_sites.fract_transf_matrix[1][1] 0.02217 _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] 0.015798 _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] 0.008127 _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 3 GDP A 1 401 401 GDP GDP . D 4 HOH A 1 501 103 HOH HOH . D 4 HOH A 2 502 47 HOH HOH . D 4 HOH A 3 503 101 HOH HOH . D 4 HOH A 4 504 15 HOH HOH . D 4 HOH A 5 505 39 HOH HOH . D 4 HOH A 6 506 92 HOH HOH . D 4 HOH A 7 507 35 HOH HOH . D 4 HOH A 8 508 21 HOH HOH . D 4 HOH A 9 509 2 HOH HOH . D 4 HOH A 10 510 106 HOH HOH . D 4 HOH A 11 511 86 HOH HOH . D 4 HOH A 12 512 117 HOH HOH . D 4 HOH A 13 513 6 HOH HOH . D 4 HOH A 14 514 49 HOH HOH . D 4 HOH A 15 515 23 HOH HOH . D 4 HOH A 16 516 110 HOH HOH . D 4 HOH A 17 517 32 HOH HOH . D 4 HOH A 18 518 79 HOH HOH . D 4 HOH A 19 519 82 HOH HOH . D 4 HOH A 20 520 68 HOH HOH . D 4 HOH A 21 521 3 HOH HOH . D 4 HOH A 22 522 60 HOH HOH . D 4 HOH A 23 523 12 HOH HOH . D 4 HOH A 24 524 48 HOH HOH . D 4 HOH A 25 525 14 HOH HOH . D 4 HOH A 26 526 77 HOH HOH . D 4 HOH A 27 527 9 HOH HOH . D 4 HOH A 28 528 73 HOH HOH . D 4 HOH A 29 529 109 HOH HOH . D 4 HOH A 30 530 46 HOH HOH . D 4 HOH A 31 531 7 HOH HOH . D 4 HOH A 32 532 53 HOH HOH . D 4 HOH A 33 533 17 HOH HOH . D 4 HOH A 34 534 80 HOH HOH . D 4 HOH A 35 535 38 HOH HOH . D 4 HOH A 36 536 28 HOH HOH . D 4 HOH A 37 537 1 HOH HOH . D 4 HOH A 38 538 4 HOH HOH . D 4 HOH A 39 539 64 HOH HOH . D 4 HOH A 40 540 90 HOH HOH . D 4 HOH A 41 541 25 HOH HOH . D 4 HOH A 42 542 54 HOH HOH . D 4 HOH A 43 543 40 HOH HOH . D 4 HOH A 44 544 51 HOH HOH . D 4 HOH A 45 545 34 HOH HOH . D 4 HOH A 46 546 85 HOH HOH . D 4 HOH A 47 547 52 HOH HOH . D 4 HOH A 48 548 50 HOH HOH . D 4 HOH A 49 549 97 HOH HOH . D 4 HOH A 50 550 33 HOH HOH . D 4 HOH A 51 551 19 HOH HOH . D 4 HOH A 52 552 88 HOH HOH . D 4 HOH A 53 553 20 HOH HOH . D 4 HOH A 54 554 5 HOH HOH . D 4 HOH A 55 555 120 HOH HOH . D 4 HOH A 56 556 122 HOH HOH . D 4 HOH A 57 557 36 HOH HOH . D 4 HOH A 58 558 70 HOH HOH . D 4 HOH A 59 559 93 HOH HOH . D 4 HOH A 60 560 56 HOH HOH . D 4 HOH A 61 561 22 HOH HOH . D 4 HOH A 62 562 74 HOH HOH . D 4 HOH A 63 563 16 HOH HOH . D 4 HOH A 64 564 59 HOH HOH . D 4 HOH A 65 565 10 HOH HOH . D 4 HOH A 66 566 104 HOH HOH . D 4 HOH A 67 567 105 HOH HOH . D 4 HOH A 68 568 45 HOH HOH . D 4 HOH A 69 569 66 HOH HOH . D 4 HOH A 70 570 24 HOH HOH . D 4 HOH A 71 571 43 HOH HOH . D 4 HOH A 72 572 30 HOH HOH . D 4 HOH A 73 573 119 HOH HOH . D 4 HOH A 74 574 62 HOH HOH . D 4 HOH A 75 575 95 HOH HOH . D 4 HOH A 76 576 121 HOH HOH . D 4 HOH A 77 577 96 HOH HOH . D 4 HOH A 78 578 26 HOH HOH . D 4 HOH A 79 579 91 HOH HOH . D 4 HOH A 80 580 8 HOH HOH . D 4 HOH A 81 581 84 HOH HOH . D 4 HOH A 82 582 58 HOH HOH . D 4 HOH A 83 583 42 HOH HOH . D 4 HOH A 84 584 81 HOH HOH . D 4 HOH A 85 585 114 HOH HOH . D 4 HOH A 86 586 69 HOH HOH . D 4 HOH A 87 587 111 HOH HOH . D 4 HOH A 88 588 55 HOH HOH . D 4 HOH A 89 589 113 HOH HOH . D 4 HOH A 90 590 108 HOH HOH . D 4 HOH A 91 591 123 HOH HOH . D 4 HOH A 92 592 118 HOH HOH . D 4 HOH A 93 593 87 HOH HOH . D 4 HOH A 94 594 94 HOH HOH . D 4 HOH A 95 595 78 HOH HOH . E 4 HOH B 1 101 115 HOH HOH . E 4 HOH B 2 102 99 HOH HOH . E 4 HOH B 3 103 44 HOH HOH . E 4 HOH B 4 104 61 HOH HOH . E 4 HOH B 5 105 31 HOH HOH . E 4 HOH B 6 106 75 HOH HOH . E 4 HOH B 7 107 72 HOH HOH . E 4 HOH B 8 108 13 HOH HOH . E 4 HOH B 9 109 37 HOH HOH . E 4 HOH B 10 110 57 HOH HOH . E 4 HOH B 11 111 100 HOH HOH . E 4 HOH B 12 112 29 HOH HOH . E 4 HOH B 13 113 41 HOH HOH . E 4 HOH B 14 114 11 HOH HOH . E 4 HOH B 15 115 116 HOH HOH . E 4 HOH B 16 116 65 HOH HOH . E 4 HOH B 17 117 18 HOH HOH . E 4 HOH B 18 118 83 HOH HOH . E 4 HOH B 19 119 76 HOH HOH . E 4 HOH B 20 120 27 HOH HOH . E 4 HOH B 21 121 89 HOH HOH . E 4 HOH B 22 122 63 HOH HOH . E 4 HOH B 23 123 71 HOH HOH . E 4 HOH B 24 124 107 HOH HOH . E 4 HOH B 25 125 98 HOH HOH . E 4 HOH B 26 126 67 HOH HOH . E 4 HOH B 27 127 112 HOH HOH . E 4 HOH B 28 128 102 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 . . . C 3 10.323 5.3 -16.268 1 30.59 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . C 3 10.267 6.742 -16.733 1 32.45 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . C 3 11.394 5.133 -15.209 1 32.58 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . C 3 8.953 4.94 -15.732 1 30.29 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . C 3 10.791 4.292 -17.446 1 32.43 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . C 3 10.158 4.264 -18.917 1 34.95 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . C 3 10.952 5.118 -19.879 1 34.51 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . C 3 8.682 4.61 -18.861 1 32.18 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . C 3 10.3 2.708 -19.304 1 36.12 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . C 3 9.332 1.799 -18.75 1 31.82 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . C 3 8.84 0.874 -19.857 1 30.68 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . C 3 8.001 1.6 -20.754 1 34.02 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . C 3 9.957 0.389 -20.775 1 32.21 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . C 3 10.648 -0.73 -20.233 1 36.72 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . C 3 9.241 0.076 -22.081 1 36.16 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . C 3 8.689 -1.266 -22.071 1 32.96 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . C 3 8.089 1.069 -22.075 1 34.46 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . C 3 8.329 2.2 -23.002 1 35.2 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . C 3 9.502 2.834 -23.216 1 37.96 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . C 3 9.362 3.841 -24.118 1 40.19 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . C 3 8.059 3.868 -24.48 1 36.47 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . C 3 7.217 4.681 -25.394 1 37.54 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . C 3 7.71 5.621 -26.058 1 39.68 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . C 3 5.918 4.388 -25.47 1 37.64 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . C 3 5.352 3.388 -24.757 1 36.62 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . C 3 4.022 3.153 -24.9 1 39.19 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . C 3 6.065 2.599 -23.909 1 36.86 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . C 3 7.391 2.786 -23.738 1 35.07 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #