data_5YLS # _model_server_result.job_id IHU3dS6AIscMGdesHjLrng _model_server_result.datetime_utc '2024-10-19 22:38:18' _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 5yls # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 5YLS # _exptl.entry_id 5YLS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 9 _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 5YLS _cell.length_a 105.767 _cell.length_b 159.054 _cell.length_c 183.151 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLS _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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,T,U,V,W,X,Y _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 9 _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 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.15 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc9 H MG MG . A MG 502 1_555 V O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 H MG MG . A MG 502 1_555 V O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc11 H MG MG . A MG 502 1_555 V O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc12 H MG MG . A MG 502 1_555 V O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc13 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc14 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc15 L MG MG . B MG 502 1_555 W O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc16 L MG MG . B MG 502 1_555 W O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc17 L MG MG . B MG 502 1_555 W O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc18 L MG MG . B MG 502 1_555 X O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc19 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc20 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc21 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc22 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc23 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc24 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc25 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc26 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc27 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc28 P MG MG . C MG 502 1_555 X O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc29 P MG MG . C MG 502 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc30 P MG MG . C MG 502 1_555 X O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc31 P MG MG . C MG 502 1_555 X O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? # _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 134 n n PB O2B GDP sing 135 n n PB O3B GDP sing 136 n n PB O3A GDP sing 137 n n O2B HOB2 GDP sing 138 n n O3B HOB3 GDP sing 139 n n O3A PA GDP sing 140 n n PA O1A GDP doub 141 n n PA O2A GDP sing 142 n n PA O5' GDP sing 143 n n O2A HOA2 GDP sing 144 n n O5' C5' GDP sing 145 n n C5' C4' GDP sing 146 n n C5' H5' GDP sing 147 n n C5' "H5''" GDP sing 148 n n C4' O4' GDP sing 149 n n C4' C3' GDP sing 150 n n C4' H4' GDP sing 151 n n O4' C1' GDP sing 152 n n C3' O3' GDP sing 153 n n C3' C2' GDP sing 154 n n C3' H3' GDP sing 155 n n O3' HO3' GDP sing 156 n n C2' O2' GDP sing 157 n n C2' C1' GDP sing 158 n n C2' H2' GDP sing 159 n n O2' HO2' GDP sing 160 n n C1' N9 GDP sing 161 n n C1' H1' GDP sing 162 n n N9 C8 GDP sing 163 n y N9 C4 GDP sing 164 n y C8 N7 GDP doub 165 n y C8 H8 GDP sing 166 n n N7 C5 GDP sing 167 n y C5 C6 GDP sing 168 n n C5 C4 GDP doub 169 n y C6 O6 GDP doub 170 n n C6 N1 GDP sing 171 n n N1 C2 GDP sing 172 n n N1 HN1 GDP sing 173 n n C2 N2 GDP sing 174 n n C2 N3 GDP doub 175 n n N2 HN21 GDP sing 176 n n N2 HN22 GDP sing 177 n n N3 C4 GDP sing 178 n n # _atom_sites.entry_id 5YLS _atom_sites.fract_transf_matrix[1][1] 0.009455 _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] 0.006287 _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] 0.00546 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GOL A 1 504 601 GOL GOL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 505 MES MES . N 11 Y50 B 1 504 1 Y50 Y50 . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 504 CA CA . R 5 GTP D 1 501 501 GTP GTP . S 6 MG D 1 502 502 MG MG . T 11 Y50 D 1 503 2 Y50 Y50 . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 11 HOH HOH . V 13 HOH A 2 602 2 HOH HOH . V 13 HOH A 3 603 1 HOH HOH . V 13 HOH A 4 604 3 HOH HOH . V 13 HOH A 5 605 4 HOH HOH . W 13 HOH B 1 601 17 HOH HOH . W 13 HOH B 2 602 18 HOH HOH . W 13 HOH B 3 603 10 HOH HOH . W 13 HOH B 4 604 12 HOH HOH . W 13 HOH B 5 605 15 HOH HOH . W 13 HOH B 6 606 16 HOH HOH . W 13 HOH B 7 607 13 HOH HOH . X 13 HOH C 1 601 5 HOH HOH . X 13 HOH C 2 602 6 HOH HOH . X 13 HOH C 3 603 7 HOH HOH . X 13 HOH C 4 604 8 HOH HOH . X 13 HOH C 5 605 14 HOH HOH . Y 13 HOH D 1 601 9 HOH HOH . Y 13 HOH D 2 602 19 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 . . . K 9 18.618 209.548 15.759 1 44.2 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . K 9 18.165 210.68 14.875 1 41.46 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . K 9 19.158 209.908 17.125 1 44.65 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . K 9 19.489 208.532 15.067 1 44.71 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . K 9 17.256 208.73 16.074 1 44.56 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . K 9 15.937 209.338 16.791 1 42.26 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . K 9 14.79 209.145 15.828 1 43.41 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . K 9 16.211 210.739 17.282 1 43.95 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . K 9 15.8 208.369 18.072 1 39.42 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . K 9 14.905 207.262 18.116 1 40.71 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . K 9 14.199 207.273 19.471 1 42.31 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . K 9 13.725 208.587 19.745 1 43.23 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . K 9 12.979 206.373 19.552 1 42.59 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . K 9 12.974 205.758 20.843 1 41.64 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . K 9 11.78 207.288 19.422 1 43.82 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . K 9 10.71 206.88 20.275 1 48.37 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . K 9 12.306 208.618 19.902 1 43.2 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . K 9 11.819 209.788 19.142 1 42.48 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . K 9 12.089 210.082 17.858 1 43.34 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . K 9 11.51 211.256 17.496 1 43.74 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . K 9 10.864 211.729 18.574 1 41.75 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . K 9 10.049 212.92 18.884 1 40.58 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . K 9 9.835 213.775 18 1 39.99 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . K 9 9.56 213.038 20.131 1 40.51 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . K 9 9.78 212.119 21.101 1 40.85 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . K 9 9.25 212.302 22.337 1 39.96 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . K 9 10.521 211.002 20.878 1 41.23 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . K 9 11.076 210.762 19.66 1 41.86 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #