data_6I0M # _model_server_result.job_id 3ZPyMrLj8aHGcAR8bpA8bA _model_server_result.datetime_utc '2024-11-26 20:16:46' _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":"Q","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 . Q 3 174.778 299.425 349.477 0.48 95.1 ? PB GDP 604 B 1 HETATM 2 P PB GDP . B . Q 3 176.713 305.157 344.426 0.52 94.28 ? PB GDP 604 B 1 HETATM 3 O O1B GDP . A . Q 3 174.24 298.802 348.213 0.48 93.91 ? O1B GDP 604 B 1 HETATM 4 O O1B GDP . B . Q 3 175.209 305.196 344.314 0.52 94.72 ? O1B GDP 604 B 1 HETATM 5 O O2B GDP . A . Q 3 175.332 298.453 350.486 0.48 96.28 ? O2B GDP 604 B 1 HETATM 6 O O2B GDP . B . Q 3 177.433 305.306 343.111 0.52 93.97 ? O2B GDP 604 B 1 HETATM 7 O O3B GDP . A . Q 3 173.895 300.498 350.059 0.48 94.72 ? O3B GDP 604 B 1 HETATM 8 O O3B GDP . B . Q 3 177.251 304.066 345.316 0.52 94.01 ? O3B GDP 604 B 1 HETATM 9 O O3A GDP . A . Q 3 176.076 300.22 348.978 0.48 93.75 ? O3A GDP 604 B 1 HETATM 10 O O3A GDP . B . Q 3 177.094 306.496 345.22 0.52 92.14 ? O3A GDP 604 B 1 HETATM 11 P PA GDP . A . Q 3 175.886 301.387 347.897 0.48 93.83 ? PA GDP 604 B 1 HETATM 12 P PA GDP . B . Q 3 176.378 306.787 346.621 0.52 91.28 ? PA GDP 604 B 1 HETATM 13 O O1A GDP . A . Q 3 176.013 300.769 346.526 0.48 93.83 ? O1A GDP 604 B 1 HETATM 14 O O1A GDP . B . Q 3 176.206 308.277 346.759 0.52 89.33 ? O1A GDP 604 B 1 HETATM 15 O O2A GDP . A . Q 3 174.645 302.159 348.272 0.48 91.45 ? O2A GDP 604 B 1 HETATM 16 O O2A GDP . B . Q 3 175.199 305.864 346.776 0.52 90.63 ? O2A GDP 604 B 1 HETATM 17 O O5' GDP . A . Q 3 177.182 302.302 348.167 0.48 94.97 ? O5' GDP 604 B 1 HETATM 18 O O5' GDP . B . Q 3 177.523 306.31 347.633 0.52 93.18 ? O5' GDP 604 B 1 HETATM 19 C C5' GDP . A . Q 3 177.074 303.722 348.26 0.48 95.32 ? C5' GDP 604 B 1 HETATM 20 C C5' GDP . B . Q 3 177.454 304.985 348.144 0.52 94.59 ? C5' GDP 604 B 1 HETATM 21 C C4' GDP . A . Q 3 178.121 304.278 349.219 0.48 93.57 ? C4' GDP 604 B 1 HETATM 22 C C4' GDP . B . Q 3 178.254 304.897 349.426 0.52 94.99 ? C4' GDP 604 B 1 HETATM 23 O O4' GDP . A . Q 3 177.532 305.293 350.031 0.48 93.63 ? O4' GDP 604 B 1 HETATM 24 O O4' GDP . B . Q 3 177.569 305.597 350.457 0.52 93.7 ? O4' GDP 604 B 1 HETATM 25 C C3' GDP . A . Q 3 178.656 303.207 350.154 0.48 95.95 ? C3' GDP 604 B 1 HETATM 26 C C3' GDP . B . Q 3 178.404 303.462 349.89 0.52 95.14 ? C3' GDP 604 B 1 HETATM 27 O O3' GDP . A . Q 3 179.956 302.777 349.734 0.48 95.89 ? O3' GDP 604 B 1 HETATM 28 O O3' GDP . B . Q 3 179.649 302.908 349.448 0.52 96.12 ? O3' GDP 604 B 1 HETATM 29 C C2' GDP . A . Q 3 178.651 303.826 351.536 0.48 94.41 ? C2' GDP 604 B 1 HETATM 30 C C2' GDP . B . Q 3 178.289 303.534 351.399 0.52 94.97 ? C2' GDP 604 B 1 HETATM 31 O O2' GDP . A . Q 3 179.97 304.168 351.971 0.48 95.45 ? O2' GDP 604 B 1 HETATM 32 O O2' GDP . B . Q 3 179.562 303.394 352.035 0.52 95.6 ? O2' GDP 604 B 1 HETATM 33 C C1' GDP . A . Q 3 177.805 305.079 351.415 0.48 93.15 ? C1' GDP 604 B 1 HETATM 34 C C1' GDP . B . Q 3 177.716 304.909 351.695 0.52 90.73 ? C1' GDP 604 B 1 HETATM 35 N N9 GDP . A . Q 3 176.541 304.887 352.163 0.48 87 ? N9 GDP 604 B 1 HETATM 36 N N9 GDP . B . Q 3 176.409 304.786 352.377 0.52 89.17 ? N9 GDP 604 B 1 HETATM 37 C C8 GDP . A . Q 3 175.638 303.932 351.901 0.48 88.04 ? C8 GDP 604 B 1 HETATM 38 C C8 GDP . B . Q 3 175.466 303.875 352.094 0.52 87.31 ? C8 GDP 604 B 1 HETATM 39 N N7 GDP . A . Q 3 174.594 304.014 352.761 0.48 89.29 ? N7 GDP 604 B 1 HETATM 40 N N7 GDP . B . Q 3 174.397 304.03 352.909 0.52 92.24 ? N7 GDP 604 B 1 HETATM 41 C C5 GDP . A . Q 3 174.826 305.037 353.596 0.48 82.23 ? C5 GDP 604 B 1 HETATM 42 C C5 GDP . B . Q 3 174.653 305.055 353.734 0.52 85.97 ? C5 GDP 604 B 1 HETATM 43 C C6 GDP . A . Q 3 174.125 305.66 354.736 0.48 89.25 ? C6 GDP 604 B 1 HETATM 44 C C6 GDP . B . Q 3 173.945 305.736 354.834 0.52 89.27 ? C6 GDP 604 B 1 HETATM 45 O O6 GDP . A . Q 3 173.027 305.229 355.131 0.48 88.28 ? O6 GDP 604 B 1 HETATM 46 O O6 GDP . B . Q 3 172.811 305.369 355.188 0.52 87.91 ? O6 GDP 604 B 1 HETATM 47 N N1 GDP . A . Q 3 174.695 306.699 355.339 0.48 87.25 ? N1 GDP 604 B 1 HETATM 48 N N1 GDP . B . Q 3 174.55 306.755 355.439 0.52 87.28 ? N1 GDP 604 B 1 HETATM 49 C C2 GDP . A . Q 3 175.877 307.18 354.933 0.48 88.23 ? C2 GDP 604 B 1 HETATM 50 C C2 GDP . B . Q 3 175.772 307.164 355.072 0.52 88.24 ? C2 GDP 604 B 1 HETATM 51 N N2 GDP . A . Q 3 176.389 308.238 355.597 0.48 88.06 ? N2 GDP 604 B 1 HETATM 52 N N2 GDP . B . Q 3 176.32 308.206 355.734 0.52 88.07 ? N2 GDP 604 B 1 HETATM 53 N N3 GDP . A . Q 3 176.578 306.662 353.897 0.48 86.39 ? N3 GDP 604 B 1 HETATM 54 N N3 GDP . B . Q 3 176.481 306.588 354.075 0.52 86.31 ? N3 GDP 604 B 1 HETATM 55 C C4 GDP . A . Q 3 176.114 305.605 353.201 0.48 106.2 ? C4 GDP 604 B 1 HETATM 56 C C4 GDP . B . Q 3 175.983 305.545 353.383 0.52 85.93 ? C4 GDP 604 B 1 HETATM 57 H H5' GDP . A . Q 3 177.212 304.165 347.272 0.48 114.83 ? H5' GDP 604 B 1 HETATM 58 H H5' GDP . B . Q 3 176.413 304.718 348.338 0.52 113.95 ? H5' GDP 604 B 1 HETATM 59 H "H5''" GDP . A . Q 3 176.077 303.991 348.614 0.48 114.83 ? "H5''" GDP 604 B 1 HETATM 60 H "H5''" GDP . B . Q 3 177.855 304.284 347.409 0.52 113.95 ? "H5''" GDP 604 B 1 HETATM 61 H H4' GDP . A . Q 3 178.955 304.696 348.637 0.48 112.73 ? H4' GDP 604 B 1 HETATM 62 H H4' GDP . B . Q 3 179.249 305.332 349.264 0.52 114.44 ? H4' GDP 604 B 1 HETATM 63 H H3' GDP . A . Q 3 177.961 302.355 350.147 0.48 115.59 ? H3' GDP 604 B 1 HETATM 64 H H3' GDP . B . Q 3 177.566 302.871 349.495 0.52 114.61 ? H3' GDP 604 B 1 HETATM 65 H HO3' GDP . A . Q 3 180.257 302.056 350.303 0.48 115.51 ? HO3' GDP 604 B 1 HETATM 66 H HO3' GDP . B . Q 3 179.703 301.981 349.718 0.52 115.79 ? HO3' GDP 604 B 1 HETATM 67 H H2' GDP . A . Q 3 178.177 303.133 352.246 0.48 113.74 ? H2' GDP 604 B 1 HETATM 68 H H2' GDP . B . Q 3 177.599 302.754 351.75 0.52 114.41 ? H2' GDP 604 B 1 HETATM 69 H HO2' GDP . A . Q 3 180.52 303.373 351.988 0.48 114.99 ? HO2' GDP 604 B 1 HETATM 70 H HO2' GDP . B . Q 3 179.95 302.542 351.793 0.52 115.17 ? HO2' GDP 604 B 1 HETATM 71 H H1' GDP . A . Q 3 178.364 305.93 351.827 0.48 112.23 ? H1' GDP 604 B 1 HETATM 72 H H1' GDP . B . Q 3 178.421 305.452 352.34 0.52 109.32 ? H1' GDP 604 B 1 HETATM 73 H H8 GDP . A . Q 3 175.727 303.199 351.108 0.48 106.1 ? H8 GDP 604 B 1 HETATM 74 H H8 GDP . B . Q 3 175.547 303.123 351.319 0.52 105.22 ? H8 GDP 604 B 1 HETATM 75 H HN1 GDP . A . Q 3 174.212 307.147 356.143 0.48 105.14 ? HN1 GDP 604 B 1 HETATM 76 H HN1 GDP . B . Q 3 174.062 307.246 356.216 0.52 105.18 ? HN1 GDP 604 B 1 HETATM 77 H HN21 GDP . A . Q 3 175.883 308.641 356.373 0.48 106.12 ? HN21 GDP 604 B 1 HETATM 78 H HN21 GDP . B . Q 3 175.81 308.653 356.483 0.52 106.13 ? HN21 GDP 604 B 1 HETATM 79 H HN22 GDP . A . Q 3 177.278 308.628 355.317 0.48 106.12 ? HN22 GDP 604 B 1 HETATM 80 H HN22 GDP . B . Q 3 177.24 308.537 355.481 0.52 106.13 ? HN22 GDP 604 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 80 #