data_4EKC # _model_server_result.job_id sa-zFc7SENyFai30PO1pbg _model_server_result.datetime_utc '2024-11-21 23:52:52' _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 4ekc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":400}' # _entry.id 4EKC # _exptl.entry_id 4EKC _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 124.13 _cell.angle_gamma 90 _cell.entry_id 4EKC _cell.length_a 139.603 _cell.length_b 124.983 _cell.length_c 97.196 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EKC _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 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,B,E,F,G,K 1 1 C,D,H,I,J,L 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 ? 3 E N N ? 3 H 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 OG SER 41 A SER 53 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc2 A OG1 THR 174 A THR 186 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc3 E O2B GDP . A GDP 400 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc4 G MG MG . A MG 402 1_555 K O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.733 ? metalc ? metalc5 G MG MG . A MG 402 1_555 K O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc6 C OG SER 41 C SER 53 1_555 J MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc7 C OG1 THR 174 C THR 186 1_555 J MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc8 H O2B GDP . C GDP 400 1_555 J MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc9 J MG MG . C MG 402 1_555 L O HOH . C HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.783 ? metalc ? metalc10 J MG MG . C MG 402 1_555 L O HOH . C HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.866 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 4EKC _atom_sites.fract_transf_matrix[1][1] 0.007163 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004855 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008001 _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] 0.012429 _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 E 3 GDP A 1 400 400 GDP GDP . F 4 ALF A 1 401 401 ALF ALF . G 5 MG A 1 402 402 MG MG . H 3 GDP C 1 400 400 GDP GDP . I 4 ALF C 1 401 401 ALF ALF . J 5 MG C 1 402 402 MG MG . K 6 HOH A 1 501 403 HOH HOH . K 6 HOH A 2 502 404 HOH HOH . K 6 HOH A 3 503 405 HOH HOH . L 6 HOH C 1 501 403 HOH HOH . L 6 HOH C 2 502 404 HOH HOH . L 6 HOH C 3 503 405 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 . . . E 3 -11.734 10.25 26.348 1 62.66 ? PB GDP 400 A 1 HETATM 2 O O1B GDP . . . E 3 -12.833 9.315 26.785 1 62.27 ? O1B GDP 400 A 1 HETATM 3 O O2B GDP . . . E 3 -12.137 11.695 26.239 1 63.41 ? O2B GDP 400 A 1 HETATM 4 O O3B GDP . . . E 3 -10.425 10.042 27.052 1 61.36 ? O3B GDP 400 A 1 HETATM 5 O O3A GDP . . . E 3 -11.436 9.813 24.825 1 68.54 ? O3A GDP 400 A 1 HETATM 6 P PA GDP . . . E 3 -10.699 10.824 23.806 1 74.79 ? PA GDP 400 A 1 HETATM 7 O O1A GDP . . . E 3 -11.747 11.534 22.987 1 74.66 ? O1A GDP 400 A 1 HETATM 8 O O2A GDP . . . E 3 -9.705 11.641 24.595 1 74.58 ? O2A GDP 400 A 1 HETATM 9 O O5' GDP . . . E 3 -9.881 9.859 22.799 1 82.59 ? O5' GDP 400 A 1 HETATM 10 C C5' GDP . . . E 3 -8.943 8.894 23.285 1 90.34 ? C5' GDP 400 A 1 HETATM 11 C C4' GDP . . . E 3 -7.817 8.557 22.293 1 95.42 ? C4' GDP 400 A 1 HETATM 12 O O4' GDP . . . E 3 -8.242 7.496 21.43 1 100.5 ? O4' GDP 400 A 1 HETATM 13 C C3' GDP . . . E 3 -7.355 9.7 21.391 1 97.81 ? C3' GDP 400 A 1 HETATM 14 O O3' GDP . . . E 3 -5.923 9.78 21.398 1 96.09 ? O3' GDP 400 A 1 HETATM 15 C C2' GDP . . . E 3 -7.858 9.361 20 1 100.6 ? C2' GDP 400 A 1 HETATM 16 O O2' GDP . . . E 3 -6.87 9.625 18.998 1 100.31 ? O2' GDP 400 A 1 HETATM 17 C C1' GDP . . . E 3 -8.198 7.877 20.051 1 103.93 ? C1' GDP 400 A 1 HETATM 18 N N9 GDP . . . E 3 -9.503 7.556 19.405 1 108.88 ? N9 GDP 400 A 1 HETATM 19 C C8 GDP . . . E 3 -10.715 8.061 19.721 1 110.66 ? C8 GDP 400 A 1 HETATM 20 N N7 GDP . . . E 3 -11.682 7.528 18.926 1 111.35 ? N7 GDP 400 A 1 HETATM 21 C C5 GDP . . . E 3 -11.094 6.66 18.082 1 110.91 ? C5 GDP 400 A 1 HETATM 22 C C6 GDP . . . E 3 -11.521 5.753 16.984 1 109.92 ? C6 GDP 400 A 1 HETATM 23 O O6 GDP . . . E 3 -12.719 5.668 16.639 1 107.56 ? O6 GDP 400 A 1 HETATM 24 N N1 GDP . . . E 3 -10.583 5.017 16.366 1 110.4 ? N1 GDP 400 A 1 HETATM 25 C C2 GDP . . . E 3 -9.277 5.081 16.712 1 111.46 ? C2 GDP 400 A 1 HETATM 26 N N2 GDP . . . E 3 -8.369 4.321 16.055 1 111.75 ? N2 GDP 400 A 1 HETATM 27 N N3 GDP . . . E 3 -8.818 5.888 17.704 1 111.99 ? N3 GDP 400 A 1 HETATM 28 C C4 GDP . . . E 3 -9.659 6.682 18.409 1 111.11 ? C4 GDP 400 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #