data_4FWP # _model_server_result.job_id IsAHkWqDZLD37NVAjuBQSg _model_server_result.datetime_utc '2024-12-02 18:32:42' _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 4fwp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 4FWP # _exptl.entry_id 4FWP _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 120 _cell.entry_id 4FWP _cell.length_a 111.489 _cell.length_b 111.489 _cell.length_c 66.888 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FWP _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -22.296 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 4FWP _atom_sites.fract_transf_matrix[1][1] 0.008969 _atom_sites.fract_transf_matrix[1][2] 0.005179 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010357 _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] 0.01495 _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 EDO A 1 501 401 EDO EDO . C 2 EDO A 1 502 402 EDO EDO . D 3 GDP A 1 503 501 GDP GDP . E 4 HOH A 1 601 1 HOH HOH . E 4 HOH A 2 602 2 HOH HOH . E 4 HOH A 3 603 3 HOH HOH . E 4 HOH A 4 604 4 HOH HOH . E 4 HOH A 5 605 5 HOH HOH . E 4 HOH A 6 606 6 HOH HOH . E 4 HOH A 7 607 7 HOH HOH . E 4 HOH A 8 608 8 HOH HOH . E 4 HOH A 9 609 9 HOH HOH . E 4 HOH A 10 610 10 HOH HOH . E 4 HOH A 11 611 11 HOH HOH . E 4 HOH A 12 612 12 HOH HOH . E 4 HOH A 13 613 13 HOH HOH . E 4 HOH A 14 614 14 HOH HOH . E 4 HOH A 15 615 15 HOH HOH . E 4 HOH A 16 616 16 HOH HOH . E 4 HOH A 17 617 17 HOH HOH . E 4 HOH A 18 618 18 HOH HOH . E 4 HOH A 19 619 19 HOH HOH . E 4 HOH A 20 620 20 HOH HOH . E 4 HOH A 21 621 21 HOH HOH . E 4 HOH A 22 622 22 HOH HOH . E 4 HOH A 23 623 23 HOH HOH . E 4 HOH A 24 624 24 HOH HOH . E 4 HOH A 25 625 25 HOH HOH . E 4 HOH A 26 626 26 HOH HOH . E 4 HOH A 27 627 27 HOH HOH . E 4 HOH A 28 628 28 HOH HOH . E 4 HOH A 29 629 29 HOH HOH . E 4 HOH A 30 630 30 HOH HOH . E 4 HOH A 31 631 31 HOH HOH . E 4 HOH A 32 632 32 HOH HOH . E 4 HOH A 33 633 33 HOH HOH . E 4 HOH A 34 634 34 HOH HOH . E 4 HOH A 35 635 35 HOH HOH . E 4 HOH A 36 636 36 HOH HOH . E 4 HOH A 37 637 37 HOH HOH . E 4 HOH A 38 638 38 HOH HOH . E 4 HOH A 39 639 39 HOH HOH . E 4 HOH A 40 640 40 HOH HOH . E 4 HOH A 41 641 41 HOH HOH . E 4 HOH A 42 642 42 HOH HOH . E 4 HOH A 43 643 43 HOH HOH . E 4 HOH A 44 644 44 HOH HOH . E 4 HOH A 45 645 45 HOH HOH . E 4 HOH A 46 646 46 HOH HOH . E 4 HOH A 47 647 47 HOH HOH . E 4 HOH A 48 648 48 HOH HOH . E 4 HOH A 49 649 49 HOH HOH . E 4 HOH A 50 650 50 HOH HOH . E 4 HOH A 51 651 51 HOH HOH . E 4 HOH A 52 652 52 HOH HOH . E 4 HOH A 53 653 53 HOH HOH . E 4 HOH A 54 654 54 HOH HOH . E 4 HOH A 55 655 55 HOH HOH . E 4 HOH A 56 656 56 HOH HOH . E 4 HOH A 57 657 57 HOH HOH . E 4 HOH A 58 658 58 HOH HOH . E 4 HOH A 59 659 59 HOH HOH . E 4 HOH A 60 660 60 HOH HOH . E 4 HOH A 61 661 61 HOH HOH . E 4 HOH A 62 662 62 HOH HOH . E 4 HOH A 63 663 63 HOH HOH . E 4 HOH A 64 664 64 HOH HOH . E 4 HOH A 65 665 65 HOH HOH . E 4 HOH A 66 666 66 HOH HOH . E 4 HOH A 67 667 67 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 . . . D 3 43.127 8.514 9.348 1 75.25 ? PB GDP 503 A 1 HETATM 2 O O1B GDP . . . D 3 42.096 8.148 10.393 1 74.85 ? O1B GDP 503 A 1 HETATM 3 O O2B GDP . . . D 3 42.527 8.393 7.964 1 74.86 ? O2B GDP 503 A 1 HETATM 4 O O3B GDP . . . D 3 43.588 9.936 9.589 1 75.07 ? O3B GDP 503 A 1 HETATM 5 O O3A GDP . . . D 3 44.379 7.505 9.441 1 73.96 ? O3A GDP 503 A 1 HETATM 6 P PA GDP . . . D 3 45.618 7.754 10.439 1 73.13 ? PA GDP 503 A 1 HETATM 7 O O1A GDP . . . D 3 45.19 8.494 11.688 1 73.09 ? O1A GDP 503 A 1 HETATM 8 O O2A GDP . . . D 3 46.746 8.465 9.731 1 72.71 ? O2A GDP 503 A 1 HETATM 9 O O5' GDP . . . D 3 46.06 6.258 10.807 1 72.1 ? O5' GDP 503 A 1 HETATM 10 C C5' GDP . . . D 3 45.181 5.411 11.535 1 70.47 ? C5' GDP 503 A 1 HETATM 11 C C4' GDP . . . D 3 45.48 3.982 11.13 1 69.39 ? C4' GDP 503 A 1 HETATM 12 O O4' GDP . . . D 3 46.884 3.729 11.232 1 68.73 ? O4' GDP 503 A 1 HETATM 13 C C3' GDP . . . D 3 44.783 2.995 12.047 1 69.1 ? C3' GDP 503 A 1 HETATM 14 O O3' GDP . . . D 3 43.554 2.555 11.46 1 69.35 ? O3' GDP 503 A 1 HETATM 15 C C2' GDP . . . D 3 45.772 1.861 12.203 1 68.51 ? C2' GDP 503 A 1 HETATM 16 O O2' GDP . . . D 3 45.481 0.844 11.244 1 68.36 ? O2' GDP 503 A 1 HETATM 17 C C1' GDP . . . D 3 47.125 2.469 11.867 1 68.29 ? C1' GDP 503 A 1 HETATM 18 N N9 GDP . . . D 3 47.949 2.643 13.093 1 67.39 ? N9 GDP 503 A 1 HETATM 19 C C8 GDP . . . D 3 47.85 3.646 13.988 1 66.87 ? C8 GDP 503 A 1 HETATM 20 N N7 GDP . . . D 3 48.754 3.5 14.99 1 66.54 ? N7 GDP 503 A 1 HETATM 21 C C5 GDP . . . D 3 49.457 2.38 14.742 1 66.6 ? C5 GDP 503 A 1 HETATM 22 C C6 GDP . . . D 3 50.564 1.635 15.399 1 66.57 ? C6 GDP 503 A 1 HETATM 23 O O6 GDP . . . D 3 51.074 2.046 16.464 1 66.73 ? O6 GDP 503 A 1 HETATM 24 N N1 GDP . . . D 3 51.007 0.51 14.814 1 66.31 ? N1 GDP 503 A 1 HETATM 25 C C2 GDP . . . D 3 50.479 0.041 13.664 1 66.19 ? C2 GDP 503 A 1 HETATM 26 N N2 GDP . . . D 3 50.98 -1.102 13.138 1 65.79 ? N2 GDP 503 A 1 HETATM 27 N N3 GDP . . . D 3 49.463 0.668 13.011 1 66.32 ? N3 GDP 503 A 1 HETATM 28 C C4 GDP . . . D 3 48.922 1.818 13.49 1 66.84 ? C4 GDP 503 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #