data_6I0M # _model_server_result.job_id eL368CdQVLNqauGRwceWOA _model_server_result.datetime_utc '2024-11-30 05:14:09' _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 6i0m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":604}' # _entry.id 6I0M # _exptl.entry_id 6I0M _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 6 _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 6I0M _cell.length_a 134.729 _cell.length_b 134.729 _cell.length_c 324.081 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6I0M _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_795 -x+2,-y+4,z -1 0 0 0 -1 0 0 0 1 269.458 538.916 0 3 'crystal symmetry operation' 3_865 -y+3,x+1,z 0 -1 0 1 0 0 0 0 1 404.187 134.729 0 4 'crystal symmetry operation' 4_485 y-1,-x+3,z 0 1 0 -1 0 0 0 0 1 -134.729 404.187 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 F N N ? 3 O N N ? 3 P N N ? 3 Q 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 123 n n PB O2B GDP sing 124 n n PB O3B GDP sing 125 n n PB O3A GDP sing 126 n n O2B HOB2 GDP sing 127 n n O3B HOB3 GDP sing 128 n n O3A PA GDP sing 129 n n PA O1A GDP doub 130 n n PA O2A GDP sing 131 n n PA O5' GDP sing 132 n n O2A HOA2 GDP sing 133 n n O5' C5' GDP sing 134 n n C5' C4' GDP sing 135 n n C5' H5' GDP sing 136 n n C5' "H5''" GDP sing 137 n n C4' O4' GDP sing 138 n n C4' C3' GDP sing 139 n n C4' H4' GDP sing 140 n n O4' C1' GDP sing 141 n n C3' O3' GDP sing 142 n n C3' C2' GDP sing 143 n n C3' H3' GDP sing 144 n n O3' HO3' GDP sing 145 n n C2' O2' GDP sing 146 n n C2' C1' GDP sing 147 n n C2' H2' GDP sing 148 n n O2' HO2' GDP sing 149 n n C1' N9 GDP sing 150 n n C1' H1' GDP sing 151 n n N9 C8 GDP sing 152 n y N9 C4 GDP sing 153 n y C8 N7 GDP doub 154 n y C8 H8 GDP sing 155 n n N7 C5 GDP sing 156 n y C5 C6 GDP sing 157 n n C5 C4 GDP doub 158 n y C6 O6 GDP doub 159 n n C6 N1 GDP sing 160 n n N1 C2 GDP sing 161 n n N1 HN1 GDP sing 162 n n C2 N2 GDP sing 163 n n C2 N3 GDP doub 164 n n N2 HN21 GDP sing 165 n n N2 HN22 GDP sing 166 n n N3 C4 GDP sing 167 n n # _atom_sites.entry_id 6I0M _atom_sites.fract_transf_matrix[1][1] 0.007422 _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] 0.007422 _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] 0.003086 _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 1 601 600 5GP 5GP . D 3 GDP A 1 602 601 GDP GDP . E 3 GDP A 1 603 602 GDP GDP . F 3 GDP A 1 604 603 GDP GDP . G 4 SO4 A 1 605 1 SO4 SO4 . H 4 SO4 A 1 606 3 SO4 SO4 . I 4 SO4 A 1 607 4 SO4 SO4 . J 4 SO4 A 1 608 5 SO4 SO4 . K 4 SO4 A 1 609 6 SO4 SO4 . L 4 SO4 A 1 610 7 SO4 SO4 . M 4 SO4 A 1 611 10 SO4 SO4 . N 2 5GP B 1 601 600 5GP 5GP . O 3 GDP B 1 602 601 GDP GDP . P 3 GDP B 1 603 602 GDP GDP . Q 3 GDP B 1 604 603 GDP GDP . R 4 SO4 B 1 605 2 SO4 SO4 . S 4 SO4 B 1 606 8 SO4 SO4 . T 4 SO4 B 1 607 9 SO4 SO4 . U 5 HOH A 1 701 41 HOH HOH . U 5 HOH A 2 702 46 HOH HOH . U 5 HOH A 3 703 2 HOH HOH . U 5 HOH A 4 704 17 HOH HOH . U 5 HOH A 5 705 74 HOH HOH . U 5 HOH A 6 706 13 HOH HOH . U 5 HOH A 7 707 48 HOH HOH . U 5 HOH A 8 708 4 HOH HOH . U 5 HOH A 9 709 28 HOH HOH . U 5 HOH A 10 710 79 HOH HOH . U 5 HOH A 11 711 12 HOH HOH . U 5 HOH A 12 712 3 HOH HOH . U 5 HOH A 13 713 16 HOH HOH . U 5 HOH A 14 714 30 HOH HOH . U 5 HOH A 15 715 39 HOH HOH . U 5 HOH A 16 716 38 HOH HOH . U 5 HOH A 17 717 14 HOH HOH . U 5 HOH A 18 718 75 HOH HOH . U 5 HOH A 19 719 44 HOH HOH . U 5 HOH A 20 720 37 HOH HOH . U 5 HOH A 21 721 26 HOH HOH . U 5 HOH A 22 722 90 HOH HOH . U 5 HOH A 23 723 9 HOH HOH . U 5 HOH A 24 724 18 HOH HOH . U 5 HOH A 25 725 92 HOH HOH . U 5 HOH A 26 726 96 HOH HOH . U 5 HOH A 27 727 47 HOH HOH . U 5 HOH A 28 728 97 HOH HOH . U 5 HOH A 29 729 78 HOH HOH . U 5 HOH A 30 730 29 HOH HOH . U 5 HOH A 31 731 21 HOH HOH . U 5 HOH A 32 732 25 HOH HOH . U 5 HOH A 33 733 32 HOH HOH . U 5 HOH A 34 734 76 HOH HOH . U 5 HOH A 35 735 91 HOH HOH . U 5 HOH A 36 736 35 HOH HOH . U 5 HOH A 37 737 83 HOH HOH . U 5 HOH A 38 738 15 HOH HOH . U 5 HOH A 39 739 20 HOH HOH . U 5 HOH A 40 740 22 HOH HOH . U 5 HOH A 41 741 100 HOH HOH . U 5 HOH A 42 742 111 HOH HOH . U 5 HOH A 43 743 40 HOH HOH . U 5 HOH A 44 744 33 HOH HOH . U 5 HOH A 45 745 36 HOH HOH . U 5 HOH A 46 746 27 HOH HOH . U 5 HOH A 47 747 19 HOH HOH . U 5 HOH A 48 748 94 HOH HOH . U 5 HOH A 49 749 77 HOH HOH . U 5 HOH A 50 750 43 HOH HOH . U 5 HOH A 51 751 95 HOH HOH . U 5 HOH A 52 752 98 HOH HOH . U 5 HOH A 53 753 93 HOH HOH . V 5 HOH B 1 701 8 HOH HOH . V 5 HOH B 2 702 89 HOH HOH . V 5 HOH B 3 703 10 HOH HOH . V 5 HOH B 4 704 88 HOH HOH . V 5 HOH B 5 705 81 HOH HOH . V 5 HOH B 6 706 87 HOH HOH . V 5 HOH B 7 707 106 HOH HOH . V 5 HOH B 8 708 67 HOH HOH . V 5 HOH B 9 709 86 HOH HOH . V 5 HOH B 10 710 24 HOH HOH . V 5 HOH B 11 711 105 HOH HOH . V 5 HOH B 12 712 64 HOH HOH . V 5 HOH B 13 713 65 HOH HOH . V 5 HOH B 14 714 53 HOH HOH . V 5 HOH B 15 715 54 HOH HOH . V 5 HOH B 16 716 112 HOH HOH . V 5 HOH B 17 717 68 HOH HOH . V 5 HOH B 18 718 108 HOH HOH . V 5 HOH B 19 719 107 HOH HOH . V 5 HOH B 20 720 110 HOH HOH . V 5 HOH B 21 721 55 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 3 181.031 300.845 397.62 0.56 86.43 ? PB GDP 604 A 1 HETATM 2 P PB GDP . B . F 3 176.239 297.632 393.012 0.44 70.46 ? PB GDP 604 A 1 HETATM 3 O O1B GDP . A . F 3 180.049 300.641 396.497 0.56 81.64 ? O1B GDP 604 A 1 HETATM 4 O O1B GDP . B . F 3 177.608 297.582 393.637 0.44 69.72 ? O1B GDP 604 A 1 HETATM 5 O O2B GDP . A . F 3 180.708 300.105 398.892 0.56 89.5 ? O2B GDP 604 A 1 HETATM 6 O O2B GDP . B . F 3 175.12 297.159 393.903 0.44 69.52 ? O2B GDP 604 A 1 HETATM 7 O O3B GDP . A . F 3 181.413 302.287 397.797 0.56 88.26 ? O3B GDP 604 A 1 HETATM 8 O O3B GDP . B . F 3 176.191 297.101 391.604 0.44 68.35 ? O3B GDP 604 A 1 HETATM 9 O O3A GDP . A . F 3 182.392 300.155 397.131 0.56 81.07 ? O3A GDP 604 A 1 HETATM 10 O O3A GDP . B . F 3 175.996 299.208 392.845 0.44 74.44 ? O3A GDP 604 A 1 HETATM 11 P PA GDP . A . F 3 182.359 299.13 395.906 0.56 78.43 ? PA GDP 604 A 1 HETATM 12 P PA GDP . B . F 3 176.78 300.23 393.806 0.44 78.74 ? PA GDP 604 A 1 HETATM 13 O O1A GDP . A . F 3 183.662 298.374 395.898 0.56 81.61 ? O1A GDP 604 A 1 HETATM 14 O O1A GDP . B . F 3 176.979 299.55 395.135 0.44 80.26 ? O1A GDP 604 A 1 HETATM 15 O O2A GDP . A . F 3 181.06 298.372 395.928 0.56 75.39 ? O2A GDP 604 A 1 HETATM 16 O O2A GDP . B . F 3 176.048 301.548 393.74 0.44 77.84 ? O2A GDP 604 A 1 HETATM 17 O O5' GDP . A . F 3 182.373 300.138 394.664 0.56 76.23 ? O5' GDP 604 A 1 HETATM 18 O O5' GDP . B . F 3 178.216 300.414 393.089 0.44 78.25 ? O5' GDP 604 A 1 HETATM 19 C C5' GDP . A . F 3 181.141 300.451 394.031 0.56 75.82 ? C5' GDP 604 A 1 HETATM 20 C C5' GDP . B . F 3 179.396 300.657 393.863 0.44 77.55 ? C5' GDP 604 A 1 HETATM 21 C C4' GDP . A . F 3 181.408 301.259 392.779 0.56 74.9 ? C4' GDP 604 A 1 HETATM 22 C C4' GDP . B . F 3 180.485 301.318 393.019 0.44 75.52 ? C4' GDP 604 A 1 HETATM 23 O O4' GDP . A . F 3 181.613 300.369 391.694 0.56 70.71 ? O4' GDP 604 A 1 HETATM 24 O O4' GDP . B . F 3 181.091 300.385 392.129 0.44 74.95 ? O4' GDP 604 A 1 HETATM 25 C C3' GDP . A . F 3 180.227 302.142 392.435 0.56 75.89 ? C3' GDP 604 A 1 HETATM 26 C C3' GDP . B . F 3 179.898 302.433 392.182 0.44 76.82 ? C3' GDP 604 A 1 HETATM 27 O O3' GDP . A . F 3 180.647 303.506 392.49 0.56 77.21 ? O3' GDP 604 A 1 HETATM 28 O O3' GDP . B . F 3 180.702 303.601 392.35 0.44 77.26 ? O3' GDP 604 A 1 HETATM 29 C C2' GDP . A . F 3 179.778 301.725 391.049 0.56 74.95 ? C2' GDP 604 A 1 HETATM 30 C C2' GDP . B . F 3 179.919 301.928 390.757 0.44 75.43 ? C2' GDP 604 A 1 HETATM 31 O O2' GDP . A . F 3 179.636 302.833 390.156 0.56 76.66 ? O2' GDP 604 A 1 HETATM 32 O O2' GDP . B . F 3 180.329 302.938 389.83 0.44 76.18 ? O2' GDP 604 A 1 HETATM 33 C C1' GDP . A . F 3 180.862 300.783 390.562 0.56 72.47 ? C1' GDP 604 A 1 HETATM 34 C C1' GDP . B . F 3 180.89 300.764 390.77 0.44 70.7 ? C1' GDP 604 A 1 HETATM 35 N N9 GDP . A . F 3 180.291 299.595 389.898 0.56 66.38 ? N9 GDP 604 A 1 HETATM 36 N N9 GDP . B . F 3 180.333 299.615 390.029 0.44 85.51 ? N9 GDP 604 A 1 HETATM 37 C C8 GDP . A . F 3 179.193 298.933 390.275 0.56 64.05 ? C8 GDP 604 A 1 HETATM 38 C C8 GDP . B . F 3 179.22 298.957 390.368 0.44 70.01 ? C8 GDP 604 A 1 HETATM 39 N N7 GDP . A . F 3 178.958 297.896 389.439 0.56 70.53 ? N7 GDP 604 A 1 HETATM 40 N N7 GDP . B . F 3 178.974 297.954 389.495 0.44 65.52 ? N7 GDP 604 A 1 HETATM 41 C C5 GDP . A . F 3 179.923 297.888 388.511 0.56 75.21 ? C5 GDP 604 A 1 HETATM 42 C C5 GDP . B . F 3 179.946 297.962 388.576 0.44 65.66 ? C5 GDP 604 A 1 HETATM 43 C C6 GDP . A . F 3 180.271 297.065 387.338 0.56 65.45 ? C6 GDP 604 A 1 HETATM 44 C C6 GDP . B . F 3 180.284 297.169 387.378 0.44 65.52 ? C6 GDP 604 A 1 HETATM 45 O O6 GDP . A . F 3 179.571 296.091 387.014 0.56 65.11 ? O6 GDP 604 A 1 HETATM 46 O O6 GDP . B . F 3 179.567 296.22 387.017 0.44 65.26 ? O6 GDP 604 A 1 HETATM 47 N N1 GDP . A . F 3 181.356 297.396 386.636 0.56 67.33 ? N1 GDP 604 A 1 HETATM 48 N N1 GDP . B . F 3 181.379 297.5 386.694 0.44 67.28 ? N1 GDP 604 A 1 HETATM 49 C C2 GDP . A . F 3 182.125 298.446 386.972 0.56 66.65 ? C2 GDP 604 A 1 HETATM 50 C C2 GDP . B . F 3 182.165 298.522 387.069 0.44 66.66 ? C2 GDP 604 A 1 HETATM 51 N N2 GDP . A . F 3 183.211 298.733 386.223 0.56 67.35 ? N2 GDP 604 A 1 HETATM 52 N N2 GDP . B . F 3 183.259 298.805 386.332 0.44 67.2 ? N2 GDP 604 A 1 HETATM 53 N N3 GDP . A . F 3 181.866 299.239 388.031 0.56 68.35 ? N3 GDP 604 A 1 HETATM 54 N N3 GDP . B . F 3 181.917 299.287 388.154 0.44 68.48 ? N3 GDP 604 A 1 HETATM 55 C C4 GDP . A . F 3 180.796 299.015 388.818 0.56 69.1 ? C4 GDP 604 A 1 HETATM 56 C C4 GDP . B . F 3 180.839 299.062 388.931 0.44 61.91 ? C4 GDP 604 A 1 HETATM 57 H H5' GDP . A . F 3 180.615 299.53 393.771 0.56 91.43 ? H5' GDP 604 A 1 HETATM 58 H H5' GDP . B . F 3 179.15 301.304 394.708 0.44 93.51 ? H5' GDP 604 A 1 HETATM 59 H "H5''" GDP . A . F 3 180.51 301.024 394.713 0.56 91.43 ? "H5''" GDP 604 A 1 HETATM 60 H "H5''" GDP . B . F 3 179.77 299.712 394.263 0.44 93.51 ? "H5''" GDP 604 A 1 HETATM 61 H H4' GDP . A . F 3 182.297 301.886 392.933 0.56 90.32 ? H4' GDP 604 A 1 HETATM 62 H H4' GDP . B . F 3 181.245 301.742 393.691 0.44 91.07 ? H4' GDP 604 A 1 HETATM 63 H H3' GDP . A . F 3 179.414 301.958 393.152 0.56 91.51 ? H3' GDP 604 A 1 HETATM 64 H H3' GDP . B . F 3 178.861 302.623 392.494 0.44 92.64 ? H3' GDP 604 A 1 HETATM 65 H HO3' GDP . A . F 3 179.892 304.083 392.313 0.56 93.1 ? HO3' GDP 604 A 1 HETATM 66 H HO3' GDP . B . F 3 180.321 304.331 391.843 0.44 93.16 ? HO3' GDP 604 A 1 HETATM 67 H H2' GDP . A . F 3 178.827 301.182 391.131 0.56 90.39 ? H2' GDP 604 A 1 HETATM 68 H H2' GDP . B . F 3 178.918 301.556 390.494 0.44 90.97 ? H2' GDP 604 A 1 HETATM 69 H HO2' GDP . A . F 3 178.984 303.452 390.511 0.56 92.43 ? HO2' GDP 604 A 1 HETATM 70 H HO2' GDP . B . F 3 179.725 303.691 389.887 0.44 91.86 ? HO2' GDP 604 A 1 HETATM 71 H H1' GDP . A . F 3 181.512 301.326 389.861 0.56 87.41 ? H1' GDP 604 A 1 HETATM 72 H H1' GDP . B . F 3 181.841 301.083 390.32 0.44 85.29 ? H1' GDP 604 A 1 HETATM 73 H H8 GDP . A . F 3 178.577 299.192 391.127 0.56 77.31 ? H8 GDP 604 A 1 HETATM 74 H H8 GDP . B . F 3 178.6 299.194 391.224 0.44 84.46 ? H8 GDP 604 A 1 HETATM 75 H HN1 GDP . A . F 3 181.615 296.825 385.806 0.56 81.25 ? HN1 GDP 604 A 1 HETATM 76 H HN1 GDP . B . F 3 181.631 296.952 385.847 0.44 81.18 ? HN1 GDP 604 A 1 HETATM 77 H HN21 GDP . A . F 3 183.438 298.16 385.423 0.56 81.27 ? HN21 GDP 604 A 1 HETATM 78 H HN21 GDP . B . F 3 183.475 298.251 385.516 0.44 81.09 ? HN21 GDP 604 A 1 HETATM 79 H HN22 GDP . A . F 3 183.797 299.519 386.464 0.56 81.27 ? HN22 GDP 604 A 1 HETATM 80 H HN22 GDP . B . F 3 183.864 299.569 386.598 0.44 81.09 ? HN22 GDP 604 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 212 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 80 #