data_5CIT # _model_server_result.job_id MnvQuuMoSQB_7da3_difTA _model_server_result.datetime_utc '2025-03-04 08:01:44' _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 5cit # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5CIT # _exptl.entry_id 5CIT _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 96.95 _cell.angle_gamma 90 _cell.entry_id 5CIT _cell.length_a 58.01 _cell.length_b 59.23 _cell.length_c 64.77 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CIT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,D,G 1 1 B,E,F,H 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 E N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OG1 THR 24 A THR 24 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc2 C O2B GDP . A GDP 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc3 D MG MG . A MG 302 1_555 G O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc4 D MG MG . A MG 302 1_555 G O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc5 D MG MG . A MG 302 1_555 G O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc6 D MG MG . A MG 302 1_555 G O HOH . A HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.749 ? metalc ? metalc7 B OG1 THR 24 B THR 24 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc8 E O2B GDP . B GDP 301 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc9 F MG MG . B MG 302 1_555 H O HOH . B HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc10 F MG MG . B MG 302 1_555 H O HOH . B HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc11 F MG MG . B MG 302 1_555 H O HOH . B HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc12 F MG MG . B MG 302 1_555 H O HOH . B HOH 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? # _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 5CIT _atom_sites.fract_transf_matrix[1][1] 0.017238 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002103 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016883 _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] 0.015554 _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 1 301 301 GDP GDP . D 3 MG A 1 302 302 MG MG . E 2 GDP B 1 301 301 GDP GDP . F 3 MG B 1 302 302 MG MG . G 4 HOH A 1 401 82 HOH HOH . G 4 HOH A 2 402 49 HOH HOH . G 4 HOH A 3 403 19 HOH HOH . G 4 HOH A 4 404 13 HOH HOH . G 4 HOH A 5 405 76 HOH HOH . G 4 HOH A 6 406 81 HOH HOH . G 4 HOH A 7 407 34 HOH HOH . G 4 HOH A 8 408 9 HOH HOH . G 4 HOH A 9 409 17 HOH HOH . G 4 HOH A 10 410 66 HOH HOH . G 4 HOH A 11 411 68 HOH HOH . G 4 HOH A 12 412 3 HOH HOH . G 4 HOH A 13 413 67 HOH HOH . G 4 HOH A 14 414 45 HOH HOH . G 4 HOH A 15 415 71 HOH HOH . G 4 HOH A 16 416 64 HOH HOH . G 4 HOH A 17 417 16 HOH HOH . G 4 HOH A 18 418 20 HOH HOH . G 4 HOH A 19 419 53 HOH HOH . G 4 HOH A 20 420 44 HOH HOH . G 4 HOH A 21 421 33 HOH HOH . G 4 HOH A 22 422 40 HOH HOH . G 4 HOH A 23 423 6 HOH HOH . G 4 HOH A 24 424 25 HOH HOH . G 4 HOH A 25 425 10 HOH HOH . G 4 HOH A 26 426 5 HOH HOH . G 4 HOH A 27 427 47 HOH HOH . G 4 HOH A 28 428 18 HOH HOH . G 4 HOH A 29 429 80 HOH HOH . G 4 HOH A 30 430 39 HOH HOH . G 4 HOH A 31 431 43 HOH HOH . G 4 HOH A 32 432 11 HOH HOH . G 4 HOH A 33 433 56 HOH HOH . G 4 HOH A 34 434 60 HOH HOH . G 4 HOH A 35 435 1 HOH HOH . G 4 HOH A 36 436 46 HOH HOH . G 4 HOH A 37 437 21 HOH HOH . G 4 HOH A 38 438 65 HOH HOH . G 4 HOH A 39 439 57 HOH HOH . H 4 HOH B 1 401 4 HOH HOH . H 4 HOH B 2 402 72 HOH HOH . H 4 HOH B 3 403 55 HOH HOH . H 4 HOH B 4 404 37 HOH HOH . H 4 HOH B 5 405 48 HOH HOH . H 4 HOH B 6 406 38 HOH HOH . H 4 HOH B 7 407 75 HOH HOH . H 4 HOH B 8 408 30 HOH HOH . H 4 HOH B 9 409 42 HOH HOH . H 4 HOH B 10 410 23 HOH HOH . H 4 HOH B 11 411 51 HOH HOH . H 4 HOH B 12 412 59 HOH HOH . H 4 HOH B 13 413 54 HOH HOH . H 4 HOH B 14 414 15 HOH HOH . H 4 HOH B 15 415 84 HOH HOH . H 4 HOH B 16 416 77 HOH HOH . H 4 HOH B 17 417 52 HOH HOH . H 4 HOH B 18 418 70 HOH HOH . H 4 HOH B 19 419 2 HOH HOH . H 4 HOH B 20 420 73 HOH HOH . H 4 HOH B 21 421 35 HOH HOH . H 4 HOH B 22 422 32 HOH HOH . H 4 HOH B 23 423 31 HOH HOH . H 4 HOH B 24 424 8 HOH HOH . H 4 HOH B 25 425 14 HOH HOH . H 4 HOH B 26 426 58 HOH HOH . H 4 HOH B 27 427 24 HOH HOH . H 4 HOH B 28 428 26 HOH HOH . H 4 HOH B 29 429 50 HOH HOH . H 4 HOH B 30 430 87 HOH HOH . H 4 HOH B 31 431 28 HOH HOH . H 4 HOH B 32 432 29 HOH HOH . H 4 HOH B 33 433 36 HOH HOH . H 4 HOH B 34 434 83 HOH HOH . H 4 HOH B 35 435 22 HOH HOH . H 4 HOH B 36 436 74 HOH HOH . H 4 HOH B 37 437 85 HOH HOH . H 4 HOH B 38 438 7 HOH HOH . H 4 HOH B 39 439 27 HOH HOH . H 4 HOH B 40 440 12 HOH HOH . H 4 HOH B 41 441 69 HOH HOH . H 4 HOH B 42 442 86 HOH HOH . H 4 HOH B 43 443 62 HOH HOH . H 4 HOH B 44 444 79 HOH HOH . H 4 HOH B 45 445 63 HOH HOH . H 4 HOH B 46 446 61 HOH HOH . H 4 HOH B 47 447 41 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 . . . C 2 24.115 20.887 5.215 1 27.67 ? PB GDP 301 A 1 HETATM 2 O O1B GDP . . . C 2 24.137 21.878 3.982 1 30.27 ? O1B GDP 301 A 1 HETATM 3 O O2B GDP . . . C 2 25.549 20.678 5.672 1 26.85 ? O2B GDP 301 A 1 HETATM 4 O O3B GDP . . . C 2 23.345 19.68 4.913 1 27.02 ? O3B GDP 301 A 1 HETATM 5 O O3A GDP . . . C 2 23.445 21.718 6.372 1 24.11 ? O3A GDP 301 A 1 HETATM 6 P PA GDP . . . C 2 23.962 22.683 7.567 1 29.51 ? PA GDP 301 A 1 HETATM 7 O O1A GDP . . . C 2 24.965 23.64 7.053 1 29.3 ? O1A GDP 301 A 1 HETATM 8 O O2A GDP . . . C 2 24.548 21.844 8.749 1 27.23 ? O2A GDP 301 A 1 HETATM 9 O O5' GDP . . . C 2 22.709 23.446 8.105 1 30.9 ? O5' GDP 301 A 1 HETATM 10 C C5' GDP . . . C 2 21.765 24.191 7.282 1 34.04 ? C5' GDP 301 A 1 HETATM 11 C C4' GDP . . . C 2 20.943 25.127 8.171 1 34.12 ? C4' GDP 301 A 1 HETATM 12 O O4' GDP . . . C 2 20.023 24.375 8.963 1 28.96 ? O4' GDP 301 A 1 HETATM 13 C C3' GDP . . . C 2 21.773 25.922 9.145 1 36.96 ? C3' GDP 301 A 1 HETATM 14 O O3' GDP . . . C 2 21.19 27.213 9.352 1 40.3 ? O3' GDP 301 A 1 HETATM 15 C C2' GDP . . . C 2 21.592 25.188 10.457 1 34.09 ? C2' GDP 301 A 1 HETATM 16 O O2' GDP . . . C 2 21.722 26.009 11.609 1 35.32 ? O2' GDP 301 A 1 HETATM 17 C C1' GDP . . . C 2 20.18 24.693 10.338 1 33.84 ? C1' GDP 301 A 1 HETATM 18 N N9 GDP . . . C 2 20.008 23.389 11.08 1 31.8 ? N9 GDP 301 A 1 HETATM 19 C C8 GDP . . . C 2 20.767 22.281 10.98 1 29.23 ? C8 GDP 301 A 1 HETATM 20 N N7 GDP . . . C 2 20.28 21.284 11.769 1 28.11 ? N7 GDP 301 A 1 HETATM 21 C C5 GDP . . . C 2 19.144 21.781 12.353 1 31.39 ? C5 GDP 301 A 1 HETATM 22 C C6 GDP . . . C 2 18.159 21.33 13.344 1 30.46 ? C6 GDP 301 A 1 HETATM 23 O O6 GDP . . . C 2 18.181 20.189 13.8 1 27.18 ? O6 GDP 301 A 1 HETATM 24 N N1 GDP . . . C 2 17.132 22.14 13.714 1 33.96 ? N1 GDP 301 A 1 HETATM 25 C C2 GDP . . . C 2 17.049 23.407 13.254 1 36.81 ? C2 GDP 301 A 1 HETATM 26 N N2 GDP . . . C 2 16.004 24.161 13.695 1 38.96 ? N2 GDP 301 A 1 HETATM 27 N N3 GDP . . . C 2 17.97 23.91 12.376 1 35.21 ? N3 GDP 301 A 1 HETATM 28 C C4 GDP . . . C 2 19.01 23.175 11.92 1 29.05 ? C4 GDP 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #