data_3HKE # _model_server_result.job_id 2PgzakYKBJZIH_Xlie_PMQ _model_server_result.datetime_utc '2024-11-15 19:23:22' _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 3hke # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":600}' # _entry.id 3HKE # _exptl.entry_id 3HKE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 90 _cell.angle_gamma 120 _cell.entry_id 3HKE _cell.length_a 326.71 _cell.length_b 326.71 _cell.length_c 54.12 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HKE _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,G,H,I,J,K,L,M,N,O,P _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 ? 7 I N N ? 7 O 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 covale ? covale1 B SG CYS 239 B CYS 241 1_555 H CAQ T13 . B T13 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.788 ? covale ? covale2 D SG CYS 239 D CYS 241 1_555 N CAQ T13 . D T13 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.79 ? # _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 3HKE _atom_sites.fract_transf_matrix[1][1] 0.003061 _atom_sites.fract_transf_matrix[1][2] 0.001767 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003534 _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] 0.018477 _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 F 4 GTP A 1 600 600 GTP GTP . G 5 MG A 1 601 601 MG MG . H 6 T13 B 1 1241 241 T13 CTU . I 7 GDP B 1 600 600 GDP GDP . J 5 MG B 1 601 601 MG MG . K 6 T13 B 1 700 700 T13 T13 . L 4 GTP C 1 600 600 GTP GTP . M 5 MG C 1 601 601 MG MG . N 6 T13 D 1 1241 241 T13 CTU . O 7 GDP D 1 600 600 GDP GDP . P 6 T13 D 1 700 700 T13 T13 . # 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 . . . I 7 89.598 72.118 5.595 1 66.97 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . I 7 90.379 73.105 6.381 1 65.84 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . I 7 90.283 70.741 5.632 1 66.35 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . I 7 88.143 71.911 6.143 1 65.73 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . I 7 89.605 72.697 4.079 1 67.24 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . I 7 90.632 72.205 2.937 1 67.31 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . I 7 91.885 71.834 3.62 1 65.97 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . I 7 89.994 71.051 2.112 1 66.43 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . I 7 90.857 73.531 2.032 1 66.62 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . I 7 90.096 73.765 0.858 1 66.02 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . I 7 90.803 74.795 -0.026 1 65.76 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . I 7 92.195 74.656 0.112 1 65.34 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . I 7 90.517 74.634 -1.519 1 66.54 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . I 7 90.486 75.888 -2.161 1 67.57 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . I 7 91.703 73.922 -2.119 1 66.3 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . I 7 92.04 74.402 -3.414 1 66.46 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . I 7 92.796 74.131 -1.077 1 65.99 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . I 7 93.479 72.833 -0.826 1 65.79 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . I 7 92.906 71.669 -0.356 1 65.92 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . I 7 93.856 70.709 -0.263 1 65.8 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . I 7 95.027 71.246 -0.664 1 65.6 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . I 7 96.292 70.699 -0.769 1 65.73 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . I 7 96.367 69.473 -0.884 1 66.37 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . I 7 97.324 71.5 -1.223 1 65.06 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . I 7 97.083 72.814 -1.571 1 64.82 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . I 7 97.92 73.427 -2.384 1 65.07 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . I 7 95.824 73.344 -1.467 1 64.95 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . I 7 94.809 72.57 -1.028 1 65.43 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 28 #