data_6YV8 # _model_server_result.job_id mIB9bV0DTcVFEToFiQFWTQ _model_server_result.datetime_utc '2024-11-21 13:45:13' _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 6yv8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6YV8 # _exptl.entry_id 6YV8 _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 90 _cell.angle_gamma 90 _cell.entry_id 6YV8 _cell.length_a 50.998 _cell.length_b 107.644 _cell.length_c 164.418 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YV8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,D 1 1 B,E,F 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 C N N ? 3 E 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 disulf ? disulf1 A SG CYS 163 A CYS 163 1_555 A SG CYS 245 A CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? disulf ? disulf2 B SG CYS 162 B CYS 163 1_555 B SG CYS 244 B CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc1 A OD2 ASP 137 A ASP 137 1_555 D MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc2 C O1B GDP . A GDP 401 1_555 D MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc3 C O1A GDP . A GDP 401 1_555 D MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc4 B OD2 ASP 136 B ASP 137 1_555 F MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc5 E O2B GDP . B GDP 401 1_555 F MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc6 E O2A GDP . B GDP 401 1_555 F MN MN . B MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? # _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 6YV8 _atom_sites.fract_transf_matrix[1][1] 0.019609 _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] 0.00929 _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] 0.006082 _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 C 3 GDP A 1 401 500 GDP GDP . D 4 MN A 1 402 401 MN MN . E 3 GDP B 1 401 500 GDP GDP . F 4 MN B 1 402 401 MN MN . # 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 18.913 48.034 -25.276 1 119.21 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . C 3 17.829 48.486 -26.229 1 121.12 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . C 3 19.798 49.225 -25.004 1 119.28 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . C 3 18.307 47.499 -24.008 1 118.38 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . C 3 19.817 46.879 -25.942 1 88.73 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . C 3 19.104 45.615 -26.631 1 87.61 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . C 3 17.662 45.912 -26.974 1 78.59 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . C 3 19.212 44.429 -25.723 1 92.25 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . C 3 19.994 45.344 -27.949 1 88.99 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . C 3 19.841 46.19 -29.101 1 89.2 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . C 3 20.115 45.395 -30.366 1 95.17 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . C 3 21.418 44.826 -30.255 1 96.36 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . C 3 19.112 44.271 -30.474 1 98.63 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . C 3 18.639 44.17 -31.832 1 97.34 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . C 3 19.909 43.025 -30.162 1 99.23 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . C 3 19.493 41.924 -30.945 1 103.46 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . C 3 21.324 43.417 -30.515 1 98.27 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . C 3 22.321 42.699 -29.69 1 99.95 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . C 3 22.547 42.883 -28.374 1 96.89 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . C 3 23.559 42.088 -27.952 1 97.11 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . C 3 24.002 41.39 -29.011 1 101.61 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . C 3 25.048 40.376 -29.256 1 111.57 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . C 3 25.773 39.994 -28.309 1 120.86 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . C 3 25.186 39.887 -30.503 1 109.53 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . C 3 24.406 40.294 -31.523 1 104.42 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . C 3 24.601 39.754 -32.749 1 102.01 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . C 3 23.425 41.217 -31.363 1 98.86 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . C 3 23.185 41.791 -30.159 1 100.08 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #