data_1IJE # _model_server_result.job_id CoHeP1IjauaTA_moBkhr_g _model_server_result.datetime_utc '2024-11-29 14:20:24' _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 1ije # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":507}' # _entry.id 1IJE # _exptl.entry_id 1IJE _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 1IJE _cell.length_a 63.712 _cell.length_b 90.418 _cell.length_c 92.362 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1IJE _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 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 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 1IJE _atom_sites.fract_transf_matrix[1][1] 0.015696 _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] 0.01106 _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] 0.010827 _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 1 507 507 GDP 5GP . D 4 HOH A 1 508 1 HOH TIP . D 4 HOH A 2 509 3 HOH TIP . D 4 HOH A 3 510 5 HOH TIP . D 4 HOH A 4 511 6 HOH TIP . D 4 HOH A 5 512 7 HOH TIP . D 4 HOH A 6 513 9 HOH TIP . D 4 HOH A 7 514 10 HOH TIP . D 4 HOH A 8 515 11 HOH TIP . D 4 HOH A 9 516 12 HOH TIP . D 4 HOH A 10 517 13 HOH TIP . D 4 HOH A 11 518 14 HOH TIP . D 4 HOH A 12 519 15 HOH TIP . D 4 HOH A 13 520 16 HOH TIP . D 4 HOH A 14 521 17 HOH TIP . D 4 HOH A 15 522 18 HOH TIP . D 4 HOH A 16 523 19 HOH TIP . D 4 HOH A 17 524 20 HOH TIP . D 4 HOH A 18 525 21 HOH TIP . D 4 HOH A 19 526 22 HOH TIP . D 4 HOH A 20 527 23 HOH TIP . D 4 HOH A 21 528 24 HOH TIP . D 4 HOH A 22 529 25 HOH TIP . D 4 HOH A 23 530 26 HOH TIP . D 4 HOH A 24 531 28 HOH TIP . D 4 HOH A 25 532 29 HOH TIP . D 4 HOH A 26 533 30 HOH TIP . D 4 HOH A 27 534 31 HOH TIP . D 4 HOH A 28 535 32 HOH TIP . D 4 HOH A 29 536 33 HOH TIP . D 4 HOH A 30 537 34 HOH TIP . D 4 HOH A 31 538 35 HOH TIP . D 4 HOH A 32 539 36 HOH TIP . D 4 HOH A 33 540 37 HOH TIP . D 4 HOH A 34 541 38 HOH TIP . D 4 HOH A 35 542 39 HOH TIP . D 4 HOH A 36 543 40 HOH TIP . D 4 HOH A 37 544 42 HOH TIP . D 4 HOH A 38 545 43 HOH TIP . D 4 HOH A 39 546 45 HOH TIP . D 4 HOH A 40 547 48 HOH TIP . D 4 HOH A 41 548 49 HOH TIP . D 4 HOH A 42 549 50 HOH TIP . D 4 HOH A 43 550 51 HOH TIP . D 4 HOH A 44 551 52 HOH TIP . D 4 HOH A 45 552 53 HOH TIP . D 4 HOH A 46 553 54 HOH TIP . D 4 HOH A 47 554 55 HOH TIP . D 4 HOH A 48 555 57 HOH TIP . D 4 HOH A 49 556 58 HOH TIP . D 4 HOH A 50 557 59 HOH TIP . D 4 HOH A 51 558 61 HOH TIP . D 4 HOH A 52 559 63 HOH TIP . D 4 HOH A 53 560 64 HOH TIP . D 4 HOH A 54 561 65 HOH TIP . D 4 HOH A 55 562 66 HOH TIP . D 4 HOH A 56 563 67 HOH TIP . D 4 HOH A 57 564 69 HOH TIP . D 4 HOH A 58 565 70 HOH TIP . D 4 HOH A 59 566 71 HOH TIP . D 4 HOH A 60 567 72 HOH TIP . D 4 HOH A 61 568 73 HOH TIP . D 4 HOH A 62 569 74 HOH TIP . D 4 HOH A 63 570 75 HOH TIP . D 4 HOH A 64 571 77 HOH TIP . D 4 HOH A 65 572 78 HOH TIP . D 4 HOH A 66 573 80 HOH TIP . D 4 HOH A 67 574 82 HOH TIP . D 4 HOH A 68 575 83 HOH TIP . D 4 HOH A 69 576 85 HOH TIP . D 4 HOH A 70 577 86 HOH TIP . D 4 HOH A 71 578 87 HOH TIP . D 4 HOH A 72 579 90 HOH TIP . D 4 HOH A 73 580 92 HOH TIP . D 4 HOH A 74 581 93 HOH TIP . D 4 HOH A 75 582 94 HOH TIP . D 4 HOH A 76 583 95 HOH TIP . D 4 HOH A 77 584 96 HOH TIP . D 4 HOH A 78 585 97 HOH TIP . D 4 HOH A 79 586 99 HOH TIP . D 4 HOH A 80 587 100 HOH TIP . D 4 HOH A 81 588 101 HOH TIP . D 4 HOH A 82 589 102 HOH TIP . D 4 HOH A 83 590 103 HOH TIP . D 4 HOH A 84 591 105 HOH TIP . D 4 HOH A 85 592 106 HOH TIP . D 4 HOH A 86 593 107 HOH TIP . D 4 HOH A 87 594 109 HOH TIP . D 4 HOH A 88 595 110 HOH TIP . D 4 HOH A 89 596 111 HOH TIP . D 4 HOH A 90 597 113 HOH TIP . D 4 HOH A 91 598 115 HOH TIP . D 4 HOH A 92 599 117 HOH TIP . D 4 HOH A 93 600 118 HOH TIP . D 4 HOH A 94 601 120 HOH TIP . D 4 HOH A 95 602 121 HOH TIP . D 4 HOH A 96 603 122 HOH TIP . D 4 HOH A 97 604 123 HOH TIP . D 4 HOH A 98 605 124 HOH TIP . D 4 HOH A 99 606 126 HOH TIP . D 4 HOH A 100 607 127 HOH TIP . D 4 HOH A 101 608 128 HOH TIP . D 4 HOH A 102 609 129 HOH TIP . D 4 HOH A 103 610 131 HOH TIP . D 4 HOH A 104 611 133 HOH TIP . D 4 HOH A 105 612 134 HOH TIP . D 4 HOH A 106 613 135 HOH TIP . D 4 HOH A 107 614 136 HOH TIP . D 4 HOH A 108 615 137 HOH TIP . E 4 HOH B 1 2 2 HOH TIP . E 4 HOH B 2 4 4 HOH TIP . E 4 HOH B 3 8 8 HOH TIP . E 4 HOH B 4 27 27 HOH TIP . E 4 HOH B 5 41 41 HOH TIP . E 4 HOH B 6 44 44 HOH TIP . E 4 HOH B 7 46 46 HOH TIP . E 4 HOH B 8 47 47 HOH TIP . E 4 HOH B 9 56 56 HOH TIP . E 4 HOH B 10 60 60 HOH TIP . E 4 HOH B 11 62 62 HOH TIP . E 4 HOH B 12 68 68 HOH TIP . E 4 HOH B 13 76 76 HOH TIP . E 4 HOH B 14 79 79 HOH TIP . E 4 HOH B 15 81 81 HOH TIP . E 4 HOH B 16 84 84 HOH TIP . E 4 HOH B 17 88 88 HOH TIP . E 4 HOH B 18 89 89 HOH TIP . E 4 HOH B 19 91 91 HOH TIP . E 4 HOH B 20 98 98 HOH TIP . E 4 HOH B 21 104 104 HOH TIP . E 4 HOH B 22 108 108 HOH TIP . E 4 HOH B 23 112 112 HOH TIP . E 4 HOH B 24 114 114 HOH TIP . E 4 HOH B 25 116 116 HOH TIP . E 4 HOH B 26 119 119 HOH TIP . E 4 HOH B 27 125 125 HOH TIP . E 4 HOH B 28 130 130 HOH TIP . E 4 HOH B 29 132 132 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 O O3A GDP . . . C 3 37.036 39.335 36.484 1 30.9 ? O3A GDP 507 A 1 HETATM 2 P PA GDP . . . C 3 36.079 40.508 36.593 1 31.9 ? PA GDP 507 A 1 HETATM 3 O O1A GDP . . . C 3 34.606 40.075 36.894 1 30.67 ? O1A GDP 507 A 1 HETATM 4 O O2A GDP . . . C 3 36.236 41.557 35.566 1 30.73 ? O2A GDP 507 A 1 HETATM 5 O O5' GDP . . . C 3 36.496 41.355 37.931 1 31.27 ? O5' GDP 507 A 1 HETATM 6 C C5' GDP . . . C 3 37.781 42.028 38.006 1 31.78 ? C5' GDP 507 A 1 HETATM 7 C C4' GDP . . . C 3 38.191 42.831 39.238 1 32.13 ? C4' GDP 507 A 1 HETATM 8 O O4' GDP . . . C 3 37.752 42.127 40.49 1 31.28 ? O4' GDP 507 A 1 HETATM 9 C C3' GDP . . . C 3 39.689 43.02 39.448 1 33.56 ? C3' GDP 507 A 1 HETATM 10 O O3' GDP . . . C 3 40.048 44.166 40.219 1 36.35 ? O3' GDP 507 A 1 HETATM 11 C C2' GDP . . . C 3 40.092 41.723 40.128 1 32.79 ? C2' GDP 507 A 1 HETATM 12 O O2' GDP . . . C 3 41.372 41.804 40.773 1 35.96 ? O2' GDP 507 A 1 HETATM 13 C C1' GDP . . . C 3 38.928 41.511 41.087 1 29.56 ? C1' GDP 507 A 1 HETATM 14 N N9 GDP . . . C 3 38.631 40.121 41.567 1 25.95 ? N9 GDP 507 A 1 HETATM 15 C C8 GDP . . . C 3 38.061 39.026 40.96 1 25.27 ? C8 GDP 507 A 1 HETATM 16 N N7 GDP . . . C 3 37.97 37.95 41.724 1 23.34 ? N7 GDP 507 A 1 HETATM 17 C C5 GDP . . . C 3 38.54 38.399 42.949 1 22.85 ? C5 GDP 507 A 1 HETATM 18 C C6 GDP . . . C 3 38.733 37.687 44.188 1 22.14 ? C6 GDP 507 A 1 HETATM 19 O O6 GDP . . . C 3 38.452 36.529 44.453 1 22.55 ? O6 GDP 507 A 1 HETATM 20 N N1 GDP . . . C 3 39.343 38.511 45.177 1 21.67 ? N1 GDP 507 A 1 HETATM 21 C C2 GDP . . . C 3 39.702 39.838 44.972 1 21.13 ? C2 GDP 507 A 1 HETATM 22 N N2 GDP . . . C 3 40.263 40.44 46.042 1 17.98 ? N2 GDP 507 A 1 HETATM 23 N N3 GDP . . . C 3 39.523 40.497 43.822 1 21.86 ? N3 GDP 507 A 1 HETATM 24 C C4 GDP . . . C 3 38.934 39.715 42.856 1 23.8 ? C4 GDP 507 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 24 #