data_6TIU # _model_server_result.job_id jdKZz--5tQzMZk6ysmEKRA _model_server_result.datetime_utc '2024-11-15 12:50:22' _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 6tiu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":503}' # _entry.id 6TIU # _exptl.entry_id 6TIU _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 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 6TIU _cell.length_a 65.97 _cell.length_b 126.35 _cell.length_c 249.79 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TIU _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 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,Q,R,S _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 7 _struct_asym.id K _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 F O1G GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 F O1B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc3 I O1B GTP . B GTP 501 1_555 J MG MG . B MG 502 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.823 ? metalc ? metalc4 N O1G GTP . C GTP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc5 N O1B GTP . C GTP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc6 P O1B GTP . D GTP 501 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? # _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 6TIU _atom_sites.fract_transf_matrix[1][1] 0.015158 _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] 0.007915 _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] 0.004003 _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 1 501 600 GTP GTP . G 5 MG A 1 502 601 MG MG . H 6 SO4 A 1 503 2 SO4 SO4 . I 4 GTP B 1 501 600 GTP GTP . J 5 MG B 1 502 601 MG MG . K 7 GDP B 1 503 700 GDP GDP . L 6 SO4 B 1 504 3 SO4 SO4 . M 6 SO4 B 1 505 9 SO4 SO4 . N 4 GTP C 1 600 600 GTP GTP . O 5 MG C 1 601 601 MG MG . P 4 GTP D 1 501 600 GTP GTP . Q 5 MG D 1 502 601 MG MG . R 6 SO4 D 1 503 1 SO4 SO4 . S 6 SO4 D 1 504 4 SO4 SO4 . # 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 . B . K 7 -5.173 82.931 91.238 0.5 67.4 ? PB GDP 503 B 1 HETATM 2 O O1B GDP . B . K 7 -5.394 83.717 90.025 0.5 68.51 ? O1B GDP 503 B 1 HETATM 3 O O2B GDP . B . K 7 -3.885 82.073 91.205 0.5 65.81 ? O2B GDP 503 B 1 HETATM 4 O O3B GDP . B . K 7 -6.298 81.96 91.579 0.5 73.08 ? O3B GDP 503 B 1 HETATM 5 O O3A GDP . B . K 7 -5.108 84.052 92.374 0.5 67.91 ? O3A GDP 503 B 1 HETATM 6 P PA GDP . B . K 7 -4.032 84.528 93.452 0.5 70.49 ? PA GDP 503 B 1 HETATM 7 O O1A GDP . B . K 7 -2.657 84.024 92.993 0.5 71.98 ? O1A GDP 503 B 1 HETATM 8 O O2A GDP . B . K 7 -4.022 86.008 93.613 0.5 70.14 ? O2A GDP 503 B 1 HETATM 9 O O5' GDP . B . K 7 -4.465 83.676 94.751 0.5 69.69 ? O5' GDP 503 B 1 HETATM 10 C C5' GDP . B . K 7 -3.839 83.73 96.047 0.5 68.39 ? C5' GDP 503 B 1 HETATM 11 C C4' GDP . B . K 7 -3.551 82.309 96.467 0.5 68.86 ? C4' GDP 503 B 1 HETATM 12 O O4' GDP . B . K 7 -2.439 81.795 95.705 0.5 65.76 ? O4' GDP 503 B 1 HETATM 13 C C3' GDP . B . K 7 -3.189 82.089 97.934 0.5 68.33 ? C3' GDP 503 B 1 HETATM 14 O O3' GDP . B . K 7 -3.717 80.868 98.45 0.5 71.14 ? O3' GDP 503 B 1 HETATM 15 C C2' GDP . B . K 7 -1.657 82.174 97.929 0.5 69.18 ? C2' GDP 503 B 1 HETATM 16 O O2' GDP . B . K 7 -1.024 81.401 98.947 0.5 67.99 ? O2' GDP 503 B 1 HETATM 17 C C1' GDP . B . K 7 -1.294 81.664 96.528 0.5 67.33 ? C1' GDP 503 B 1 HETATM 18 N N9 GDP . B . K 7 -0.195 82.417 95.912 0.5 68.58 ? N9 GDP 503 B 1 HETATM 19 C C8 GDP . B . K 7 -0.244 83.647 95.308 0.5 72.38 ? C8 GDP 503 B 1 HETATM 20 N N7 GDP . B . K 7 0.919 84.057 94.866 0.5 75.54 ? N7 GDP 503 B 1 HETATM 21 C C5 GDP . B . K 7 1.79 83.03 95.201 0.5 71.54 ? C5 GDP 503 B 1 HETATM 22 C C6 GDP . B . K 7 3.212 82.865 94.98 0.5 71.7 ? C6 GDP 503 B 1 HETATM 23 O O6 GDP . B . K 7 3.988 83.666 94.457 0.5 74.38 ? O6 GDP 503 B 1 HETATM 24 N N1 GDP . B . K 7 3.676 81.656 95.467 0.5 71.68 ? N1 GDP 503 B 1 HETATM 25 C C2 GDP . B . K 7 2.911 80.711 96.104 0.5 70.45 ? C2 GDP 503 B 1 HETATM 26 N N2 GDP . B . K 7 3.543 79.623 96.556 0.5 72.69 ? N2 GDP 503 B 1 HETATM 27 N N3 GDP . B . K 7 1.605 80.852 96.324 0.5 69.89 ? N3 GDP 503 B 1 HETATM 28 C C4 GDP . B . K 7 1.112 82.015 95.848 0.5 70.89 ? C4 GDP 503 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #