data_4OR6 # _model_server_result.job_id X_v07fybggVdBzy_tjCPNw _model_server_result.datetime_utc '2024-11-26 02:39:23' _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 4or6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 4OR6 # _exptl.entry_id 4OR6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 4OR6 _cell.length_a 42.974 _cell.length_b 90.151 _cell.length_c 95.706 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OR6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D 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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 4OR6 _atom_sites.fract_transf_matrix[1][1] 0.02327 _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] 0.011093 _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] 0.010449 _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 GDP A 1 501 1 GDP GDP . D 2 GDP B 1 501 1 GDP GDP . E 3 HOH A 1 601 2 HOH HOH . E 3 HOH A 2 602 5 HOH HOH . E 3 HOH A 3 603 6 HOH HOH . E 3 HOH A 4 604 7 HOH HOH . E 3 HOH A 5 605 14 HOH HOH . E 3 HOH A 6 606 17 HOH HOH . E 3 HOH A 7 607 23 HOH HOH . E 3 HOH A 8 608 24 HOH HOH . E 3 HOH A 9 609 25 HOH HOH . E 3 HOH A 10 610 26 HOH HOH . E 3 HOH A 11 611 28 HOH HOH . E 3 HOH A 12 612 29 HOH HOH . E 3 HOH A 13 613 31 HOH HOH . E 3 HOH A 14 614 34 HOH HOH . E 3 HOH A 15 615 37 HOH HOH . E 3 HOH A 16 616 41 HOH HOH . E 3 HOH A 17 617 45 HOH HOH . E 3 HOH A 18 618 47 HOH HOH . E 3 HOH A 19 619 48 HOH HOH . E 3 HOH A 20 620 52 HOH HOH . E 3 HOH A 21 621 53 HOH HOH . E 3 HOH A 22 622 54 HOH HOH . E 3 HOH A 23 623 55 HOH HOH . E 3 HOH A 24 624 56 HOH HOH . E 3 HOH A 25 625 60 HOH HOH . E 3 HOH A 26 626 61 HOH HOH . E 3 HOH A 27 627 67 HOH HOH . E 3 HOH A 28 628 70 HOH HOH . E 3 HOH A 29 629 76 HOH HOH . E 3 HOH A 30 630 77 HOH HOH . E 3 HOH A 31 631 79 HOH HOH . E 3 HOH A 32 632 81 HOH HOH . E 3 HOH A 33 633 84 HOH HOH . E 3 HOH A 34 634 86 HOH HOH . E 3 HOH A 35 635 91 HOH HOH . E 3 HOH A 36 636 94 HOH HOH . E 3 HOH A 37 637 101 HOH HOH . E 3 HOH A 38 638 121 HOH HOH . E 3 HOH A 39 639 127 HOH HOH . E 3 HOH A 40 640 128 HOH HOH . E 3 HOH A 41 641 136 HOH HOH . E 3 HOH A 42 642 138 HOH HOH . E 3 HOH A 43 643 139 HOH HOH . E 3 HOH A 44 644 140 HOH HOH . E 3 HOH A 45 645 141 HOH HOH . E 3 HOH A 46 646 145 HOH HOH . E 3 HOH A 47 647 150 HOH HOH . E 3 HOH A 48 648 154 HOH HOH . E 3 HOH A 49 649 155 HOH HOH . E 3 HOH A 50 650 156 HOH HOH . E 3 HOH A 51 651 157 HOH HOH . E 3 HOH A 52 652 160 HOH HOH . E 3 HOH A 53 653 161 HOH HOH . E 3 HOH A 54 654 162 HOH HOH . E 3 HOH A 55 655 167 HOH HOH . E 3 HOH A 56 656 168 HOH HOH . E 3 HOH A 57 657 10 HOH HOH . E 3 HOH A 58 658 15 HOH HOH . E 3 HOH A 59 659 18 HOH HOH . E 3 HOH A 60 660 22 HOH HOH . E 3 HOH A 61 661 43 HOH HOH . E 3 HOH A 62 662 73 HOH HOH . E 3 HOH A 63 663 85 HOH HOH . E 3 HOH A 64 664 102 HOH HOH . E 3 HOH A 65 665 105 HOH HOH . E 3 HOH A 66 666 106 HOH HOH . E 3 HOH A 67 667 117 HOH HOH . E 3 HOH A 68 668 124 HOH HOH . E 3 HOH A 69 669 125 HOH HOH . E 3 HOH A 70 670 129 HOH HOH . E 3 HOH A 71 671 131 HOH HOH . E 3 HOH A 72 672 159 HOH HOH . E 3 HOH A 73 673 169 HOH HOH . E 3 HOH A 74 674 170 HOH HOH . E 3 HOH A 75 675 173 HOH HOH . F 3 HOH B 1 601 4 HOH HOH . F 3 HOH B 2 602 8 HOH HOH . F 3 HOH B 3 603 9 HOH HOH . F 3 HOH B 4 604 11 HOH HOH . F 3 HOH B 5 605 12 HOH HOH . F 3 HOH B 6 606 13 HOH HOH . F 3 HOH B 7 607 16 HOH HOH . F 3 HOH B 8 608 19 HOH HOH . F 3 HOH B 9 609 20 HOH HOH . F 3 HOH B 10 610 21 HOH HOH . F 3 HOH B 11 611 27 HOH HOH . F 3 HOH B 12 612 30 HOH HOH . F 3 HOH B 13 613 32 HOH HOH . F 3 HOH B 14 614 33 HOH HOH . F 3 HOH B 15 615 35 HOH HOH . F 3 HOH B 16 616 36 HOH HOH . F 3 HOH B 17 617 38 HOH HOH . F 3 HOH B 18 618 39 HOH HOH . F 3 HOH B 19 619 40 HOH HOH . F 3 HOH B 20 620 42 HOH HOH . F 3 HOH B 21 621 44 HOH HOH . F 3 HOH B 22 622 46 HOH HOH . F 3 HOH B 23 623 49 HOH HOH . F 3 HOH B 24 624 50 HOH HOH . F 3 HOH B 25 625 57 HOH HOH . F 3 HOH B 26 626 58 HOH HOH . F 3 HOH B 27 627 59 HOH HOH . F 3 HOH B 28 628 63 HOH HOH . F 3 HOH B 29 629 64 HOH HOH . F 3 HOH B 30 630 65 HOH HOH . F 3 HOH B 31 631 66 HOH HOH . F 3 HOH B 32 632 68 HOH HOH . F 3 HOH B 33 633 75 HOH HOH . F 3 HOH B 34 634 83 HOH HOH . F 3 HOH B 35 635 87 HOH HOH . F 3 HOH B 36 636 88 HOH HOH . F 3 HOH B 37 637 89 HOH HOH . F 3 HOH B 38 638 95 HOH HOH . F 3 HOH B 39 639 96 HOH HOH . F 3 HOH B 40 640 97 HOH HOH . F 3 HOH B 41 641 98 HOH HOH . F 3 HOH B 42 642 99 HOH HOH . F 3 HOH B 43 643 100 HOH HOH . F 3 HOH B 44 644 107 HOH HOH . F 3 HOH B 45 645 108 HOH HOH . F 3 HOH B 46 646 109 HOH HOH . F 3 HOH B 47 647 110 HOH HOH . F 3 HOH B 48 648 111 HOH HOH . F 3 HOH B 49 649 112 HOH HOH . F 3 HOH B 50 650 113 HOH HOH . F 3 HOH B 51 651 114 HOH HOH . F 3 HOH B 52 652 115 HOH HOH . F 3 HOH B 53 653 116 HOH HOH . F 3 HOH B 54 654 119 HOH HOH . F 3 HOH B 55 655 120 HOH HOH . F 3 HOH B 56 656 123 HOH HOH . F 3 HOH B 57 657 134 HOH HOH . F 3 HOH B 58 658 135 HOH HOH . F 3 HOH B 59 659 137 HOH HOH . F 3 HOH B 60 660 142 HOH HOH . F 3 HOH B 61 661 143 HOH HOH . F 3 HOH B 62 662 144 HOH HOH . F 3 HOH B 63 663 146 HOH HOH . F 3 HOH B 64 664 148 HOH HOH . F 3 HOH B 65 665 151 HOH HOH . F 3 HOH B 66 666 152 HOH HOH . F 3 HOH B 67 667 158 HOH HOH . F 3 HOH B 68 668 163 HOH HOH . F 3 HOH B 69 669 165 HOH HOH . F 3 HOH B 70 670 62 HOH HOH . F 3 HOH B 71 671 71 HOH HOH . F 3 HOH B 72 672 74 HOH HOH . F 3 HOH B 73 673 78 HOH HOH . F 3 HOH B 74 674 80 HOH HOH . F 3 HOH B 75 675 103 HOH HOH . F 3 HOH B 76 676 104 HOH HOH . F 3 HOH B 77 677 118 HOH HOH . F 3 HOH B 78 678 126 HOH HOH . F 3 HOH B 79 679 130 HOH HOH . F 3 HOH B 80 680 132 HOH HOH . F 3 HOH B 81 681 133 HOH HOH . F 3 HOH B 82 682 171 HOH HOH . F 3 HOH B 83 683 172 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 . . . D 2 22.381 -64.949 -0.596 1 28.5 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . D 2 22.588 -64.043 0.595 1 38.36 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . D 2 23.544 -65.904 -0.714 1 32.31 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . D 2 22.292 -64.116 -1.853 1 21.29 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . D 2 21.021 -65.791 -0.424 1 25.95 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . D 2 19.616 -65.069 -0.109 1 21.13 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . D 2 19.784 -63.934 0.873 1 28.14 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . D 2 18.6 -66.067 0.393 1 27.59 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . D 2 19.174 -64.516 -1.55 1 27.91 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . D 2 18.742 -65.434 -2.547 1 22.99 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . D 2 17.661 -64.787 -3.395 1 20.81 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . D 2 17.803 -65.234 -4.74 1 17.9 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . D 2 16.287 -65.225 -2.922 1 23.91 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . D 2 15.473 -64.07 -2.714 1 23.1 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . D 2 15.709 -66.055 -4.049 1 18.62 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . D 2 14.331 -65.736 -4.253 1 26.35 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . D 2 16.547 -65.671 -5.255 1 17.75 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . D 2 16.773 -66.825 -6.153 1 24.84 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . D 2 17.021 -68.097 -5.79 1 15.19 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . D 2 17.194 -68.885 -6.884 1 24.25 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . D 2 17.068 -68.1 -7.971 1 18.59 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . D 2 17.136 -68.28 -9.439 1 18.03 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . D 2 17.363 -69.404 -9.935 1 28.59 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . D 2 16.947 -67.203 -10.215 1 20.23 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . D 2 16.701 -65.98 -9.706 1 19.17 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . D 2 16.52 -64.938 -10.553 1 11.93 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . D 2 16.626 -65.744 -8.373 1 17.54 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . D 2 16.796 -66.745 -7.481 1 18.9 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #