data_5TC3 # _model_server_result.job_id gQ3FkE2_5Cdi3RAgfcUqUA _model_server_result.datetime_utc '2024-11-18 05:40:01' _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 5tc3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":603}' # _entry.id 5TC3 # _exptl.entry_id 5TC3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 5TC3 _cell.length_a 147.88 _cell.length_b 147.88 _cell.length_c 103.542 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TC3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M 1 2 A,B,C,D,E,F,G,H,I,J,K,L,M 1 3 A,B,C,D,E,F,G,H,I,J,K,L,M 1 4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 F N N ? 4 J N N ? 4 K 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 178 n n PB O2B GDP sing 179 n n PB O3B GDP sing 180 n n PB O3A GDP sing 181 n n O2B HOB2 GDP sing 182 n n O3B HOB3 GDP sing 183 n n O3A PA GDP sing 184 n n PA O1A GDP doub 185 n n PA O2A GDP sing 186 n n PA O5' GDP sing 187 n n O2A HOA2 GDP sing 188 n n O5' C5' GDP sing 189 n n C5' C4' GDP sing 190 n n C5' H5' GDP sing 191 n n C5' "H5''" GDP sing 192 n n C4' O4' GDP sing 193 n n C4' C3' GDP sing 194 n n C4' H4' GDP sing 195 n n O4' C1' GDP sing 196 n n C3' O3' GDP sing 197 n n C3' C2' GDP sing 198 n n C3' H3' GDP sing 199 n n O3' HO3' GDP sing 200 n n C2' O2' GDP sing 201 n n C2' C1' GDP sing 202 n n C2' H2' GDP sing 203 n n O2' HO2' GDP sing 204 n n C1' N9 GDP sing 205 n n C1' H1' GDP sing 206 n n N9 C8 GDP sing 207 n y N9 C4 GDP sing 208 n y C8 N7 GDP doub 209 n y C8 H8 GDP sing 210 n n N7 C5 GDP sing 211 n y C5 C6 GDP sing 212 n n C5 C4 GDP doub 213 n y C6 O6 GDP doub 214 n n C6 N1 GDP sing 215 n n N1 C2 GDP sing 216 n n N1 HN1 GDP sing 217 n n C2 N2 GDP sing 218 n n C2 N3 GDP doub 219 n n N2 HN21 GDP sing 220 n n N2 HN22 GDP sing 221 n n N3 C4 GDP sing 222 n n # _atom_sites.entry_id 5TC3 _atom_sites.fract_transf_matrix[1][1] 0.006762 _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] 0.006762 _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] 0.009658 _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 2 5GP A 1 600 600 5GP 5GP . D 3 ATP A 1 601 601 ATP ATP . E 4 GDP A 1 602 602 GDP GDP . F 4 GDP A 1 603 603 GDP GDP . G 5 ACT A 1 604 604 ACT ACT . H 2 5GP B 1 600 600 5GP 5GP . I 3 ATP B 1 601 601 ATP ATP . J 4 GDP B 1 602 602 GDP GDP . K 4 GDP B 1 603 603 GDP GDP . L 6 HOH A 1 701 25 HOH HOH . L 6 HOH A 2 702 36 HOH HOH . L 6 HOH A 3 703 16 HOH HOH . L 6 HOH A 4 704 20 HOH HOH . L 6 HOH A 5 705 17 HOH HOH . L 6 HOH A 6 706 23 HOH HOH . L 6 HOH A 7 707 7 HOH HOH . L 6 HOH A 8 708 1 HOH HOH . L 6 HOH A 9 709 12 HOH HOH . L 6 HOH A 10 710 2 HOH HOH . L 6 HOH A 11 711 24 HOH HOH . L 6 HOH A 12 712 21 HOH HOH . L 6 HOH A 13 713 37 HOH HOH . L 6 HOH A 14 714 43 HOH HOH . L 6 HOH A 15 715 46 HOH HOH . L 6 HOH A 16 716 39 HOH HOH . L 6 HOH A 17 717 41 HOH HOH . L 6 HOH A 18 718 19 HOH HOH . L 6 HOH A 19 719 22 HOH HOH . L 6 HOH A 20 720 47 HOH HOH . L 6 HOH A 21 721 49 HOH HOH . L 6 HOH A 22 722 53 HOH HOH . L 6 HOH A 23 723 40 HOH HOH . L 6 HOH A 24 724 52 HOH HOH . L 6 HOH A 25 725 51 HOH HOH . L 6 HOH A 26 726 45 HOH HOH . L 6 HOH A 27 727 44 HOH HOH . L 6 HOH A 28 728 48 HOH HOH . M 6 HOH B 1 701 8 HOH HOH . M 6 HOH B 2 702 13 HOH HOH . M 6 HOH B 3 703 27 HOH HOH . M 6 HOH B 4 704 15 HOH HOH . M 6 HOH B 5 705 3 HOH HOH . M 6 HOH B 6 706 6 HOH HOH . M 6 HOH B 7 707 11 HOH HOH . M 6 HOH B 8 708 31 HOH HOH . M 6 HOH B 9 709 30 HOH HOH . M 6 HOH B 10 710 29 HOH HOH . M 6 HOH B 11 711 5 HOH HOH . M 6 HOH B 12 712 14 HOH HOH . M 6 HOH B 13 713 26 HOH HOH . M 6 HOH B 14 714 28 HOH HOH . M 6 HOH B 15 715 9 HOH HOH . M 6 HOH B 16 716 32 HOH HOH . M 6 HOH B 17 717 10 HOH HOH . M 6 HOH B 18 718 34 HOH HOH . M 6 HOH B 19 719 33 HOH HOH . M 6 HOH B 20 720 54 HOH HOH . M 6 HOH B 21 721 35 HOH HOH . M 6 HOH B 22 722 50 HOH HOH . M 6 HOH B 23 723 42 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 . A . F 4 -50.586 1.347 17.763 0.66 67.84 ? PB GDP 603 A 1 HETATM 2 P PB GDP . B . F 4 -49.529 -0.281 16.382 0.34 68.21 ? PB GDP 603 A 1 HETATM 3 O O1B GDP . A . F 4 -50.083 1.012 16.379 0.66 67.71 ? O1B GDP 603 A 1 HETATM 4 O O1B GDP . B . F 4 -48.521 0.265 17.365 0.34 67.4 ? O1B GDP 603 A 1 HETATM 5 O O2B GDP . A . F 4 -49.454 1.903 18.59 0.66 67.75 ? O2B GDP 603 A 1 HETATM 6 O O2B GDP . B . F 4 -48.83 -1.277 15.493 0.34 66.87 ? O2B GDP 603 A 1 HETATM 7 O O3B GDP . A . F 4 -51.663 2.393 17.662 0.66 67.61 ? O3B GDP 603 A 1 HETATM 8 O O3B GDP . B . F 4 -50.135 0.835 15.556 0.34 67.37 ? O3B GDP 603 A 1 HETATM 9 O O3A GDP . A . F 4 -51.185 0.048 18.452 0.66 68.3 ? O3A GDP 603 A 1 HETATM 10 O O3A GDP . B . F 4 -50.668 -1.02 17.19 0.34 68.97 ? O3A GDP 603 A 1 HETATM 11 P PA GDP . A . F 4 -52.176 -0.979 17.745 0.66 71.77 ? PA GDP 603 A 1 HETATM 12 P PA GDP . B . F 4 -51.756 -0.264 18.057 0.34 69.43 ? PA GDP 603 A 1 HETATM 13 O O1A GDP . A . F 4 -51.479 -1.663 16.592 0.66 69.23 ? O1A GDP 603 A 1 HETATM 14 O O1A GDP . B . F 4 -51.995 -1.057 19.323 0.34 69.67 ? O1A GDP 603 A 1 HETATM 15 O O2A GDP . A . F 4 -52.623 -2.033 18.735 0.66 69.01 ? O2A GDP 603 A 1 HETATM 16 O O2A GDP . B . F 4 -51.239 1.116 18.396 0.34 68.36 ? O2A GDP 603 A 1 HETATM 17 O O5' GDP . A . F 4 -53.441 -0.171 17.219 0.66 70.45 ? O5' GDP 603 A 1 HETATM 18 O O5' GDP . B . F 4 -53.138 -0.128 17.287 0.34 70.09 ? O5' GDP 603 A 1 HETATM 19 C C5' GDP . A . F 4 -54.6 -0.145 18.03 0.66 72.36 ? C5' GDP 603 A 1 HETATM 20 C C5' GDP . B . F 4 -54.298 -0.105 18.101 0.34 72.33 ? C5' GDP 603 A 1 HETATM 21 C C4' GDP . A . F 4 -55.701 0.589 17.367 0.66 73.36 ? C4' GDP 603 A 1 HETATM 22 C C4' GDP . B . F 4 -55.445 0.555 17.437 0.34 71.75 ? C4' GDP 603 A 1 HETATM 23 O O4' GDP . A . F 4 -55.218 1.935 16.894 0.66 71.86 ? O4' GDP 603 A 1 HETATM 24 O O4' GDP . B . F 4 -55.044 1.908 16.911 0.34 71.87 ? O4' GDP 603 A 1 HETATM 25 C C3' GDP . A . F 4 -56.208 -0.159 16.201 0.66 72.48 ? C3' GDP 603 A 1 HETATM 26 C C3' GDP . B . F 4 -55.938 -0.249 16.306 0.34 72.32 ? C3' GDP 603 A 1 HETATM 27 O O3' GDP . A . F 4 -57.67 -0.216 16.259 0.66 72.7 ? O3' GDP 603 A 1 HETATM 28 O O3' GDP . B . F 4 -57.398 -0.314 16.373 0.34 72.3 ? O3' GDP 603 A 1 HETATM 29 C C2' GDP . A . F 4 -55.784 0.563 15.018 0.66 72.51 ? C2' GDP 603 A 1 HETATM 30 C C2' GDP . B . F 4 -55.521 0.431 15.097 0.34 72.34 ? C2' GDP 603 A 1 HETATM 31 O O2' GDP . A . F 4 -56.802 0.475 13.973 0.66 72.7 ? O2' GDP 603 A 1 HETATM 32 O O2' GDP . B . F 4 -56.495 0.221 14.03 0.34 72.68 ? O2' GDP 603 A 1 HETATM 33 C C1' GDP . A . F 4 -55.606 1.962 15.439 0.66 72.01 ? C1' GDP 603 A 1 HETATM 34 C C1' GDP . B . F 4 -55.438 1.856 15.458 0.34 71.96 ? C1' GDP 603 A 1 HETATM 35 N N9 GDP . A . F 4 -54.615 2.578 14.699 0.66 71.8 ? N9 GDP 603 A 1 HETATM 36 N N9 GDP . B . F 4 -54.492 2.532 14.707 0.34 71.36 ? N9 GDP 603 A 1 HETATM 37 C C8 GDP . A . F 4 -53.307 2.451 14.905 0.66 71.8 ? C8 GDP 603 A 1 HETATM 38 C C8 GDP . B . F 4 -53.176 2.49 14.902 0.34 71.33 ? C8 GDP 603 A 1 HETATM 39 N N7 GDP . A . F 4 -52.645 3.173 14.027 0.66 71.09 ? N7 GDP 603 A 1 HETATM 40 N N7 GDP . B . F 4 -52.568 3.253 14.018 0.34 71.67 ? N7 GDP 603 A 1 HETATM 41 C C5 GDP . A . F 4 -53.506 3.793 13.228 0.66 72.18 ? C5 GDP 603 A 1 HETATM 42 C C5 GDP . B . F 4 -53.476 3.818 13.229 0.34 71.2 ? C5 GDP 603 A 1 HETATM 43 C C6 GDP . A . F 4 -53.367 4.711 12.094 0.66 71.18 ? C6 GDP 603 A 1 HETATM 44 C C6 GDP . B . F 4 -53.409 4.744 12.095 0.34 71.17 ? C6 GDP 603 A 1 HETATM 45 O O6 GDP . A . F 4 -52.266 5.047 11.713 0.66 71.1 ? O6 GDP 603 A 1 HETATM 46 O O6 GDP . B . F 4 -52.333 5.148 11.704 0.34 71.12 ? O6 GDP 603 A 1 HETATM 47 N N1 GDP . A . F 4 -54.5 5.195 11.455 0.66 71.48 ? N1 GDP 603 A 1 HETATM 48 N N1 GDP . B . F 4 -54.579 5.156 11.47 0.34 71.36 ? N1 GDP 603 A 1 HETATM 49 C C2 GDP . A . F 4 -55.81 4.8 11.904 0.66 71.29 ? C2 GDP 603 A 1 HETATM 50 C C2 GDP . B . F 4 -55.855 4.678 11.933 0.34 71.27 ? C2 GDP 603 A 1 HETATM 51 N N2 GDP . A . F 4 -56.956 5.306 11.24 0.66 71.49 ? N2 GDP 603 A 1 HETATM 52 N N2 GDP . B . F 4 -57.042 5.106 11.287 0.34 71.5 ? N2 GDP 603 A 1 HETATM 53 N N3 GDP . A . F 4 -55.949 3.952 12.953 0.66 71.42 ? N3 GDP 603 A 1 HETATM 54 N N3 GDP . B . F 4 -55.926 3.822 12.981 0.34 71.42 ? N3 GDP 603 A 1 HETATM 55 C C4 GDP . A . F 4 -54.783 3.429 13.641 0.66 71.45 ? C4 GDP 603 A 1 HETATM 56 C C4 GDP . B . F 4 -54.722 3.374 13.654 0.34 71.1 ? C4 GDP 603 A 1 HETATM 57 H H5' GDP . A . F 4 -54.386 0.302 18.877 0.66 86.83 ? H5' GDP 603 A 1 HETATM 58 H H5' GDP . B . F 4 -54.546 -1.026 18.328 0.34 86.8 ? H5' GDP 603 A 1 HETATM 59 H "H5''" GDP . A . F 4 -54.886 -1.064 18.216 0.66 86.83 ? "H5''" GDP 603 A 1 HETATM 60 H "H5''" GDP . B . F 4 -54.092 0.381 18.927 0.34 86.8 ? "H5''" GDP 603 A 1 HETATM 61 H H4' GDP . A . F 4 -56.429 0.717 18.005 0.66 88.03 ? H4' GDP 603 A 1 HETATM 62 H H4' GDP . B . F 4 -56.165 0.668 18.086 0.34 86.1 ? H4' GDP 603 A 1 HETATM 63 H H3' GDP . A . F 4 -55.837 -1.06 16.194 0.66 86.98 ? H3' GDP 603 A 1 HETATM 64 H H3' GDP . B . F 4 -55.558 -1.145 16.337 0.34 86.78 ? H3' GDP 603 A 1 HETATM 65 H HO3' GDP . A . F 4 -57.97 -0.774 15.637 0.66 87.24 ? HO3' GDP 603 A 1 HETATM 66 H HO3' GDP . B . F 4 -57.697 -0.892 15.769 0.34 86.76 ? HO3' GDP 603 A 1 HETATM 67 H H2' GDP . A . F 4 -54.937 0.201 14.691 0.66 87.01 ? H2' GDP 603 A 1 HETATM 68 H H2' GDP . B . F 4 -54.643 0.106 14.817 0.34 86.8 ? H2' GDP 603 A 1 HETATM 69 H HO2' GDP . A . F 4 -56.816 -0.348 13.641 0.66 87.23 ? HO2' GDP 603 A 1 HETATM 70 H HO2' GDP . B . F 4 -56.495 -0.635 13.794 0.34 87.22 ? HO2' GDP 603 A 1 HETATM 71 H H1' GDP . A . F 4 -56.447 2.447 15.331 0.66 86.41 ? H1' GDP 603 A 1 HETATM 72 H H1' GDP . B . F 4 -56.312 2.277 15.34 0.34 86.36 ? H1' GDP 603 A 1 HETATM 73 H H8 GDP . A . F 4 -52.9 1.901 15.6 0.66 86.17 ? H8 GDP 603 A 1 HETATM 74 H H8 GDP . B . F 4 -52.728 1.965 15.591 0.34 85.59 ? H8 GDP 603 A 1 HETATM 75 H HN1 GDP . A . F 4 -54.415 5.765 10.75 0.66 85.78 ? HN1 GDP 603 A 1 HETATM 76 H HN1 GDP . B . F 4 -54.538 5.731 10.764 0.34 85.63 ? HN1 GDP 603 A 1 HETATM 77 H HN21 GDP . A . F 4 -57.794 5.059 11.518 0.66 85.79 ? HN21 GDP 603 A 1 HETATM 78 H HN21 GDP . B . F 4 -57.857 4.803 11.578 0.34 85.79 ? HN21 GDP 603 A 1 HETATM 79 H HN22 GDP . A . F 4 -56.859 5.877 10.533 0.66 85.79 ? HN22 GDP 603 A 1 HETATM 80 H HN22 GDP . B . F 4 -56.995 5.683 10.58 0.34 85.79 ? HN22 GDP 603 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 540 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 80 #