data_3B1W # _model_server_result.job_id f7RGKEpzhcyg-Eax8cd3cw _model_server_result.datetime_utc '2024-12-02 13:57:56' _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 3b1w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":300}' # _entry.id 3B1W # _exptl.entry_id 3B1W _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 4 _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 3B1W _cell.length_a 64.6 _cell.length_b 92.1 _cell.length_c 206.8 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B1W _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N 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 3B1W _atom_sites.fract_transf_matrix[1][1] 0.015483 _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] 0.010855 _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] 0.004835 _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 E 2 GDP A 1 300 300 GDP GDP . F 2 GDP B 1 300 300 GDP GDP . G 2 GDP C 1 300 300 GDP GDP . H 2 GDP D 1 300 300 GDP GDP . I 3 HOH A 1 271 1 HOH HOH . I 3 HOH A 2 272 2 HOH HOH . I 3 HOH A 3 273 3 HOH HOH . I 3 HOH A 4 274 6 HOH HOH . I 3 HOH A 5 275 7 HOH HOH . I 3 HOH A 6 276 8 HOH HOH . I 3 HOH A 7 277 9 HOH HOH . I 3 HOH A 8 278 10 HOH HOH . I 3 HOH A 9 279 21 HOH HOH . I 3 HOH A 10 280 24 HOH HOH . I 3 HOH A 11 281 28 HOH HOH . I 3 HOH A 12 282 41 HOH HOH . I 3 HOH A 13 283 47 HOH HOH . I 3 HOH A 14 284 71 HOH HOH . I 3 HOH A 15 285 77 HOH HOH . I 3 HOH A 16 286 78 HOH HOH . I 3 HOH A 17 287 79 HOH HOH . I 3 HOH A 18 288 80 HOH HOH . I 3 HOH A 19 289 81 HOH HOH . I 3 HOH A 20 290 82 HOH HOH . I 3 HOH A 21 291 83 HOH HOH . I 3 HOH A 22 292 84 HOH HOH . I 3 HOH A 23 293 85 HOH HOH . I 3 HOH A 24 294 86 HOH HOH . I 3 HOH A 25 295 87 HOH HOH . I 3 HOH A 26 296 88 HOH HOH . I 3 HOH A 27 297 89 HOH HOH . I 3 HOH A 28 298 90 HOH HOH . I 3 HOH A 29 299 91 HOH HOH . I 3 HOH A 30 301 92 HOH HOH . I 3 HOH A 31 302 93 HOH HOH . I 3 HOH A 32 303 94 HOH HOH . I 3 HOH A 33 304 95 HOH HOH . I 3 HOH A 34 305 104 HOH HOH . I 3 HOH A 35 306 108 HOH HOH . J 3 HOH B 1 271 4 HOH HOH . J 3 HOH B 2 272 5 HOH HOH . J 3 HOH B 3 273 11 HOH HOH . J 3 HOH B 4 274 12 HOH HOH . J 3 HOH B 5 275 13 HOH HOH . J 3 HOH B 6 276 14 HOH HOH . J 3 HOH B 7 277 15 HOH HOH . J 3 HOH B 8 278 16 HOH HOH . J 3 HOH B 9 279 17 HOH HOH . J 3 HOH B 10 280 45 HOH HOH . J 3 HOH B 11 281 54 HOH HOH . J 3 HOH B 12 282 56 HOH HOH . J 3 HOH B 13 283 59 HOH HOH . J 3 HOH B 14 284 60 HOH HOH . J 3 HOH B 15 285 61 HOH HOH . J 3 HOH B 16 286 62 HOH HOH . J 3 HOH B 17 287 63 HOH HOH . J 3 HOH B 18 288 64 HOH HOH . J 3 HOH B 19 289 65 HOH HOH . J 3 HOH B 20 290 66 HOH HOH . J 3 HOH B 21 291 67 HOH HOH . J 3 HOH B 22 292 68 HOH HOH . J 3 HOH B 23 293 69 HOH HOH . J 3 HOH B 24 294 72 HOH HOH . J 3 HOH B 25 295 73 HOH HOH . J 3 HOH B 26 296 74 HOH HOH . J 3 HOH B 27 297 96 HOH HOH . J 3 HOH B 28 298 97 HOH HOH . J 3 HOH B 29 299 103 HOH HOH . J 3 HOH B 30 301 107 HOH HOH . J 3 HOH B 31 302 110 HOH HOH . K 3 HOH C 1 271 18 HOH HOH . K 3 HOH C 2 272 23 HOH HOH . K 3 HOH C 3 273 25 HOH HOH . K 3 HOH C 4 274 27 HOH HOH . K 3 HOH C 5 275 29 HOH HOH . K 3 HOH C 6 276 30 HOH HOH . K 3 HOH C 7 277 31 HOH HOH . K 3 HOH C 8 278 32 HOH HOH . K 3 HOH C 9 279 39 HOH HOH . K 3 HOH C 10 280 40 HOH HOH . K 3 HOH C 11 281 44 HOH HOH . K 3 HOH C 12 282 46 HOH HOH . K 3 HOH C 13 283 52 HOH HOH . K 3 HOH C 14 284 53 HOH HOH . K 3 HOH C 15 285 55 HOH HOH . K 3 HOH C 16 286 57 HOH HOH . K 3 HOH C 17 287 58 HOH HOH . K 3 HOH C 18 288 70 HOH HOH . K 3 HOH C 19 289 98 HOH HOH . K 3 HOH C 20 290 99 HOH HOH . K 3 HOH C 21 291 100 HOH HOH . K 3 HOH C 22 292 101 HOH HOH . K 3 HOH C 23 293 102 HOH HOH . K 3 HOH C 24 294 105 HOH HOH . L 3 HOH D 1 271 19 HOH HOH . L 3 HOH D 2 272 20 HOH HOH . L 3 HOH D 3 273 22 HOH HOH . L 3 HOH D 4 274 26 HOH HOH . L 3 HOH D 5 275 33 HOH HOH . L 3 HOH D 6 276 34 HOH HOH . L 3 HOH D 7 277 35 HOH HOH . L 3 HOH D 8 278 36 HOH HOH . L 3 HOH D 9 279 37 HOH HOH . L 3 HOH D 10 280 38 HOH HOH . L 3 HOH D 11 281 42 HOH HOH . L 3 HOH D 12 282 43 HOH HOH . L 3 HOH D 13 283 48 HOH HOH . L 3 HOH D 14 284 49 HOH HOH . L 3 HOH D 15 285 50 HOH HOH . L 3 HOH D 16 286 51 HOH HOH . L 3 HOH D 17 287 75 HOH HOH . L 3 HOH D 18 288 76 HOH HOH . L 3 HOH D 19 289 106 HOH HOH . L 3 HOH D 20 290 109 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 . . . F 2 28.065 -46.48 -41.232 1 42.31 ? PB GDP 300 B 1 HETATM 2 O O1B GDP . . . F 2 28.294 -47.937 -41.357 1 43.97 ? O1B GDP 300 B 1 HETATM 3 O O2B GDP . . . F 2 27.586 -46.055 -39.751 1 46.09 ? O2B GDP 300 B 1 HETATM 4 O O3B GDP . . . F 2 26.911 -45.943 -42.214 1 40.51 ? O3B GDP 300 B 1 HETATM 5 O O3A GDP . . . F 2 29.383 -45.635 -41.534 1 42.11 ? O3A GDP 300 B 1 HETATM 6 P PA GDP . . . F 2 29.316 -44.202 -42.279 1 42.21 ? PA GDP 300 B 1 HETATM 7 O O1A GDP . . . F 2 28.93 -44.308 -43.712 1 41.82 ? O1A GDP 300 B 1 HETATM 8 O O2A GDP . . . F 2 28.28 -43.301 -41.427 1 41.55 ? O2A GDP 300 B 1 HETATM 9 O O5' GDP . . . F 2 30.749 -43.554 -42.077 1 44.26 ? O5' GDP 300 B 1 HETATM 10 C C5' GDP . . . F 2 31.432 -43.666 -40.821 1 45.86 ? C5' GDP 300 B 1 HETATM 11 C C4' GDP . . . F 2 32.62 -42.663 -40.748 1 47.06 ? C4' GDP 300 B 1 HETATM 12 O O4' GDP . . . F 2 33.737 -43.254 -41.486 1 47.54 ? O4' GDP 300 B 1 HETATM 13 C C3' GDP . . . F 2 32.363 -41.289 -41.402 1 47.88 ? C3' GDP 300 B 1 HETATM 14 O O3' GDP . . . F 2 33.15 -40.273 -40.758 1 48.34 ? O3' GDP 300 B 1 HETATM 15 C C2' GDP . . . F 2 32.834 -41.528 -42.842 1 48.49 ? C2' GDP 300 B 1 HETATM 16 O O2' GDP . . . F 2 33.16 -40.319 -43.523 1 51.57 ? O2' GDP 300 B 1 HETATM 17 C C1' GDP . . . F 2 34.086 -42.365 -42.588 1 47.38 ? C1' GDP 300 B 1 HETATM 18 N N9 GDP . . . F 2 34.421 -43.327 -43.637 1 46.56 ? N9 GDP 300 B 1 HETATM 19 C C8 GDP . . . F 2 33.565 -44.078 -44.334 1 45.07 ? C8 GDP 300 B 1 HETATM 20 N N7 GDP . . . F 2 34.259 -44.831 -45.179 1 45.14 ? N7 GDP 300 B 1 HETATM 21 C C5 GDP . . . F 2 35.557 -44.563 -45.029 1 46.35 ? C5 GDP 300 B 1 HETATM 22 C C6 GDP . . . F 2 36.721 -45.042 -45.636 1 46.9 ? C6 GDP 300 B 1 HETATM 23 O O6 GDP . . . F 2 36.687 -45.895 -46.522 1 46.92 ? O6 GDP 300 B 1 HETATM 24 N N1 GDP . . . F 2 37.961 -44.539 -45.222 1 47.83 ? N1 GDP 300 B 1 HETATM 25 C C2 GDP . . . F 2 38 -43.566 -44.212 1 47.84 ? C2 GDP 300 B 1 HETATM 26 N N2 GDP . . . F 2 39.177 -43.083 -43.821 1 48.81 ? N2 GDP 300 B 1 HETATM 27 N N3 GDP . . . F 2 36.861 -43.124 -43.648 1 45.55 ? N3 GDP 300 B 1 HETATM 28 C C4 GDP . . . F 2 35.66 -43.599 -44.033 1 46.37 ? C4 GDP 300 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #