data_5H5I # _model_server_result.job_id FT6s4jUZv53OihFP5Oa8Gw _model_server_result.datetime_utc '2025-03-29 05:57:57' _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 5h5i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5H5I # _exptl.entry_id 5H5I _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.13 _cell.angle_gamma 90 _cell.entry_id 5H5I _cell.length_a 64.757 _cell.length_b 59.279 _cell.length_c 81.77 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5H5I _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 5H5I _atom_sites.fract_transf_matrix[1][1] 0.015442 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005357 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016869 _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] 0.012944 _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 GDP A 1 401 1 GDP GDP . C 3 HOH A 1 501 124 HOH HOH . C 3 HOH A 2 502 69 HOH HOH . C 3 HOH A 3 503 68 HOH HOH . C 3 HOH A 4 504 117 HOH HOH . C 3 HOH A 5 505 99 HOH HOH . C 3 HOH A 6 506 64 HOH HOH . C 3 HOH A 7 507 122 HOH HOH . C 3 HOH A 8 508 106 HOH HOH . C 3 HOH A 9 509 58 HOH HOH . C 3 HOH A 10 510 16 HOH HOH . C 3 HOH A 11 511 142 HOH HOH . C 3 HOH A 12 512 31 HOH HOH . C 3 HOH A 13 513 30 HOH HOH . C 3 HOH A 14 514 90 HOH HOH . C 3 HOH A 15 515 33 HOH HOH . C 3 HOH A 16 516 84 HOH HOH . C 3 HOH A 17 517 138 HOH HOH . C 3 HOH A 18 518 24 HOH HOH . C 3 HOH A 19 519 71 HOH HOH . C 3 HOH A 20 520 1 HOH HOH . C 3 HOH A 21 521 5 HOH HOH . C 3 HOH A 22 522 9 HOH HOH . C 3 HOH A 23 523 48 HOH HOH . C 3 HOH A 24 524 129 HOH HOH . C 3 HOH A 25 525 4 HOH HOH . C 3 HOH A 26 526 78 HOH HOH . C 3 HOH A 27 527 75 HOH HOH . C 3 HOH A 28 528 61 HOH HOH . C 3 HOH A 29 529 50 HOH HOH . C 3 HOH A 30 530 47 HOH HOH . C 3 HOH A 31 531 76 HOH HOH . C 3 HOH A 32 532 96 HOH HOH . C 3 HOH A 33 533 88 HOH HOH . C 3 HOH A 34 534 103 HOH HOH . C 3 HOH A 35 535 15 HOH HOH . C 3 HOH A 36 536 100 HOH HOH . C 3 HOH A 37 537 21 HOH HOH . C 3 HOH A 38 538 94 HOH HOH . C 3 HOH A 39 539 60 HOH HOH . C 3 HOH A 40 540 57 HOH HOH . C 3 HOH A 41 541 74 HOH HOH . C 3 HOH A 42 542 3 HOH HOH . C 3 HOH A 43 543 23 HOH HOH . C 3 HOH A 44 544 91 HOH HOH . C 3 HOH A 45 545 87 HOH HOH . C 3 HOH A 46 546 37 HOH HOH . C 3 HOH A 47 547 108 HOH HOH . C 3 HOH A 48 548 116 HOH HOH . C 3 HOH A 49 549 26 HOH HOH . C 3 HOH A 50 550 95 HOH HOH . C 3 HOH A 51 551 44 HOH HOH . C 3 HOH A 52 552 12 HOH HOH . C 3 HOH A 53 553 42 HOH HOH . C 3 HOH A 54 554 6 HOH HOH . C 3 HOH A 55 555 81 HOH HOH . C 3 HOH A 56 556 25 HOH HOH . C 3 HOH A 57 557 39 HOH HOH . C 3 HOH A 58 558 118 HOH HOH . C 3 HOH A 59 559 136 HOH HOH . C 3 HOH A 60 560 8 HOH HOH . C 3 HOH A 61 561 45 HOH HOH . C 3 HOH A 62 562 140 HOH HOH . C 3 HOH A 63 563 17 HOH HOH . C 3 HOH A 64 564 102 HOH HOH . C 3 HOH A 65 565 89 HOH HOH . C 3 HOH A 66 566 139 HOH HOH . C 3 HOH A 67 567 70 HOH HOH . C 3 HOH A 68 568 2 HOH HOH . C 3 HOH A 69 569 54 HOH HOH . C 3 HOH A 70 570 14 HOH HOH . C 3 HOH A 71 571 111 HOH HOH . C 3 HOH A 72 572 107 HOH HOH . C 3 HOH A 73 573 131 HOH HOH . C 3 HOH A 74 574 51 HOH HOH . C 3 HOH A 75 575 7 HOH HOH . C 3 HOH A 76 576 10 HOH HOH . C 3 HOH A 77 577 119 HOH HOH . C 3 HOH A 78 578 72 HOH HOH . C 3 HOH A 79 579 80 HOH HOH . C 3 HOH A 80 580 62 HOH HOH . C 3 HOH A 81 581 101 HOH HOH . C 3 HOH A 82 582 128 HOH HOH . C 3 HOH A 83 583 83 HOH HOH . C 3 HOH A 84 584 59 HOH HOH . C 3 HOH A 85 585 19 HOH HOH . C 3 HOH A 86 586 20 HOH HOH . C 3 HOH A 87 587 65 HOH HOH . C 3 HOH A 88 588 110 HOH HOH . C 3 HOH A 89 589 63 HOH HOH . C 3 HOH A 90 590 82 HOH HOH . C 3 HOH A 91 591 92 HOH HOH . C 3 HOH A 92 592 49 HOH HOH . C 3 HOH A 93 593 35 HOH HOH . C 3 HOH A 94 594 98 HOH HOH . C 3 HOH A 95 595 114 HOH HOH . C 3 HOH A 96 596 73 HOH HOH . C 3 HOH A 97 597 38 HOH HOH . C 3 HOH A 98 598 109 HOH HOH . C 3 HOH A 99 599 97 HOH HOH . C 3 HOH A 100 600 120 HOH HOH . C 3 HOH A 101 601 52 HOH HOH . C 3 HOH A 102 602 125 HOH HOH . C 3 HOH A 103 603 123 HOH HOH . C 3 HOH A 104 604 66 HOH HOH . C 3 HOH A 105 605 132 HOH HOH . C 3 HOH A 106 606 85 HOH HOH . C 3 HOH A 107 607 79 HOH HOH . C 3 HOH A 108 608 137 HOH HOH . C 3 HOH A 109 609 55 HOH HOH . C 3 HOH A 110 610 112 HOH HOH . C 3 HOH A 111 611 141 HOH HOH . C 3 HOH A 112 612 53 HOH HOH . C 3 HOH A 113 613 13 HOH HOH . C 3 HOH A 114 614 36 HOH HOH . C 3 HOH A 115 615 40 HOH HOH . C 3 HOH A 116 616 43 HOH HOH . C 3 HOH A 117 617 32 HOH HOH . C 3 HOH A 118 618 126 HOH HOH . C 3 HOH A 119 619 46 HOH HOH . C 3 HOH A 120 620 115 HOH HOH . C 3 HOH A 121 621 127 HOH HOH . C 3 HOH A 122 622 22 HOH HOH . C 3 HOH A 123 623 86 HOH HOH . C 3 HOH A 124 624 135 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 . . . B 2 44.633 -76.592 104.756 1 31.41 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 45.567 -75.433 104.731 1 31.96 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 44.997 -77.673 105.676 1 30.81 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 43.156 -76.289 104.749 1 31.94 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 44.774 -77.283 103.291 1 31.61 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 44.909 -76.554 101.848 1 35.56 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 46.345 -76.495 101.426 1 37.89 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 44.156 -75.271 101.759 1 36.25 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 44.206 -77.617 100.921 1 34.7 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 42.771 -77.665 100.894 1 31.4 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 42.313 -77.68 99.456 1 32.48 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 42.489 -76.387 98.875 1 31.89 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 43.067 -78.636 98.561 1 30.8 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 42.534 -79.944 98.628 1 33.19 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 42.894 -78.024 97.172 1 30.11 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 41.715 -78.452 96.521 1 32.07 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 42.732 -76.554 97.462 1 32.16 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 43.963 -75.836 97.128 1 31.02 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 45.272 -76.212 97.338 1 32.35 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 46.096 -75.24 96.951 1 32.03 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 45.309 -74.237 96.472 1 33.5 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 45.451 -72.911 95.851 1 33.67 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 46.567 -72.39 95.655 1 35.51 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 44.34 -72.214 95.53 1 30.2 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 43.075 -72.683 95.693 1 27.7 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 42.008 -71.91 95.359 1 30.3 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 42.851 -73.867 96.219 1 28 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 43.9 -74.656 96.607 1 31.15 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #