data_3AH8 # _model_server_result.job_id igkCTHwKjFDhKFrt91vgew _model_server_result.datetime_utc '2024-12-26 13:01:46' _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 3ah8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1}' # _entry.id 3AH8 # _exptl.entry_id 3AH8 _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 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 3AH8 _cell.length_a 173.336 _cell.length_b 173.336 _cell.length_c 60.946 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AH8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 D C ACE 1 Y ACE 1 1_555 D N HL2 2 Y HL2 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 D C HL2 2 Y HL2 2 1_555 D OH HL2 3 Y HL2 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 D C HL2 3 Y HL2 3 1_555 D N OTH 4 Y OTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale4 D N HL2 3 Y HL2 3 1_555 D C MAA 9 Y MAA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale5 D C OTH 4 Y OTH 4 1_555 D OG1 THC 5 Y THC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale6 D C THC 5 Y THC 5 1_555 D OA HF2 6 Y HF2 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale7 D C HF2 6 Y HF2 6 1_555 D N DAM 7 Y DAM 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 ? covale ? covale8 D C DAM 7 Y DAM 7 1_555 D N ALA 8 Y ALA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale9 D C ALA 8 Y ALA 8 1_555 D N MAA 9 Y MAA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? # _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 102 n n PB O2B GDP sing 103 n n PB O3B GDP sing 104 n n PB O3A GDP sing 105 n n O2B HOB2 GDP sing 106 n n O3B HOB3 GDP sing 107 n n O3A PA GDP sing 108 n n PA O1A GDP doub 109 n n PA O2A GDP sing 110 n n PA O5' GDP sing 111 n n O2A HOA2 GDP sing 112 n n O5' C5' GDP sing 113 n n C5' C4' GDP sing 114 n n C5' H5' GDP sing 115 n n C5' "H5''" GDP sing 116 n n C4' O4' GDP sing 117 n n C4' C3' GDP sing 118 n n C4' H4' GDP sing 119 n n O4' C1' GDP sing 120 n n C3' O3' GDP sing 121 n n C3' C2' GDP sing 122 n n C3' H3' GDP sing 123 n n O3' HO3' GDP sing 124 n n C2' O2' GDP sing 125 n n C2' C1' GDP sing 126 n n C2' H2' GDP sing 127 n n O2' HO2' GDP sing 128 n n C1' N9 GDP sing 129 n n C1' H1' GDP sing 130 n n N9 C8 GDP sing 131 n y N9 C4 GDP sing 132 n y C8 N7 GDP doub 133 n y C8 H8 GDP sing 134 n n N7 C5 GDP sing 135 n y C5 C6 GDP sing 136 n n C5 C4 GDP doub 137 n y C6 O6 GDP doub 138 n n C6 N1 GDP sing 139 n n N1 C2 GDP sing 140 n n N1 HN1 GDP sing 141 n n C2 N2 GDP sing 142 n n C2 N3 GDP doub 143 n n N2 HN21 GDP sing 144 n n N2 HN22 GDP sing 145 n n N3 C4 GDP sing 146 n n # _atom_sites.entry_id 3AH8 _atom_sites.fract_transf_matrix[1][1] 0.005769 _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] 0.005769 _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] 0.016408 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id E _pdbx_nonpoly_scheme.entity_id 5 _pdbx_nonpoly_scheme.mon_id GDP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id GDP _pdbx_nonpoly_scheme.auth_mon_id GDP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . E 5 19.675 -22.079 -32.93 1 91.77 ? PB GDP 1 A 1 HETATM 2 O O1B GDP . . . E 5 20.193 -23.498 -33.001 1 92.12 ? O1B GDP 1 A 1 HETATM 3 O O2B GDP . . . E 5 19.314 -21.805 -31.497 1 91.26 ? O2B GDP 1 A 1 HETATM 4 O O3B GDP . . . E 5 18.475 -21.914 -33.833 1 91.39 ? O3B GDP 1 A 1 HETATM 5 O O3A GDP . . . E 5 20.849 -21.08 -33.382 1 92.14 ? O3A GDP 1 A 1 HETATM 6 P PA GDP . . . E 5 20.835 -20.38 -34.821 1 91.63 ? PA GDP 1 A 1 HETATM 7 O O1A GDP . . . E 5 19.52 -20.631 -35.511 1 92.64 ? O1A GDP 1 A 1 HETATM 8 O O2A GDP . . . E 5 21.968 -20.86 -35.68 1 91.72 ? O2A GDP 1 A 1 HETATM 9 O O5' GDP . . . E 5 20.988 -18.822 -34.454 1 91.73 ? O5' GDP 1 A 1 HETATM 10 C C5' GDP . . . E 5 22.227 -18.257 -34.037 1 91.26 ? C5' GDP 1 A 1 HETATM 11 C C4' GDP . . . E 5 22.549 -17.014 -34.867 1 91.1 ? C4' GDP 1 A 1 HETATM 12 O O4' GDP . . . E 5 23.963 -16.806 -34.847 1 91.1 ? O4' GDP 1 A 1 HETATM 13 C C3' GDP . . . E 5 22.164 -17.162 -36.334 1 91.13 ? C3' GDP 1 A 1 HETATM 14 O O3' GDP . . . E 5 21.791 -15.887 -36.871 1 90.76 ? O3' GDP 1 A 1 HETATM 15 C C2' GDP . . . E 5 23.426 -17.608 -37.028 1 91.16 ? C2' GDP 1 A 1 HETATM 16 O O2' GDP . . . E 5 23.51 -17.042 -38.344 1 92.54 ? O2' GDP 1 A 1 HETATM 17 C C1' GDP . . . E 5 24.551 -17.144 -36.109 1 90.23 ? C1' GDP 1 A 1 HETATM 18 N N9 GDP . . . E 5 25.548 -18.226 -35.938 1 89.46 ? N9 GDP 1 A 1 HETATM 19 C C8 GDP . . . E 5 25.278 -19.519 -35.717 1 89.35 ? C8 GDP 1 A 1 HETATM 20 N N7 GDP . . . E 5 26.422 -20.237 -35.617 1 89.35 ? N7 GDP 1 A 1 HETATM 21 C C5 GDP . . . E 5 27.46 -19.405 -35.784 1 89.37 ? C5 GDP 1 A 1 HETATM 22 C C6 GDP . . . E 5 28.946 -19.516 -35.792 1 90.01 ? C6 GDP 1 A 1 HETATM 23 O O6 GDP . . . E 5 29.527 -20.619 -35.612 1 90.05 ? O6 GDP 1 A 1 HETATM 24 N N1 GDP . . . E 5 29.654 -18.393 -35.996 1 89.47 ? N1 GDP 1 A 1 HETATM 25 C C2 GDP . . . E 5 29.055 -17.199 -36.188 1 89.65 ? C2 GDP 1 A 1 HETATM 26 N N2 GDP . . . E 5 29.822 -16.104 -36.391 1 89.85 ? N2 GDP 1 A 1 HETATM 27 N N3 GDP . . . E 5 27.707 -17.033 -36.18 1 89.74 ? N3 GDP 1 A 1 HETATM 28 C C4 GDP . . . E 5 26.871 -18.077 -35.988 1 89.36 ? C4 GDP 1 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #