data_4KV9 # _model_server_result.job_id FiAsaBX6PvdDe89I6eUuFQ _model_server_result.datetime_utc '2025-07-09 02:42:27' _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 4kv9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 4KV9 # _exptl.entry_id 4KV9 _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 112.17 _cell.angle_gamma 90 _cell.entry_id 4KV9 _cell.length_a 160.9 _cell.length_b 45.05 _cell.length_c 95.49 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KV9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 4KV9 _atom_sites.fract_transf_matrix[1][1] 0.006215 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002533 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022198 _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] 0.011308 _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 1 500 500 GDP GDP . D 2 GDP B 1 500 500 GDP GDP . E 3 HOH A 1 601 2 HOH HOH . E 3 HOH A 2 602 3 HOH HOH . E 3 HOH A 3 603 7 HOH HOH . E 3 HOH A 4 604 9 HOH HOH . E 3 HOH A 5 605 10 HOH HOH . E 3 HOH A 6 606 12 HOH HOH . E 3 HOH A 7 607 14 HOH HOH . E 3 HOH A 8 608 20 HOH HOH . E 3 HOH A 9 609 21 HOH HOH . E 3 HOH A 10 610 22 HOH HOH . E 3 HOH A 11 611 23 HOH HOH . E 3 HOH A 12 612 24 HOH HOH . E 3 HOH A 13 613 26 HOH HOH . E 3 HOH A 14 614 28 HOH HOH . E 3 HOH A 15 615 32 HOH HOH . E 3 HOH A 16 616 36 HOH HOH . E 3 HOH A 17 617 37 HOH HOH . E 3 HOH A 18 618 39 HOH HOH . E 3 HOH A 19 619 40 HOH HOH . E 3 HOH A 20 620 41 HOH HOH . E 3 HOH A 21 621 44 HOH HOH . E 3 HOH A 22 622 46 HOH HOH . E 3 HOH A 23 623 47 HOH HOH . E 3 HOH A 24 624 49 HOH HOH . E 3 HOH A 25 625 50 HOH HOH . E 3 HOH A 26 626 55 HOH HOH . E 3 HOH A 27 627 56 HOH HOH . E 3 HOH A 28 628 58 HOH HOH . E 3 HOH A 29 629 59 HOH HOH . E 3 HOH A 30 630 62 HOH HOH . E 3 HOH A 31 631 67 HOH HOH . E 3 HOH A 32 632 68 HOH HOH . E 3 HOH A 33 633 70 HOH HOH . E 3 HOH A 34 634 71 HOH HOH . E 3 HOH A 35 635 76 HOH HOH . E 3 HOH A 36 636 77 HOH HOH . E 3 HOH A 37 637 78 HOH HOH . E 3 HOH A 38 638 79 HOH HOH . E 3 HOH A 39 639 80 HOH HOH . E 3 HOH A 40 640 81 HOH HOH . E 3 HOH A 41 641 82 HOH HOH . E 3 HOH A 42 642 85 HOH HOH . E 3 HOH A 43 643 86 HOH HOH . E 3 HOH A 44 644 89 HOH HOH . E 3 HOH A 45 645 90 HOH HOH . E 3 HOH A 46 646 92 HOH HOH . E 3 HOH A 47 647 95 HOH HOH . E 3 HOH A 48 648 96 HOH HOH . E 3 HOH A 49 649 97 HOH HOH . E 3 HOH A 50 650 98 HOH HOH . E 3 HOH A 51 651 99 HOH HOH . E 3 HOH A 52 652 101 HOH HOH . E 3 HOH A 53 653 102 HOH HOH . E 3 HOH A 54 654 104 HOH HOH . E 3 HOH A 55 655 106 HOH HOH . E 3 HOH A 56 656 107 HOH HOH . E 3 HOH A 57 657 108 HOH HOH . E 3 HOH A 58 658 110 HOH HOH . E 3 HOH A 59 659 112 HOH HOH . E 3 HOH A 60 660 115 HOH HOH . E 3 HOH A 61 661 117 HOH HOH . E 3 HOH A 62 662 118 HOH HOH . E 3 HOH A 63 663 119 HOH HOH . E 3 HOH A 64 664 122 HOH HOH . E 3 HOH A 65 665 123 HOH HOH . E 3 HOH A 66 666 124 HOH HOH . E 3 HOH A 67 667 127 HOH HOH . E 3 HOH A 68 668 129 HOH HOH . E 3 HOH A 69 669 131 HOH HOH . E 3 HOH A 70 670 132 HOH HOH . F 3 HOH B 1 601 73 HOH HOH . F 3 HOH B 2 602 111 HOH HOH . F 3 HOH B 3 603 1 HOH HOH . F 3 HOH B 4 604 4 HOH HOH . F 3 HOH B 5 605 5 HOH HOH . F 3 HOH B 6 606 6 HOH HOH . F 3 HOH B 7 607 8 HOH HOH . F 3 HOH B 8 608 11 HOH HOH . F 3 HOH B 9 609 13 HOH HOH . F 3 HOH B 10 610 15 HOH HOH . F 3 HOH B 11 611 16 HOH HOH . F 3 HOH B 12 612 17 HOH HOH . F 3 HOH B 13 613 18 HOH HOH . F 3 HOH B 14 614 19 HOH HOH . F 3 HOH B 15 615 25 HOH HOH . F 3 HOH B 16 616 27 HOH HOH . F 3 HOH B 17 617 29 HOH HOH . F 3 HOH B 18 618 30 HOH HOH . F 3 HOH B 19 619 31 HOH HOH . F 3 HOH B 20 620 33 HOH HOH . F 3 HOH B 21 621 34 HOH HOH . F 3 HOH B 22 622 35 HOH HOH . F 3 HOH B 23 623 38 HOH HOH . F 3 HOH B 24 624 43 HOH HOH . F 3 HOH B 25 625 45 HOH HOH . F 3 HOH B 26 626 48 HOH HOH . F 3 HOH B 27 627 51 HOH HOH . F 3 HOH B 28 628 52 HOH HOH . F 3 HOH B 29 629 53 HOH HOH . F 3 HOH B 30 630 54 HOH HOH . F 3 HOH B 31 631 57 HOH HOH . F 3 HOH B 32 632 60 HOH HOH . F 3 HOH B 33 633 61 HOH HOH . F 3 HOH B 34 634 63 HOH HOH . F 3 HOH B 35 635 64 HOH HOH . F 3 HOH B 36 636 65 HOH HOH . F 3 HOH B 37 637 66 HOH HOH . F 3 HOH B 38 638 69 HOH HOH . F 3 HOH B 39 639 72 HOH HOH . F 3 HOH B 40 640 74 HOH HOH . F 3 HOH B 41 641 75 HOH HOH . F 3 HOH B 42 642 84 HOH HOH . F 3 HOH B 43 643 87 HOH HOH . F 3 HOH B 44 644 88 HOH HOH . F 3 HOH B 45 645 91 HOH HOH . F 3 HOH B 46 646 93 HOH HOH . F 3 HOH B 47 647 100 HOH HOH . F 3 HOH B 48 648 103 HOH HOH . F 3 HOH B 49 649 105 HOH HOH . F 3 HOH B 50 650 109 HOH HOH . F 3 HOH B 51 651 113 HOH HOH . F 3 HOH B 52 652 114 HOH HOH . F 3 HOH B 53 653 116 HOH HOH . F 3 HOH B 54 654 120 HOH HOH . F 3 HOH B 55 655 121 HOH HOH . F 3 HOH B 56 656 125 HOH HOH . F 3 HOH B 57 657 126 HOH HOH . F 3 HOH B 58 658 128 HOH HOH . F 3 HOH B 59 659 130 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 8.876 0.327 26.594 1 39.81 ? PB GDP 500 B 1 HETATM 2 O O1B GDP . . . D 2 9.996 1.264 26.939 1 39.56 ? O1B GDP 500 B 1 HETATM 3 O O2B GDP . . . D 2 7.809 1.059 25.82 1 46.32 ? O2B GDP 500 B 1 HETATM 4 O O3B GDP . . . D 2 9.345 -0.855 25.778 1 31.47 ? O3B GDP 500 B 1 HETATM 5 O O3A GDP . . . D 2 8.216 -0.381 27.884 1 39.63 ? O3A GDP 500 B 1 HETATM 6 P PA GDP . . . D 2 8.378 0.064 29.422 1 42.4 ? PA GDP 500 B 1 HETATM 7 O O1A GDP . . . D 2 9.787 -0.14 29.944 1 42.56 ? O1A GDP 500 B 1 HETATM 8 O O2A GDP . . . D 2 7.903 1.487 29.487 1 37.79 ? O2A GDP 500 B 1 HETATM 9 O O5' GDP . . . D 2 7.449 -1.034 30.1 1 41.96 ? O5' GDP 500 B 1 HETATM 10 C C5' GDP . . . D 2 6.061 -1.09 29.767 1 39.38 ? C5' GDP 500 B 1 HETATM 11 C C4' GDP . . . D 2 5.296 -1.832 30.845 1 36.6 ? C4' GDP 500 B 1 HETATM 12 O O4' GDP . . . D 2 5.712 -3.2 30.985 1 41.1 ? O4' GDP 500 B 1 HETATM 13 C C3' GDP . . . D 2 5.442 -1.182 32.2 1 43.18 ? C3' GDP 500 B 1 HETATM 14 O O3' GDP . . . D 2 4.183 -1.38 32.854 1 45.57 ? O3' GDP 500 B 1 HETATM 15 C C2' GDP . . . D 2 6.428 -2.089 32.877 1 39.88 ? C2' GDP 500 B 1 HETATM 16 O O2' GDP . . . D 2 6.241 -2.068 34.283 1 42.77 ? O2' GDP 500 B 1 HETATM 17 C C1' GDP . . . D 2 6.056 -3.448 32.346 1 37.73 ? C1' GDP 500 B 1 HETATM 18 N N9 GDP . . . D 2 7.237 -4.296 32.361 1 34.44 ? N9 GDP 500 B 1 HETATM 19 C C8 GDP . . . D 2 8.508 -3.86 32.14 1 33.89 ? C8 GDP 500 B 1 HETATM 20 N N7 GDP . . . D 2 9.36 -4.908 32.187 1 33.96 ? N7 GDP 500 B 1 HETATM 21 C C5 GDP . . . D 2 8.653 -6.02 32.437 1 30.59 ? C5 GDP 500 B 1 HETATM 22 C C6 GDP . . . D 2 8.955 -7.451 32.593 1 38.77 ? C6 GDP 500 B 1 HETATM 23 O O6 GDP . . . D 2 10.13 -7.871 32.525 1 37.39 ? O6 GDP 500 B 1 HETATM 24 N N1 GDP . . . D 2 7.935 -8.28 32.847 1 38.48 ? N1 GDP 500 B 1 HETATM 25 C C2 GDP . . . D 2 6.666 -7.855 32.904 1 33.57 ? C2 GDP 500 B 1 HETATM 26 N N2 GDP . . . D 2 5.69 -8.768 33.14 1 32.51 ? N2 GDP 500 B 1 HETATM 27 N N3 GDP . . . D 2 6.32 -6.561 32.766 1 32.75 ? N3 GDP 500 B 1 HETATM 28 C C4 GDP . . . D 2 7.249 -5.617 32.535 1 33.64 ? C4 GDP 500 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #