data_7DN9 # _model_server_result.job_id QQbfsxJRxNZgSP51rMPmmQ _model_server_result.datetime_utc '2024-11-25 20:30:34' _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 7dn9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":202}' # _entry.id 7DN9 # _exptl.entry_id 7DN9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.8 _cell.angle_gamma 90 _cell.entry_id 7DN9 _cell.length_a 104.711 _cell.length_b 105.576 _cell.length_c 105.839 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DN9 _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K 1 1 C,D,L,M,N 2 1 E,F,O,P,Q 3 1 G,H,R,S,T 4 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 ? 5 K N N ? 5 N N N ? 5 Q N N ? 5 T 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 B OG1 THR 32 B THR 48 1_555 J MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc2 J MG MG . B MG 201 1_555 K O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc3 M MG MG . D MG 201 1_555 N O1B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc4 F OG1 THR 32 F THR 48 1_555 P MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc5 P MG MG . F MG 201 1_555 Q O1B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc6 H OG1 THR 32 H THR 48 1_555 S MG MG . H MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc7 S MG MG . H MG 201 1_555 T O3B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc8 S MG MG . H MG 201 1_555 T O1B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? # _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 7DN9 _atom_sites.fract_transf_matrix[1][1] 0.00955 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002524 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009472 _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] 0.009773 _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 I 3 NAD A 1 401 401 NAD NAD . J 4 MG B 1 201 201 MG MG . K 5 GDP B 1 202 202 GDP GDP . L 3 NAD C 1 401 401 NAD NAD . M 4 MG D 1 201 201 MG MG . N 5 GDP D 1 202 202 GDP GDP . O 3 NAD E 1 401 401 NAD NAD . P 4 MG F 1 201 201 MG MG . Q 5 GDP F 1 202 202 GDP GDP . R 3 NAD G 1 401 401 NAD NAD . S 4 MG H 1 201 201 MG MG . T 5 GDP H 1 202 202 GDP GDP . # 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 . . . T 5 20.354 59.503 -39.045 1 34.04 ? PB GDP 202 H 1 HETATM 2 O O1B GDP . . . T 5 19.038 60.237 -38.962 1 37.82 ? O1B GDP 202 H 1 HETATM 3 O O2B GDP . . . T 5 21.411 60.281 -38.299 1 35.2 ? O2B GDP 202 H 1 HETATM 4 O O3B GDP . . . T 5 20.198 58.136 -38.423 1 40.85 ? O3B GDP 202 H 1 HETATM 5 O O3A GDP . . . T 5 20.8 59.348 -40.586 1 40.57 ? O3A GDP 202 H 1 HETATM 6 P PA GDP . . . T 5 19.944 58.445 -41.608 1 35.63 ? PA GDP 202 H 1 HETATM 7 O O1A GDP . . . T 5 20.358 56.997 -41.51 1 32.82 ? O1A GDP 202 H 1 HETATM 8 O O2A GDP . . . T 5 18.467 58.6 -41.343 1 46.06 ? O2A GDP 202 H 1 HETATM 9 O O5' GDP . . . T 5 20.328 59.031 -43.057 1 34.79 ? O5' GDP 202 H 1 HETATM 10 C C5' GDP . . . T 5 19.303 59.52 -43.918 1 42.45 ? C5' GDP 202 H 1 HETATM 11 C C4' GDP . . . T 5 19.79 59.537 -45.359 1 42.52 ? C4' GDP 202 H 1 HETATM 12 O O4' GDP . . . T 5 21.215 59.626 -45.408 1 45.99 ? O4' GDP 202 H 1 HETATM 13 C C3' GDP . . . T 5 19.393 58.269 -46.097 1 47.61 ? C3' GDP 202 H 1 HETATM 14 O O3' GDP . . . T 5 18.402 58.579 -47.081 1 56.66 ? O3' GDP 202 H 1 HETATM 15 C C2' GDP . . . T 5 20.656 57.771 -46.77 1 47.41 ? C2' GDP 202 H 1 HETATM 16 O O2' GDP . . . T 5 20.438 57.619 -48.177 1 56.76 ? O2' GDP 202 H 1 HETATM 17 C C1' GDP . . . T 5 21.703 58.841 -46.5 1 46.64 ? C1' GDP 202 H 1 HETATM 18 N N9 GDP . . . T 5 23.012 58.219 -46.172 1 39.7 ? N9 GDP 202 H 1 HETATM 19 C C8 GDP . . . T 5 23.35 57.644 -45.002 1 38.56 ? C8 GDP 202 H 1 HETATM 20 N N7 GDP . . . T 5 24.624 57.176 -45.039 1 33.91 ? N7 GDP 202 H 1 HETATM 21 C C5 GDP . . . T 5 25.122 57.452 -46.257 1 34.24 ? C5 GDP 202 H 1 HETATM 22 C C6 GDP . . . T 5 26.407 57.234 -46.963 1 40.12 ? C6 GDP 202 H 1 HETATM 23 O O6 GDP . . . T 5 27.362 56.659 -46.398 1 42.58 ? O6 GDP 202 H 1 HETATM 24 N N1 GDP . . . T 5 26.514 57.675 -48.223 1 37.75 ? N1 GDP 202 H 1 HETATM 25 C C2 GDP . . . T 5 25.504 58.3 -48.856 1 32.36 ? C2 GDP 202 H 1 HETATM 26 N N2 GDP . . . T 5 25.695 58.714 -50.13 1 32.57 ? N2 GDP 202 H 1 HETATM 27 N N3 GDP . . . T 5 24.301 58.533 -48.272 1 31.5 ? N3 GDP 202 H 1 HETATM 28 C C4 GDP . . . T 5 24.057 58.139 -46.999 1 35.01 ? C4 GDP 202 H 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #