data_4N9W # _model_server_result.job_id 7okbTM34e4kpuhR_nqtswA _model_server_result.datetime_utc '2024-11-05 00:30:42' _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 4n9w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4N9W # _exptl.entry_id 4N9W _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 97.69 _cell.angle_gamma 90 _cell.entry_id 4N9W _cell.length_a 37.507 _cell.length_b 75.515 _cell.length_c 59.326 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4N9W _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 _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 92 n n PB O2B GDP sing 93 n n PB O3B GDP sing 94 n n PB O3A GDP sing 95 n n O2B HOB2 GDP sing 96 n n O3B HOB3 GDP sing 97 n n O3A PA GDP sing 98 n n PA O1A GDP doub 99 n n PA O2A GDP sing 100 n n PA O5' GDP sing 101 n n O2A HOA2 GDP sing 102 n n O5' C5' GDP sing 103 n n C5' C4' GDP sing 104 n n C5' H5' GDP sing 105 n n C5' "H5''" GDP sing 106 n n C4' O4' GDP sing 107 n n C4' C3' GDP sing 108 n n C4' H4' GDP sing 109 n n O4' C1' GDP sing 110 n n C3' O3' GDP sing 111 n n C3' C2' GDP sing 112 n n C3' H3' GDP sing 113 n n O3' HO3' GDP sing 114 n n C2' O2' GDP sing 115 n n C2' C1' GDP sing 116 n n C2' H2' GDP sing 117 n n O2' HO2' GDP sing 118 n n C1' N9 GDP sing 119 n n C1' H1' GDP sing 120 n n N9 C8 GDP sing 121 n y N9 C4 GDP sing 122 n y C8 N7 GDP doub 123 n y C8 H8 GDP sing 124 n n N7 C5 GDP sing 125 n y C5 C6 GDP sing 126 n n C5 C4 GDP doub 127 n y C6 O6 GDP doub 128 n n C6 N1 GDP sing 129 n n N1 C2 GDP sing 130 n n N1 HN1 GDP sing 131 n n C2 N2 GDP sing 132 n n C2 N3 GDP doub 133 n n N2 HN21 GDP sing 134 n n N2 HN22 GDP sing 135 n n N3 C4 GDP sing 136 n n # _atom_sites.entry_id 4N9W _atom_sites.fract_transf_matrix[1][1] 0.026662 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0036 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013242 _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] 0.017009 _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 2 EDO EDO . D 4 HOH A 1 501 1 HOH HOH . D 4 HOH A 2 502 2 HOH HOH . D 4 HOH A 3 503 3 HOH HOH . D 4 HOH A 4 504 4 HOH HOH . D 4 HOH A 5 505 5 HOH HOH . D 4 HOH A 6 506 6 HOH HOH . D 4 HOH A 7 507 7 HOH HOH . D 4 HOH A 8 508 8 HOH HOH . D 4 HOH A 9 509 9 HOH HOH . D 4 HOH A 10 510 10 HOH HOH . D 4 HOH A 11 511 11 HOH HOH . D 4 HOH A 12 512 12 HOH HOH . D 4 HOH A 13 513 13 HOH HOH . D 4 HOH A 14 514 14 HOH HOH . D 4 HOH A 15 515 15 HOH HOH . D 4 HOH A 16 516 16 HOH HOH . D 4 HOH A 17 517 17 HOH HOH . D 4 HOH A 18 518 18 HOH HOH . D 4 HOH A 19 519 19 HOH HOH . D 4 HOH A 20 520 20 HOH HOH . D 4 HOH A 21 521 21 HOH HOH . D 4 HOH A 22 522 22 HOH HOH . D 4 HOH A 23 523 23 HOH HOH . D 4 HOH A 24 524 24 HOH HOH . D 4 HOH A 25 525 25 HOH HOH . D 4 HOH A 26 526 26 HOH HOH . D 4 HOH A 27 527 27 HOH HOH . D 4 HOH A 28 528 28 HOH HOH . D 4 HOH A 29 529 29 HOH HOH . D 4 HOH A 30 530 30 HOH HOH . D 4 HOH A 31 531 31 HOH HOH . D 4 HOH A 32 532 32 HOH HOH . D 4 HOH A 33 533 33 HOH HOH . D 4 HOH A 34 534 34 HOH HOH . D 4 HOH A 35 535 35 HOH HOH . D 4 HOH A 36 536 36 HOH HOH . D 4 HOH A 37 537 37 HOH HOH . D 4 HOH A 38 538 38 HOH HOH . D 4 HOH A 39 539 39 HOH HOH . D 4 HOH A 40 540 40 HOH HOH . D 4 HOH A 41 541 41 HOH HOH . D 4 HOH A 42 542 42 HOH HOH . D 4 HOH A 43 543 43 HOH HOH . D 4 HOH A 44 544 44 HOH HOH . D 4 HOH A 45 545 45 HOH HOH . D 4 HOH A 46 546 46 HOH HOH . D 4 HOH A 47 547 47 HOH HOH . D 4 HOH A 48 548 48 HOH HOH . D 4 HOH A 49 549 49 HOH HOH . D 4 HOH A 50 550 50 HOH HOH . D 4 HOH A 51 551 51 HOH HOH . D 4 HOH A 52 552 52 HOH HOH . D 4 HOH A 53 553 53 HOH HOH . D 4 HOH A 54 554 54 HOH HOH . D 4 HOH A 55 555 55 HOH HOH . D 4 HOH A 56 556 56 HOH HOH . D 4 HOH A 57 557 57 HOH HOH . D 4 HOH A 58 558 58 HOH HOH . D 4 HOH A 59 559 59 HOH HOH . D 4 HOH A 60 560 60 HOH HOH . D 4 HOH A 61 561 61 HOH HOH . D 4 HOH A 62 562 62 HOH HOH . D 4 HOH A 63 563 63 HOH HOH . D 4 HOH A 64 564 64 HOH HOH . D 4 HOH A 65 565 65 HOH HOH . D 4 HOH A 66 566 66 HOH HOH . D 4 HOH A 67 567 68 HOH HOH . D 4 HOH A 68 568 70 HOH HOH . D 4 HOH A 69 569 71 HOH HOH . D 4 HOH A 70 570 72 HOH HOH . D 4 HOH A 71 571 73 HOH HOH . D 4 HOH A 72 572 74 HOH HOH . D 4 HOH A 73 573 75 HOH HOH . D 4 HOH A 74 574 76 HOH HOH . D 4 HOH A 75 575 77 HOH HOH . D 4 HOH A 76 576 78 HOH HOH . D 4 HOH A 77 577 79 HOH HOH . D 4 HOH A 78 578 80 HOH HOH . D 4 HOH A 79 579 81 HOH HOH . D 4 HOH A 80 580 82 HOH HOH . D 4 HOH A 81 581 83 HOH HOH . D 4 HOH A 82 582 84 HOH HOH . D 4 HOH A 83 583 85 HOH HOH . D 4 HOH A 84 584 86 HOH HOH . D 4 HOH A 85 585 88 HOH HOH . D 4 HOH A 86 586 89 HOH HOH . D 4 HOH A 87 587 90 HOH HOH . D 4 HOH A 88 588 91 HOH HOH . D 4 HOH A 89 589 92 HOH HOH . D 4 HOH A 90 590 93 HOH HOH . D 4 HOH A 91 591 94 HOH HOH . D 4 HOH A 92 592 95 HOH HOH . D 4 HOH A 93 593 96 HOH HOH . D 4 HOH A 94 594 97 HOH HOH . D 4 HOH A 95 595 98 HOH HOH . D 4 HOH A 96 596 99 HOH HOH . D 4 HOH A 97 597 100 HOH HOH . D 4 HOH A 98 598 101 HOH HOH . D 4 HOH A 99 599 102 HOH HOH . D 4 HOH A 100 600 103 HOH HOH . D 4 HOH A 101 601 104 HOH HOH . D 4 HOH A 102 602 105 HOH HOH . D 4 HOH A 103 603 106 HOH HOH . D 4 HOH A 104 604 107 HOH HOH . D 4 HOH A 105 605 108 HOH HOH . D 4 HOH A 106 606 109 HOH HOH . D 4 HOH A 107 607 110 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 1.697 4.403 17.277 1 73.02 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 1.735 3.676 15.951 1 70.87 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 0.888 5.693 17.176 1 71.48 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 1.128 3.482 18.344 1 71.94 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 3.203 4.779 17.675 1 83.58 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 4.141 3.606 18.247 1 84.24 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 3.512 2.23 18.128 1 82.87 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 4.563 3.924 19.667 1 86.86 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 5.37 3.782 17.23 1 45.51 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 5.707 5.095 16.829 1 28.41 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 6.862 5.028 15.857 1 27.3 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 6.929 6.32 15.243 1 29.96 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 8.195 4.836 16.549 1 25.41 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 9.184 4.366 15.634 1 24.87 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 8.553 6.265 16.971 1 22.33 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 9.944 6.483 17.235 1 23.19 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 8.077 7.011 15.726 1 27.57 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 7.75 8.414 16.055 1 29.55 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 6.72 8.85 16.8 1 32.96 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 6.774 10.195 16.883 1 32.03 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 7.824 10.619 16.152 1 25.23 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 8.432 11.919 15.796 1 27.64 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 7.948 12.986 16.23 1 36.18 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 9.526 11.939 15.042 1 31.06 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 10.069 10.8 14.564 1 33.05 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 11.178 10.779 13.786 1 26.26 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 9.552 9.58 14.844 1 22.68 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 8.46 9.436 15.613 1 22.09 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #