data_5TC3 # _model_server_result.job_id 2otcztYN4cK4PwFgsLJnXA _model_server_result.datetime_utc '2024-11-18 05:59:57' _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":"K","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 . K 4 -50.636 -1.214 -27.504 0.65 66.74 ? PB GDP 603 B 1 HETATM 2 P PB GDP . B . K 4 -49.18 0.035 -25.497 0.35 63.26 ? PB GDP 603 B 1 HETATM 3 O O1B GDP . A . K 4 -49.874 -1.279 -28.805 0.65 65.73 ? O1B GDP 603 B 1 HETATM 4 O O1B GDP . B . K 4 -49.053 -0.539 -24.102 0.35 59.36 ? O1B GDP 603 B 1 HETATM 5 O O2B GDP . A . K 4 -49.855 -1.926 -26.433 0.65 64.92 ? O2B GDP 603 B 1 HETATM 6 O O2B GDP . B . K 4 -49.001 1.531 -25.434 0.35 62.19 ? O2B GDP 603 B 1 HETATM 7 O O3B GDP . A . K 4 -51.966 -1.899 -27.694 0.65 65.9 ? O3B GDP 603 B 1 HETATM 8 O O3B GDP . B . K 4 -48.138 -0.52 -26.439 0.35 64.75 ? O3B GDP 603 B 1 HETATM 9 O O3A GDP . A . K 4 -50.862 0.294 -27.054 0.65 65.69 ? O3A GDP 603 B 1 HETATM 10 O O3A GDP . B . K 4 -50.631 -0.283 -26.039 0.35 65.49 ? O3A GDP 603 B 1 HETATM 11 P PA GDP . A . K 4 -52.177 1.123 -27.37 0.65 65.85 ? PA GDP 603 B 1 HETATM 12 P PA GDP . B . K 4 -50.971 -0.498 -27.571 0.35 67.35 ? PA GDP 603 B 1 HETATM 13 O O1A GDP . A . K 4 -52.255 1.374 -28.859 0.65 66.52 ? O1A GDP 603 B 1 HETATM 14 O O1A GDP . B . K 4 -50.965 -1.978 -27.88 0.35 65.63 ? O1A GDP 603 B 1 HETATM 15 O O2A GDP . A . K 4 -52.139 2.447 -26.643 0.65 64.95 ? O2A GDP 603 B 1 HETATM 16 O O2A GDP . B . K 4 -49.939 0.204 -28.422 0.35 65.95 ? O2A GDP 603 B 1 HETATM 17 O O5' GDP . A . K 4 -53.434 0.269 -26.902 0.65 68.21 ? O5' GDP 603 B 1 HETATM 18 O O5' GDP . B . K 4 -52.396 0.1 -27.922 0.35 67.37 ? O5' GDP 603 B 1 HETATM 19 C C5' GDP . A . K 4 -54.436 -0.029 -27.855 0.65 69.12 ? C5' GDP 603 B 1 HETATM 20 C C5' GDP . B . K 4 -53.285 0.481 -26.891 0.35 68.18 ? C5' GDP 603 B 1 HETATM 21 C C4' GDP . A . K 4 -55.621 -0.67 -27.232 0.65 70.6 ? C4' GDP 603 B 1 HETATM 22 C C4' GDP . B . K 4 -54.587 -0.185 -27.089 0.35 70.15 ? C4' GDP 603 B 1 HETATM 23 O O4' GDP . A . K 4 -55.274 -2.034 -26.69 0.65 70.31 ? O4' GDP 603 B 1 HETATM 24 O O4' GDP . B . K 4 -54.458 -1.654 -26.793 0.35 70.31 ? O4' GDP 603 B 1 HETATM 25 C C3' GDP . A . K 4 -56.123 0.134 -26.106 0.65 70.72 ? C3' GDP 603 B 1 HETATM 26 C C3' GDP . B . K 4 -55.573 0.34 -26.137 0.35 70.27 ? C3' GDP 603 B 1 HETATM 27 O O3' GDP . A . K 4 -57.584 0.064 -26.079 0.65 70.84 ? O3' GDP 603 B 1 HETATM 28 O O3' GDP . B . K 4 -56.915 0.133 -26.675 0.35 70.77 ? O3' GDP 603 B 1 HETATM 29 C C2' GDP . A . K 4 -55.577 -0.468 -24.91 0.65 71.25 ? C2' GDP 603 B 1 HETATM 30 C C2' GDP . B . K 4 -55.376 -0.448 -24.94 0.35 71.13 ? C2' GDP 603 B 1 HETATM 31 O O2' GDP . A . K 4 -56.428 -0.2 -23.755 0.65 71.4 ? O2' GDP 603 B 1 HETATM 32 O O2' GDP . B . K 4 -56.571 -0.425 -24.103 0.35 71.29 ? O2' GDP 603 B 1 HETATM 33 C C1' GDP . A . K 4 -55.528 -1.909 -25.209 0.65 70.58 ? C1' GDP 603 B 1 HETATM 34 C C1' GDP . B . K 4 -55.093 -1.808 -25.432 0.35 70.46 ? C1' GDP 603 B 1 HETATM 35 N N9 GDP . A . K 4 -54.52 -2.533 -24.498 0.65 71.09 ? N9 GDP 603 B 1 HETATM 36 N N9 GDP . B . K 4 -54.227 -2.5 -24.6 0.35 71.21 ? N9 GDP 603 B 1 HETATM 37 C C8 GDP . A . K 4 -53.215 -2.418 -24.735 0.65 71.42 ? C8 GDP 603 B 1 HETATM 38 C C8 GDP . B . K 4 -52.898 -2.505 -24.698 0.35 70.89 ? C8 GDP 603 B 1 HETATM 39 N N7 GDP . A . K 4 -52.538 -3.148 -23.874 0.65 70.7 ? N7 GDP 603 B 1 HETATM 40 N N7 GDP . B . K 4 -52.38 -3.272 -23.762 0.35 70.91 ? N7 GDP 603 B 1 HETATM 41 C C5 GDP . A . K 4 -53.386 -3.761 -23.055 0.65 71.11 ? C5 GDP 603 B 1 HETATM 42 C C5 GDP . B . K 4 -53.36 -3.792 -23.03 0.35 71.3 ? C5 GDP 603 B 1 HETATM 43 C C6 GDP . A . K 4 -53.229 -4.68 -21.926 0.65 70.6 ? C6 GDP 603 B 1 HETATM 44 C C6 GDP . B . K 4 -53.402 -4.697 -21.879 0.35 70.63 ? C6 GDP 603 B 1 HETATM 45 O O6 GDP . A . K 4 -52.122 -5.027 -21.572 0.65 70.65 ? O6 GDP 603 B 1 HETATM 46 O O6 GDP . B . K 4 -52.371 -5.129 -21.406 0.35 70.68 ? O6 GDP 603 B 1 HETATM 47 N N1 GDP . A . K 4 -54.349 -5.156 -21.261 0.65 70.97 ? N1 GDP 603 B 1 HETATM 48 N N1 GDP . B . K 4 -54.625 -5.061 -21.331 0.35 71.03 ? N1 GDP 603 B 1 HETATM 49 C C2 GDP . A . K 4 -55.665 -4.749 -21.677 0.65 70.99 ? C2 GDP 603 B 1 HETATM 50 C C2 GDP . B . K 4 -55.848 -4.551 -21.89 0.35 70.98 ? C2 GDP 603 B 1 HETATM 51 N N2 GDP . A . K 4 -56.799 -5.245 -20.985 0.65 71.09 ? N2 GDP 603 B 1 HETATM 52 N N2 GDP . B . K 4 -57.087 -4.933 -21.317 0.35 71.13 ? N2 GDP 603 B 1 HETATM 53 N N3 GDP . A . K 4 -55.823 -3.897 -22.722 0.65 71.1 ? N3 GDP 603 B 1 HETATM 54 N N3 GDP . B . K 4 -55.817 -3.714 -22.955 0.35 71.07 ? N3 GDP 603 B 1 HETATM 55 C C4 GDP . A . K 4 -54.669 -3.384 -23.437 0.65 70.76 ? C4 GDP 603 B 1 HETATM 56 C C4 GDP . B . K 4 -54.557 -3.315 -23.551 0.35 69.78 ? C4 GDP 603 B 1 HETATM 57 H H5' GDP . A . K 4 -54.714 0.8 -28.299 0.65 82.95 ? H5' GDP 603 B 1 HETATM 58 H H5' GDP . B . K 4 -53.405 1.454 -26.901 0.35 81.82 ? H5' GDP 603 B 1 HETATM 59 H "H5''" GDP . A . K 4 -54.064 -0.64 -28.525 0.65 82.95 ? "H5''" GDP 603 B 1 HETATM 60 H "H5''" GDP . B . K 4 -52.914 0.207 -26.026 0.35 81.82 ? "H5''" GDP 603 B 1 HETATM 61 H H4' GDP . A . K 4 -56.325 -0.761 -27.901 0.65 84.72 ? H4' GDP 603 B 1 HETATM 62 H H4' GDP . B . K 4 -54.898 -0.051 -28.004 0.35 84.18 ? H4' GDP 603 B 1 HETATM 63 H H3' GDP . A . K 4 -55.827 1.058 -26.188 0.65 84.86 ? H3' GDP 603 B 1 HETATM 64 H H3' GDP . B . K 4 -55.413 1.285 -25.96 0.35 84.33 ? H3' GDP 603 B 1 HETATM 65 H HO3' GDP . A . K 4 -57.843 -0.773 -26.224 0.65 85 ? HO3' GDP 603 B 1 HETATM 66 H HO3' GDP . B . K 4 -57.514 0.469 -26.113 0.35 84.93 ? HO3' GDP 603 B 1 HETATM 67 H H2' GDP . A . K 4 -54.675 -0.13 -24.747 0.65 85.5 ? H2' GDP 603 B 1 HETATM 68 H H2' GDP . B . K 4 -54.61 -0.108 -24.438 0.35 85.36 ? H2' GDP 603 B 1 HETATM 69 H HO2' GDP . A . K 4 -56.134 0.523 -23.332 0.65 85.68 ? HO2' GDP 603 B 1 HETATM 70 H HO2' GDP . B . K 4 -56.687 0.392 -23.775 0.35 85.55 ? HO2' GDP 603 B 1 HETATM 71 H H1' GDP . A . K 4 -56.387 -2.319 -24.988 0.65 84.7 ? H1' GDP 603 B 1 HETATM 72 H H1' GDP . B . K 4 -55.93 -2.304 -25.516 0.35 84.55 ? H1' GDP 603 B 1 HETATM 73 H H8 GDP . A . K 4 -52.819 -1.871 -25.438 0.65 85.71 ? H8 GDP 603 B 1 HETATM 74 H H8 GDP . B . K 4 -52.385 -2.01 -25.363 0.35 85.07 ? H8 GDP 603 B 1 HETATM 75 H HN1 GDP . A . K 4 -54.251 -5.728 -20.558 0.65 85.16 ? HN1 GDP 603 B 1 HETATM 76 H HN1 GDP . B . K 4 -54.652 -5.623 -20.615 0.35 85.23 ? HN1 GDP 603 B 1 HETATM 77 H HN21 GDP . A . K 4 -57.642 -4.99 -21.244 0.65 85.31 ? HN21 GDP 603 B 1 HETATM 78 H HN21 GDP . B . K 4 -57.872 -4.613 -21.667 0.35 85.36 ? HN21 GDP 603 B 1 HETATM 79 H HN22 GDP . A . K 4 -56.691 -5.818 -20.282 0.65 85.31 ? HN22 GDP 603 B 1 HETATM 80 H HN22 GDP . B . K 4 -57.104 -5.498 -20.599 0.35 85.36 ? HN22 GDP 603 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 80 #