data_1FNM # _model_server_result.job_id 93DJkEvc4lNdZ4vmbIWraw _model_server_result.datetime_utc '2024-11-28 02:24:54' _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 1fnm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":900}' # _entry.id 1FNM # _exptl.entry_id 1FNM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 1FNM _cell.length_a 76.696 _cell.length_b 85.973 _cell.length_c 113.367 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1FNM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _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 3 _struct_asym.id C _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 metalc ? metalc1 A OG1 THR 26 A THR 26 1_555 B MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc2 A OE2 GLU 295 A GLU 295 3_655 B MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc3 C O3B GDP . A GDP 900 1_555 B MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? # _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 1FNM _atom_sites.fract_transf_matrix[1][1] 0.013038 _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] 0.011632 _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] 0.008821 _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 MG A 1 950 950 MG MG . C 3 GDP A 1 900 900 GDP GDP . D 4 HOH A 1 1001 1001 HOH HOH . D 4 HOH A 2 1002 1002 HOH HOH . D 4 HOH A 3 1003 1003 HOH HOH . D 4 HOH A 4 1004 1004 HOH HOH . D 4 HOH A 5 1005 1005 HOH HOH . D 4 HOH A 6 1006 1006 HOH HOH . D 4 HOH A 7 1007 1007 HOH HOH . D 4 HOH A 8 1008 1008 HOH HOH . D 4 HOH A 9 1009 1009 HOH HOH . D 4 HOH A 10 1010 1010 HOH HOH . D 4 HOH A 11 1011 1011 HOH HOH . D 4 HOH A 12 1012 1012 HOH HOH . D 4 HOH A 13 1013 1013 HOH HOH . D 4 HOH A 14 1014 1014 HOH HOH . D 4 HOH A 15 1015 1015 HOH HOH . D 4 HOH A 16 1016 1016 HOH HOH . D 4 HOH A 17 1017 1017 HOH HOH . D 4 HOH A 18 1018 1018 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 3 40.686 18.554 37.746 1 32.48 ? PB GDP 900 A 1 HETATM 2 O O1B GDP . . . C 3 39.233 18.635 37.89 1 32.48 ? O1B GDP 900 A 1 HETATM 3 O O2B GDP . . . C 3 41.356 17.65 38.675 1 32.48 ? O2B GDP 900 A 1 HETATM 4 O O3B GDP . . . C 3 41.117 18.198 36.366 1 32.48 ? O3B GDP 900 A 1 HETATM 5 O O3A GDP . . . C 3 41.239 20.015 38.083 1 32.48 ? O3A GDP 900 A 1 HETATM 6 P PA GDP . . . C 3 41.982 21.12 37.124 1 32.48 ? PA GDP 900 A 1 HETATM 7 O O1A GDP . . . C 3 41.08 21.522 36.033 1 32.48 ? O1A GDP 900 A 1 HETATM 8 O O2A GDP . . . C 3 43.288 20.571 36.735 1 32.48 ? O2A GDP 900 A 1 HETATM 9 O O5' GDP . . . C 3 42.163 22.249 38.213 1 32.48 ? O5' GDP 900 A 1 HETATM 10 C C5' GDP . . . C 3 41.026 22.946 38.768 1 32.48 ? C5' GDP 900 A 1 HETATM 11 C C4' GDP . . . C 3 41.339 24.412 39.022 1 32.48 ? C4' GDP 900 A 1 HETATM 12 O O4' GDP . . . C 3 42.475 24.458 39.933 1 32.48 ? O4' GDP 900 A 1 HETATM 13 C C3' GDP . . . C 3 41.764 25.158 37.773 1 32.48 ? C3' GDP 900 A 1 HETATM 14 O O3' GDP . . . C 3 41.288 26.498 37.971 1 32.48 ? O3' GDP 900 A 1 HETATM 15 C C2' GDP . . . C 3 43.301 25.016 37.845 1 32.48 ? C2' GDP 900 A 1 HETATM 16 O O2' GDP . . . C 3 43.997 26.006 37.066 1 32.48 ? O2' GDP 900 A 1 HETATM 17 C C1' GDP . . . C 3 43.572 25.157 39.337 1 32.48 ? C1' GDP 900 A 1 HETATM 18 N N9 GDP . . . C 3 44.855 24.5 39.725 1 32.48 ? N9 GDP 900 A 1 HETATM 19 C C8 GDP . . . C 3 45.385 23.262 39.347 1 32.48 ? C8 GDP 900 A 1 HETATM 20 N N7 GDP . . . C 3 46.558 22.977 39.867 1 32.48 ? N7 GDP 900 A 1 HETATM 21 C C5 GDP . . . C 3 46.823 24.104 40.643 1 32.48 ? C5 GDP 900 A 1 HETATM 22 C C6 GDP . . . C 3 47.929 24.434 41.463 1 32.48 ? C6 GDP 900 A 1 HETATM 23 O O6 GDP . . . C 3 48.962 23.759 41.673 1 32.48 ? O6 GDP 900 A 1 HETATM 24 N N1 GDP . . . C 3 47.81 25.67 42.088 1 32.48 ? N1 GDP 900 A 1 HETATM 25 C C2 GDP . . . C 3 46.73 26.537 41.955 1 32.48 ? C2 GDP 900 A 1 HETATM 26 N N2 GDP . . . C 3 46.764 27.686 42.622 1 32.48 ? N2 GDP 900 A 1 HETATM 27 N N3 GDP . . . C 3 45.671 26.25 41.179 1 32.48 ? N3 GDP 900 A 1 HETATM 28 C C4 GDP . . . C 3 45.774 25.037 40.564 1 32.48 ? C4 GDP 900 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #