data_4H54 # _model_server_result.job_id SDHscn8v_VLdAErbgFkCcQ _model_server_result.datetime_utc '2024-11-22 11:28:48' _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 4h54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":404}' # _entry.id 4H54 # _exptl.entry_id 4H54 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 120 _cell.entry_id 4H54 _cell.length_a 102.593 _cell.length_b 102.593 _cell.length_c 129.156 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4H54 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N ? 3 I N N ? 3 K 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 NE2 HIS 22 A HIS 22 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc2 A NE2 HIS 79 A HIS 79 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc3 A NE2 HIS 83 A HIS 83 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc4 A OD2 ASP 165 A ASP 165 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.727 ? metalc ? metalc5 A O ILE 166 A ILE 166 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc6 A OE2 GLU 208 A GLU 208 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc7 A OE1 GLU 208 A GLU 208 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc8 D O3G GAV . A GAV 402 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc9 D O2B GAV . A GAV 402 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc10 B NE2 HIS 22 B HIS 22 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc11 B NE2 HIS 79 B HIS 79 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc12 B NE2 HIS 83 B HIS 83 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc13 B OD2 ASP 165 B ASP 165 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc14 B O ILE 166 B ILE 166 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.677 ? metalc ? metalc15 B OE1 GLU 208 B GLU 208 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc16 B OE2 GLU 208 B GLU 208 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc17 I O2B GAV . B GAV 402 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc18 I O3B GAV . B GAV 402 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc19 I O3G GAV . B GAV 402 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.672 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GAV _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE" _chem_comp.type non-polymer _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 O6 C6 GAV doub 159 n n C6 C5 GAV sing 160 n n C5 C4 GAV doub 161 n y C4 N3 GAV sing 162 n n N3 C2 GAV doub 163 n n C2 N2 GAV sing 164 n n C6 N1 GAV sing 165 n n C2 N1 GAV sing 166 n n C5 N7 GAV sing 167 n y N7 C8 GAV doub 168 n y C4 N9 GAV sing 169 n y C8 N9 GAV sing 170 n y N9 C1' GAV sing 171 n n C1' C2' GAV sing 172 n n C2' O2' GAV sing 173 n n C2' C3' GAV sing 174 n n C3' O3' GAV sing 175 n n C1' O4' GAV sing 176 n n C3' C4' GAV sing 177 n n O4' C4' GAV sing 178 n n C4' C5' GAV sing 179 n n C5' O5' GAV sing 180 n n O5' PA GAV sing 181 n n PA S1A GAV sing 182 n n PA O2A GAV doub 183 n n PA O3A GAV sing 184 n n O3A PB GAV sing 185 n n PB O1B GAV sing 186 n n PB O2B GAV doub 187 n n PB O3B GAV sing 188 n n O3B PG GAV sing 189 n n PG O1G GAV sing 190 n n PG O3G GAV doub 191 n n PG O2G GAV sing 192 n n N1 H1 GAV sing 193 n n N2 H2N1 GAV sing 194 n n N2 H2N2 GAV sing 195 n n C8 H8 GAV sing 196 n n C1' H1' GAV sing 197 n n C2' H2' GAV sing 198 n n O2' HA GAV sing 199 n n C3' H3' GAV sing 200 n n O3' HB GAV sing 201 n n C4' H4' GAV sing 202 n n C5' "H5'1" GAV sing 203 n n C5' "H5'2" GAV sing 204 n n S1A H1A GAV sing 205 n n O1B H1B GAV sing 206 n n O1G H1G GAV sing 207 n n O2G H2G GAV sing 208 n n # _atom_sites.entry_id 4H54 _atom_sites.fract_transf_matrix[1][1] 0.009747 _atom_sites.fract_transf_matrix[1][2] 0.005628 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011255 _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] 0.007743 _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 2 ZN A 1 401 400 ZN ZN . D 3 GAV A 1 402 600 GAV GAV . E 4 MG A 1 403 601 MG MG . F 3 GAV A 1 404 700 GAV GAV . G 5 C2E A 1 405 701 C2E C2E . H 2 ZN B 1 401 400 ZN ZN . I 3 GAV B 1 402 600 GAV GAV . J 4 MG B 1 403 601 MG MG . K 3 GAV B 1 404 700 GAV GAV . # 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 O O6 GAV . . . F 3 35.382 -50.109 14.212 1 26.76 ? O6 GAV 404 A 1 HETATM 2 C C6 GAV . . . F 3 35.328 -51.338 14.091 1 29.65 ? C6 GAV 404 A 1 HETATM 3 C C5 GAV . . . F 3 34.478 -52.091 14.893 1 34.84 ? C5 GAV 404 A 1 HETATM 4 C C4 GAV . . . F 3 34.405 -53.472 14.765 1 39.96 ? C4 GAV 404 A 1 HETATM 5 N N3 GAV . . . F 3 35.177 -54.098 13.845 1 39.3 ? N3 GAV 404 A 1 HETATM 6 C C2 GAV . . . F 3 36.031 -53.363 13.036 1 32.72 ? C2 GAV 404 A 1 HETATM 7 N N2 GAV . . . F 3 36.788 -53.982 12.13 1 32.76 ? N2 GAV 404 A 1 HETATM 8 N N1 GAV . . . F 3 36.111 -51.986 13.159 1 28.51 ? N1 GAV 404 A 1 HETATM 9 N N7 GAV . . . F 3 33.63 -51.734 15.864 1 37.32 ? N7 GAV 404 A 1 HETATM 10 C C8 GAV . . . F 3 33.013 -52.827 16.352 1 46.12 ? C8 GAV 404 A 1 HETATM 11 N N9 GAV . . . F 3 33.486 -53.924 15.684 1 53.33 ? N9 GAV 404 A 1 HETATM 12 C C1' GAV . . . F 3 33.08 -55.323 15.942 1 97.75 ? C1' GAV 404 A 1 HETATM 13 C C2' GAV . . . F 3 34.173 -56.026 16.731 1 114.04 ? C2' GAV 404 A 1 HETATM 14 O O2' GAV . . . F 3 34.269 -57.374 16.34 1 120.41 ? O2' GAV 404 A 1 HETATM 15 C C3' GAV . . . F 3 33.755 -55.914 18.185 1 124.64 ? C3' GAV 404 A 1 HETATM 16 O O3' GAV . . . F 3 33.994 -57.107 18.896 1 232.12 ? O3' GAV 404 A 1 HETATM 17 O O4' GAV . . . F 3 31.935 -55.359 16.771 1 113.03 ? O4' GAV 404 A 1 HETATM 18 C C4' GAV . . . F 3 32.268 -55.586 18.133 1 128.82 ? C4' GAV 404 A 1 HETATM 19 C C5' GAV . . . F 3 31.885 -54.366 18.969 1 119.06 ? C5' GAV 404 A 1 HETATM 20 O O5' GAV . . . F 3 31.552 -54.732 20.29 1 144.25 ? O5' GAV 404 A 1 HETATM 21 P PA GAV . . . F 3 30.729 -53.716 21.233 1 137.42 ? PA GAV 404 A 1 HETATM 22 S S1A GAV . . . F 3 29.201 -54.347 21.654 1 216.41 ? S1A GAV 404 A 1 HETATM 23 O O2A GAV . . . F 3 30.606 -52.371 20.566 1 88.97 ? O2A GAV 404 A 1 HETATM 24 O O3A GAV . . . F 3 31.624 -53.603 22.568 1 142.85 ? O3A GAV 404 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 24 #