data_7OJA # _model_server_result.job_id Gsvye0Nc_IAGgkFQfF2GOQ _model_server_result.datetime_utc '2025-07-20 08:58:31' _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 7oja # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7OJA # _exptl.entry_id 7OJA _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 105.747 _cell.angle_gamma 90 _cell.entry_id 7OJA _cell.length_a 67 _cell.length_b 53.194 _cell.length_c 84.078 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OJA _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _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,D,E,F,G _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 79 n n PB O2B GDP sing 80 n n PB O3B GDP sing 81 n n PB O3A GDP sing 82 n n O2B HOB2 GDP sing 83 n n O3B HOB3 GDP sing 84 n n O3A PA GDP sing 85 n n PA O1A GDP doub 86 n n PA O2A GDP sing 87 n n PA O5' GDP sing 88 n n O2A HOA2 GDP sing 89 n n O5' C5' GDP sing 90 n n C5' C4' GDP sing 91 n n C5' H5' GDP sing 92 n n C5' "H5''" GDP sing 93 n n C4' O4' GDP sing 94 n n C4' C3' GDP sing 95 n n C4' H4' GDP sing 96 n n O4' C1' GDP sing 97 n n C3' O3' GDP sing 98 n n C3' C2' GDP sing 99 n n C3' H3' GDP sing 100 n n O3' HO3' GDP sing 101 n n C2' O2' GDP sing 102 n n C2' C1' GDP sing 103 n n C2' H2' GDP sing 104 n n O2' HO2' GDP sing 105 n n C1' N9 GDP sing 106 n n C1' H1' GDP sing 107 n n N9 C8 GDP sing 108 n y N9 C4 GDP sing 109 n y C8 N7 GDP doub 110 n y C8 H8 GDP sing 111 n n N7 C5 GDP sing 112 n y C5 C6 GDP sing 113 n n C5 C4 GDP doub 114 n y C6 O6 GDP doub 115 n n C6 N1 GDP sing 116 n n N1 C2 GDP sing 117 n n N1 HN1 GDP sing 118 n n C2 N2 GDP sing 119 n n C2 N3 GDP doub 120 n n N2 HN21 GDP sing 121 n n N2 HN22 GDP sing 122 n n N3 C4 GDP sing 123 n n # _atom_sites.entry_id 7OJA _atom_sites.fract_transf_matrix[1][1] 0.014925 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004209 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018799 _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] 0.012358 _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 EDO A 1 402 1 EDO EDO . D 3 EDO A 1 403 2 EDO EDO . E 4 SO4 A 1 404 1 SO4 SO4 . F 4 SO4 A 1 405 2 SO4 SO4 . G 5 HOH A 1 501 27 HOH HOH . G 5 HOH A 2 502 2 HOH HOH . G 5 HOH A 3 503 43 HOH HOH . G 5 HOH A 4 504 89 HOH HOH . G 5 HOH A 5 505 19 HOH HOH . G 5 HOH A 6 506 41 HOH HOH . G 5 HOH A 7 507 51 HOH HOH . G 5 HOH A 8 508 9 HOH HOH . G 5 HOH A 9 509 53 HOH HOH . G 5 HOH A 10 510 14 HOH HOH . G 5 HOH A 11 511 56 HOH HOH . G 5 HOH A 12 512 17 HOH HOH . G 5 HOH A 13 513 4 HOH HOH . G 5 HOH A 14 514 38 HOH HOH . G 5 HOH A 15 515 32 HOH HOH . G 5 HOH A 16 516 58 HOH HOH . G 5 HOH A 17 517 3 HOH HOH . G 5 HOH A 18 518 29 HOH HOH . G 5 HOH A 19 519 24 HOH HOH . G 5 HOH A 20 520 31 HOH HOH . G 5 HOH A 21 521 20 HOH HOH . G 5 HOH A 22 522 88 HOH HOH . G 5 HOH A 23 523 22 HOH HOH . G 5 HOH A 24 524 25 HOH HOH . G 5 HOH A 25 525 15 HOH HOH . G 5 HOH A 26 526 13 HOH HOH . G 5 HOH A 27 527 79 HOH HOH . G 5 HOH A 28 528 7 HOH HOH . G 5 HOH A 29 529 40 HOH HOH . G 5 HOH A 30 530 8 HOH HOH . G 5 HOH A 31 531 84 HOH HOH . G 5 HOH A 32 532 37 HOH HOH . G 5 HOH A 33 533 16 HOH HOH . G 5 HOH A 34 534 42 HOH HOH . G 5 HOH A 35 535 77 HOH HOH . G 5 HOH A 36 536 60 HOH HOH . G 5 HOH A 37 537 85 HOH HOH . G 5 HOH A 38 538 5 HOH HOH . G 5 HOH A 39 539 10 HOH HOH . G 5 HOH A 40 540 55 HOH HOH . G 5 HOH A 41 541 18 HOH HOH . G 5 HOH A 42 542 23 HOH HOH . G 5 HOH A 43 543 12 HOH HOH . G 5 HOH A 44 544 52 HOH HOH . G 5 HOH A 45 545 33 HOH HOH . G 5 HOH A 46 546 48 HOH HOH . G 5 HOH A 47 547 67 HOH HOH . G 5 HOH A 48 548 11 HOH HOH . G 5 HOH A 49 549 1 HOH HOH . G 5 HOH A 50 550 45 HOH HOH . G 5 HOH A 51 551 61 HOH HOH . G 5 HOH A 52 552 65 HOH HOH . G 5 HOH A 53 553 75 HOH HOH . G 5 HOH A 54 554 63 HOH HOH . G 5 HOH A 55 555 34 HOH HOH . G 5 HOH A 56 556 44 HOH HOH . G 5 HOH A 57 557 49 HOH HOH . G 5 HOH A 58 558 57 HOH HOH . G 5 HOH A 59 559 71 HOH HOH . G 5 HOH A 60 560 28 HOH HOH . G 5 HOH A 61 561 6 HOH HOH . G 5 HOH A 62 562 21 HOH HOH . G 5 HOH A 63 563 59 HOH HOH . G 5 HOH A 64 564 36 HOH HOH . G 5 HOH A 65 565 46 HOH HOH . G 5 HOH A 66 566 30 HOH HOH . G 5 HOH A 67 567 50 HOH HOH . G 5 HOH A 68 568 74 HOH HOH . G 5 HOH A 69 569 35 HOH HOH . G 5 HOH A 70 570 47 HOH HOH . G 5 HOH A 71 571 80 HOH HOH . G 5 HOH A 72 572 69 HOH HOH . G 5 HOH A 73 573 76 HOH HOH . G 5 HOH A 74 574 83 HOH HOH . G 5 HOH A 75 575 72 HOH HOH . G 5 HOH A 76 576 26 HOH HOH . G 5 HOH A 77 577 78 HOH HOH . G 5 HOH A 78 578 64 HOH HOH . G 5 HOH A 79 579 39 HOH HOH . G 5 HOH A 80 580 82 HOH HOH . G 5 HOH A 81 581 81 HOH HOH . G 5 HOH A 82 582 87 HOH HOH . G 5 HOH A 83 583 86 HOH HOH . G 5 HOH A 84 584 73 HOH HOH . G 5 HOH A 85 585 66 HOH HOH . G 5 HOH A 86 586 54 HOH HOH . G 5 HOH A 87 587 68 HOH HOH . G 5 HOH A 88 588 70 HOH HOH . G 5 HOH A 89 589 62 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 7.286 -8.362 26.7 1 35.06 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 7.821 -6.951 26.708 1 35.14 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 8.261 -9.303 27.369 1 40.41 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 5.971 -8.412 27.439 1 44.36 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 7.072 -8.857 25.183 1 41.29 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 6.888 -7.842 23.944 1 32.26 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 8.221 -7.307 23.478 1 37.71 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 5.929 -6.715 24.251 1 33.97 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 6.279 -8.83 22.832 1 36.36 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 4.999 -9.413 23.05 1 29.79 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 4.271 -9.571 21.727 1 34.92 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 3.846 -8.293 21.25 1 35.5 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 5.14 -10.16 20.625 1 35.17 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 5.038 -11.58 20.607 1 37.61 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 4.623 -9.507 19.359 1 33.66 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 3.543 -10.251 18.794 1 36.61 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 4.053 -8.187 19.835 1 31.32 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 4.949 -7.033 19.599 1 31.9 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 6.136 -6.799 20.191 1 41.1 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 6.665 -5.626 19.754 1 33.8 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 5.797 -5.086 18.879 1 35.58 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 5.727 -3.86 18.05 1 31.14 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 6.642 -3.012 18.06 1 38.07 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 4.65 -3.684 17.282 1 32.94 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 3.647 -4.58 17.241 1 38.09 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 2.589 -4.33 16.44 1 38.71 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 3.637 -5.72 17.971 1 35.83 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 4.667 -6.017 18.79 1 43.23 ? C4 GDP 401 A 1 HETATM 29 H H4' GDP . . . B 2 3.431 -10.248 21.933 1 41.95 ? H4' GDP 401 A 1 HETATM 30 H H3' GDP . . . B 2 6.214 -9.97 20.76 1 42.25 ? H3' GDP 401 A 1 HETATM 31 H HO3' GDP . . . B 2 5.914 -11.965 20.467 1 45.18 ? HO3' GDP 401 A 1 HETATM 32 H H2' GDP . . . B 2 5.414 -9.428 18.6 1 40.45 ? H2' GDP 401 A 1 HETATM 33 H HO2' GDP . . . B 2 3.646 -10.29 17.833 1 43.99 ? HO2' GDP 401 A 1 HETATM 34 H H1' GDP . . . B 2 3.13 -8.016 19.261 1 37.64 ? H1' GDP 401 A 1 HETATM 35 H H8 GDP . . . B 2 6.604 -7.455 20.914 1 49.38 ? H8 GDP 401 A 1 HETATM 36 H HN1 GDP . . . B 2 4.583 -2.827 16.696 1 39.58 ? HN1 GDP 401 A 1 HETATM 37 H HN21 GDP . . . B 2 1.827 -4.985 16.403 1 46.51 ? HN21 GDP 401 A 1 HETATM 38 H HN22 GDP . . . B 2 2.56 -3.492 15.882 1 46.51 ? HN22 GDP 401 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #