data_5H7O # _model_server_result.job_id 3o-412j1qB5K9Z5MaNDJRg _model_server_result.datetime_utc '2024-11-26 11:14:03' _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 5h7o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 5H7O # _exptl.entry_id 5H7O _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 5H7O _cell.length_a 105.199 _cell.length_b 157.029 _cell.length_c 182.576 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5H7O _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.01 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc7 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.84 ? metalc ? metalc8 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc9 H MG MG . A MG 502 1_555 V O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc10 H MG MG . A MG 502 1_555 V O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc11 H MG MG . A MG 502 1_555 V O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc12 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc13 K O2A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc14 L MG MG . B MG 502 1_555 W O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc15 L MG MG . B MG 502 1_555 W O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc16 L MG MG . B MG 502 1_555 X O HOH . C HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc17 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc18 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc19 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? metalc ? metalc20 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc21 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc22 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc23 O O3G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc24 O O2B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc25 P MG MG . C MG 502 1_555 X O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc26 P MG MG . C MG 502 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc27 P MG MG . C MG 502 1_555 X O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc28 P MG MG . C MG 502 1_555 X O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc29 R O2G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc30 R O3G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc31 R O2B GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? # _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 188 n n PB O2B GDP sing 189 n n PB O3B GDP sing 190 n n PB O3A GDP sing 191 n n O2B HOB2 GDP sing 192 n n O3B HOB3 GDP sing 193 n n O3A PA GDP sing 194 n n PA O1A GDP doub 195 n n PA O2A GDP sing 196 n n PA O5' GDP sing 197 n n O2A HOA2 GDP sing 198 n n O5' C5' GDP sing 199 n n C5' C4' GDP sing 200 n n C5' H5' GDP sing 201 n n C5' "H5''" GDP sing 202 n n C4' O4' GDP sing 203 n n C4' C3' GDP sing 204 n n C4' H4' GDP sing 205 n n O4' C1' GDP sing 206 n n C3' O3' GDP sing 207 n n C3' C2' GDP sing 208 n n C3' H3' GDP sing 209 n n O3' HO3' GDP sing 210 n n C2' O2' GDP sing 211 n n C2' C1' GDP sing 212 n n C2' H2' GDP sing 213 n n O2' HO2' GDP sing 214 n n C1' N9 GDP sing 215 n n C1' H1' GDP sing 216 n n N9 C8 GDP sing 217 n y N9 C4 GDP sing 218 n y C8 N7 GDP doub 219 n y C8 H8 GDP sing 220 n n N7 C5 GDP sing 221 n y C5 C6 GDP sing 222 n n C5 C4 GDP doub 223 n y C6 O6 GDP doub 224 n n C6 N1 GDP sing 225 n n N1 C2 GDP sing 226 n n N1 HN1 GDP sing 227 n n C2 N2 GDP sing 228 n n C2 N3 GDP doub 229 n n N2 HN21 GDP sing 230 n n N2 HN22 GDP sing 231 n n N3 C4 GDP sing 232 n n # _atom_sites.entry_id 5H7O _atom_sites.fract_transf_matrix[1][1] 0.009506 _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] 0.006368 _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] 0.005477 _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 7Q7 B 1 504 1 7Q7 D01 . 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 7Q7 D 1 503 2 7Q7 D01 . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 8 HOH HOH . V 13 HOH A 2 602 2 HOH HOH . V 13 HOH A 3 603 3 HOH HOH . V 13 HOH A 4 604 5 HOH HOH . V 13 HOH A 5 605 4 HOH HOH . V 13 HOH A 6 606 1 HOH HOH . W 13 HOH B 1 601 16 HOH HOH . W 13 HOH B 2 602 17 HOH HOH . W 13 HOH B 3 603 15 HOH HOH . W 13 HOH B 4 604 21 HOH HOH . W 13 HOH B 5 605 12 HOH HOH . W 13 HOH B 6 606 13 HOH HOH . W 13 HOH B 7 607 20 HOH HOH . W 13 HOH B 8 608 11 HOH HOH . X 13 HOH C 1 601 24 HOH HOH . X 13 HOH C 2 602 25 HOH HOH . X 13 HOH C 3 603 23 HOH HOH . X 13 HOH C 4 604 22 HOH HOH . X 13 HOH C 5 605 19 HOH HOH . X 13 HOH C 6 606 14 HOH HOH . X 13 HOH C 7 607 18 HOH HOH . X 13 HOH C 8 608 7 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 -18.381 49.623 -15.827 1 29.44 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . K 9 -18.967 50.064 -17.148 1 29.88 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . K 9 -17.825 50.722 -14.959 1 29.4 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . K 9 -19.238 48.636 -15.083 1 28.84 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . K 9 -17.111 48.718 -16.251 1 28.6 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . K 9 -15.734 49.244 -16.908 1 26.69 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . K 9 -15.961 50.612 -17.506 1 28.16 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . K 9 -14.662 49.068 -15.868 1 27.64 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . K 9 -15.569 48.186 -18.11 1 27.17 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . K 9 -14.553 47.192 -18.185 1 28.66 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . K 9 -13.974 47.204 -19.592 1 29.8 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . K 9 -13.549 48.527 -19.909 1 30.26 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . K 9 -12.747 46.329 -19.745 1 30.32 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . K 9 -12.736 45.75 -21.056 1 30.78 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . K 9 -11.575 47.269 -19.565 1 30.99 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . K 9 -10.428 46.902 -20.345 1 32.91 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . K 9 -12.13 48.596 -20.029 1 30.41 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . K 9 -11.647 49.744 -19.23 1 30.41 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . K 9 -11.892 49.99 -17.93 1 30.82 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . K 9 -11.314 51.155 -17.543 1 31.07 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . K 9 -10.696 51.668 -18.618 1 30.46 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . K 9 -9.895 52.869 -18.918 1 30.54 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . K 9 -9.656 53.702 -18.023 1 30.22 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . K 9 -9.44 53.029 -20.173 1 30.9 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . K 9 -9.682 52.142 -21.163 1 30.51 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . K 9 -9.184 52.376 -22.404 1 30.26 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . K 9 -10.407 51.018 -20.952 1 30.02 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . K 9 -10.92 50.738 -19.728 1 30.27 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #