data_6I0M # _model_server_result.job_id cM3Kvqq98A-GcNlL9TqiRw _model_server_result.datetime_utc '2024-11-26 20:17:04' _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":"P","auth_seq_id":603}' # _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 . . . P 3 173.908 309.228 368.748 1 88.63 ? PB GDP 603 B 1 HETATM 2 O O1B GDP . . . P 3 174.572 309.808 367.534 1 83.91 ? O1B GDP 603 B 1 HETATM 3 O O2B GDP . . . P 3 172.84 310.087 369.365 1 91.2 ? O2B GDP 603 B 1 HETATM 4 O O3B GDP . . . P 3 174.863 308.617 369.726 1 91.19 ? O3B GDP 603 B 1 HETATM 5 O O3A GDP . . . P 3 173.086 307.962 368.238 1 91.33 ? O3A GDP 603 B 1 HETATM 6 P PA GDP . . . P 3 173.396 307.207 366.864 1 94.39 ? PA GDP 603 B 1 HETATM 7 O O1A GDP . . . P 3 174.774 307.546 366.379 1 98.45 ? O1A GDP 603 B 1 HETATM 8 O O2A GDP . . . P 3 173.047 305.768 367.084 1 97.07 ? O2A GDP 603 B 1 HETATM 9 O O5' GDP . . . P 3 172.306 307.856 365.883 1 89.65 ? O5' GDP 603 B 1 HETATM 10 C C5' GDP . . . P 3 171.103 307.147 365.616 1 87.4 ? C5' GDP 603 B 1 HETATM 11 C C4' GDP . . . P 3 170.631 307.381 364.188 1 87.33 ? C4' GDP 603 B 1 HETATM 12 O O4' GDP . . . P 3 169.701 308.456 364.103 1 89.47 ? O4' GDP 603 B 1 HETATM 13 C C3' GDP . . . P 3 171.774 307.719 363.255 1 87.81 ? C3' GDP 603 B 1 HETATM 14 O O3' GDP . . . P 3 172.017 306.603 362.396 1 86.97 ? O3' GDP 603 B 1 HETATM 15 C C2' GDP . . . P 3 171.322 308.952 362.496 1 88.9 ? C2' GDP 603 B 1 HETATM 16 O O2' GDP . . . P 3 171.475 308.815 361.081 1 88.19 ? O2' GDP 603 B 1 HETATM 17 C C1' GDP . . . P 3 169.859 309.112 362.848 1 90.88 ? C1' GDP 603 B 1 HETATM 18 N N9 GDP . . . P 3 169.469 310.528 362.993 1 94.32 ? N9 GDP 603 B 1 HETATM 19 C C8 GDP . . . P 3 168.45 311.118 362.354 1 95.94 ? C8 GDP 603 B 1 HETATM 20 N N7 GDP . . . P 3 168.362 312.424 362.696 1 96.33 ? N7 GDP 603 B 1 HETATM 21 C C5 GDP . . . P 3 169.347 312.681 363.566 1 95.84 ? C5 GDP 603 B 1 HETATM 22 C C6 GDP . . . P 3 169.82 313.856 364.319 1 95.87 ? C6 GDP 603 B 1 HETATM 23 O O6 GDP . . . P 3 169.247 314.955 364.205 1 95.97 ? O6 GDP 603 B 1 HETATM 24 N N1 GDP . . . P 3 170.875 313.71 365.121 1 96.44 ? N1 GDP 603 B 1 HETATM 25 C C2 GDP . . . P 3 171.503 312.531 365.253 1 96.05 ? C2 GDP 603 B 1 HETATM 26 N N2 GDP . . . P 3 172.568 312.449 366.081 1 95.29 ? N2 GDP 603 B 1 HETATM 27 N N3 GDP . . . P 3 171.125 311.413 364.595 1 96.73 ? N3 GDP 603 B 1 HETATM 28 C C4 GDP . . . P 3 170.08 311.43 363.748 1 95.81 ? C4 GDP 603 B 1 HETATM 29 H H5' GDP . . . P 3 171.269 306.079 365.773 1 105.32 ? H5' GDP 603 B 1 HETATM 30 H "H5''" GDP . . . P 3 170.328 307.471 366.313 1 105.32 ? "H5''" GDP 603 B 1 HETATM 31 H H4' GDP . . . P 3 170.155 306.458 363.828 1 105.24 ? H4' GDP 603 B 1 HETATM 32 H H3' GDP . . . P 3 172.67 307.959 363.845 1 105.82 ? H3' GDP 603 B 1 HETATM 33 H H2' GDP . . . P 3 171.879 309.826 362.86 1 107.13 ? H2' GDP 603 B 1 HETATM 34 H HO2' GDP . . . P 3 172.405 308.652 360.872 1 106.27 ? HO2' GDP 603 B 1 HETATM 35 H H1' GDP . . . P 3 169.245 308.621 362.081 1 109.51 ? H1' GDP 603 B 1 HETATM 36 H H8 GDP . . . P 3 167.785 310.617 361.661 1 115.58 ? H8 GDP 603 B 1 HETATM 37 H HN1 GDP . . . P 3 171.221 314.531 365.657 1 116.18 ? HN1 GDP 603 B 1 HETATM 38 H HN21 GDP . . . P 3 172.878 313.267 366.587 1 114.79 ? HN21 GDP 603 B 1 HETATM 39 H HN22 GDP . . . P 3 173.054 311.571 366.193 1 114.79 ? HN22 GDP 603 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #