data_7EVH # _model_server_result.job_id 3lkMdxuhx2MBtLycYb4Fow _model_server_result.datetime_utc '2025-01-31 02:54:12' _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 7evh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7EVH # _exptl.entry_id 7EVH _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 1 _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 7EVH _cell.length_a 40.3 _cell.length_b 93.342 _cell.length_c 100.118 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EVH _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 7EVH _atom_sites.fract_transf_matrix[1][1] 0.024814 _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] 0.010713 _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] 0.009988 _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 B 2 GDP A 1 501 501 GDP GDP . C 3 PO4 A 1 502 501 PO4 PO4 . D 4 HOH A 1 601 25 HOH HOH . D 4 HOH A 2 602 3 HOH HOH . D 4 HOH A 3 603 9 HOH HOH . D 4 HOH A 4 604 44 HOH HOH . D 4 HOH A 5 605 8 HOH HOH . D 4 HOH A 6 606 43 HOH HOH . D 4 HOH A 7 607 5 HOH HOH . D 4 HOH A 8 608 17 HOH HOH . D 4 HOH A 9 609 26 HOH HOH . D 4 HOH A 10 610 34 HOH HOH . D 4 HOH A 11 611 16 HOH HOH . D 4 HOH A 12 612 15 HOH HOH . D 4 HOH A 13 613 4 HOH HOH . D 4 HOH A 14 614 28 HOH HOH . D 4 HOH A 15 615 32 HOH HOH . D 4 HOH A 16 616 11 HOH HOH . D 4 HOH A 17 617 35 HOH HOH . D 4 HOH A 18 618 45 HOH HOH . D 4 HOH A 19 619 7 HOH HOH . D 4 HOH A 20 620 10 HOH HOH . D 4 HOH A 21 621 41 HOH HOH . D 4 HOH A 22 622 1 HOH HOH . D 4 HOH A 23 623 27 HOH HOH . D 4 HOH A 24 624 23 HOH HOH . D 4 HOH A 25 625 36 HOH HOH . D 4 HOH A 26 626 29 HOH HOH . D 4 HOH A 27 627 2 HOH HOH . D 4 HOH A 28 628 19 HOH HOH . D 4 HOH A 29 629 33 HOH HOH . D 4 HOH A 30 630 14 HOH HOH . D 4 HOH A 31 631 30 HOH HOH . D 4 HOH A 32 632 18 HOH HOH . D 4 HOH A 33 633 13 HOH HOH . D 4 HOH A 34 634 12 HOH HOH . D 4 HOH A 35 635 6 HOH HOH . D 4 HOH A 36 636 21 HOH HOH . D 4 HOH A 37 637 31 HOH HOH . D 4 HOH A 38 638 22 HOH HOH . D 4 HOH A 39 639 20 HOH HOH . D 4 HOH A 40 640 42 HOH HOH . D 4 HOH A 41 641 38 HOH HOH . D 4 HOH A 42 642 37 HOH HOH . D 4 HOH A 43 643 24 HOH HOH . D 4 HOH A 44 644 40 HOH HOH . D 4 HOH A 45 645 39 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 . B 2 38.226 52.123 33.241 0.59 28.42 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . A . B 2 38.902 50.92 32.41 0.59 33.47 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . A . B 2 38.491 51.985 34.72 0.59 20.45 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . A . B 2 36.744 52.132 32.952 0.59 31.22 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . A . B 2 38.946 53.441 32.655 0.59 43.15 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . A . B 2 38.176 54.84 32.44 0.59 47.42 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . A . B 2 39.049 55.988 32.889 0.59 51.55 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . A . B 2 36.856 54.851 33.174 0.59 30.46 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . A . B 2 37.923 54.888 30.853 0.59 47.85 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . A . B 2 38.685 55.735 30.026 0.59 37.76 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . A . B 2 37.767 56.855 29.575 0.59 40.62 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . A . B 2 36.843 57.108 30.603 0.59 45.68 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . A . B 2 38.507 58.148 29.304 0.59 44.19 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . A . B 2 38.019 58.616 28.082 0.59 57.98 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . A . B 2 38.015 59.126 30.329 0.59 41.59 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . A . B 2 37.776 60.379 29.734 0.59 44.66 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . A . B 2 36.713 58.495 30.765 0.59 39.69 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . A . B 2 36.533 58.798 32.176 0.59 32.08 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . A . B 2 37.089 58.223 33.291 0.59 27.58 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . A . B 2 36.589 58.876 34.368 0.59 29.32 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . A . B 2 35.729 59.833 33.945 0.59 33.9 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . A . B 2 34.949 60.787 34.578 0.59 34.43 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . A . B 2 34.916 60.893 35.816 0.59 28.08 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . A . B 2 34.171 61.63 33.803 0.59 34 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . A . B 2 34.159 61.55 32.435 0.59 48.29 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . A . B 2 33.413 62.371 31.711 0.59 59.49 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . A . B 2 34.937 60.61 31.829 0.59 39.62 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . A . B 2 35.697 59.783 32.566 0.59 26.44 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #