data_8DCA # _model_server_result.job_id yk-DQC6QbmrYn-We1mMjTg _model_server_result.datetime_utc '2024-11-16 02:20:53' _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 8dca # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 8DCA # _exptl.entry_id 8DCA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 8DCA _cell.length_a 81.161 _cell.length_b 138.864 _cell.length_c 149.877 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DCA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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,E,F,G,H,I,J,K,L,M,N,O,X 1 1 B,D,P,Q,R,S,T,U,V,W,Y 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 E N N ? 3 P N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C GLC 1 C 1 GLC A 502 SUC 2 n C FRU 2 C 2 FRU A 502 SUC 2 n D GLC 1 D 1 GLC B 502 SUC 2 n D FRU 2 D 2 FRU B 502 SUC # 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 covale ? covale1 C C1 GLC . C GLC 1 1_555 C O2 FRU . C FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale2 D C1 GLC . D GLC 1 1_555 D O2 FRU . D FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? metalc ? metalc1 A OD2 ASP 115 A ASP 95 1_555 O CO CO . A CO 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc2 A NE2 HIS 223 A HIS 203 1_555 O CO CO . A CO 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc3 A NE2 HIS 254 A HIS 234 1_555 N CO CO . A CO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc4 A NE2 HIS 349 A HIS 329 1_555 N CO CO . A CO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc5 E O1B GTP . A GTP 501 1_555 N CO CO . A CO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc6 E O2A GTP . A GTP 501 1_555 N CO CO . A CO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc7 E O3G GTP . A GTP 501 1_555 O CO CO . A CO 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc8 E O1B GTP . A GTP 501 1_555 O CO CO . A CO 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc9 N CO CO . A CO 510 1_555 X O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc10 B OD2 ASP 115 B ASP 95 1_555 V CO CO . B CO 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc11 B NE2 HIS 223 B HIS 203 1_555 V CO CO . B CO 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc12 B NE2 HIS 254 B HIS 234 1_555 W CO CO . B CO 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc13 B NE2 HIS 349 B HIS 329 1_555 W CO CO . B CO 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc14 P O1G GTP . B GTP 501 1_555 V CO CO . B CO 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc15 P O1B GTP . B GTP 501 1_555 V CO CO . B CO 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc16 P O1B GTP . B GTP 501 1_555 W CO CO . B CO 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc17 P O2A GTP . B GTP 501 1_555 W CO CO . B CO 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-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 PG O1G GTP doub 190 n n PG O2G GTP sing 191 n n PG O3G GTP sing 192 n n PG O3B GTP sing 193 n n O2G HOG2 GTP sing 194 n n O3G HOG3 GTP sing 195 n n O3B PB GTP sing 196 n n PB O1B GTP doub 197 n n PB O2B GTP sing 198 n n PB O3A GTP sing 199 n n O2B HOB2 GTP sing 200 n n O3A PA GTP sing 201 n n PA O1A GTP doub 202 n n PA O2A GTP sing 203 n n PA O5' GTP sing 204 n n O2A HOA2 GTP sing 205 n n O5' C5' GTP sing 206 n n C5' C4' GTP sing 207 n n C5' H5' GTP sing 208 n n C5' "H5''" GTP sing 209 n n C4' O4' GTP sing 210 n n C4' C3' GTP sing 211 n n C4' H4' GTP sing 212 n n O4' C1' GTP sing 213 n n C3' O3' GTP sing 214 n n C3' C2' GTP sing 215 n n C3' H3' GTP sing 216 n n O3' HO3' GTP sing 217 n n C2' O2' GTP sing 218 n n C2' C1' GTP sing 219 n n C2' H2' GTP sing 220 n n O2' HO2' GTP sing 221 n n C1' N9 GTP sing 222 n n C1' H1' GTP sing 223 n n N9 C8 GTP sing 224 n y N9 C4 GTP sing 225 n y C8 N7 GTP doub 226 n y C8 H8 GTP sing 227 n n N7 C5 GTP sing 228 n y C5 C6 GTP sing 229 n n C5 C4 GTP doub 230 n y C6 O6 GTP doub 231 n n C6 N1 GTP sing 232 n n N1 C2 GTP sing 233 n n N1 HN1 GTP sing 234 n n C2 N2 GTP sing 235 n n C2 N3 GTP doub 236 n n N2 HN21 GTP sing 237 n n N2 HN22 GTP sing 238 n n N3 C4 GTP sing 239 n n # _atom_sites.entry_id 8DCA _atom_sites.fract_transf_matrix[1][1] 0.012321 _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] 0.007201 _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] 0.006672 _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 E 3 GTP A 1 501 501 GTP GTP . F 4 GOL A 1 502 503 GOL GOL . G 5 SO4 A 1 503 3 SO4 SO4 . H 5 SO4 A 1 504 4 SO4 SO4 . I 5 SO4 A 1 505 8 SO4 SO4 . J 5 SO4 A 1 506 13 SO4 SO4 . K 5 SO4 A 1 507 14 SO4 SO4 . L 5 SO4 A 1 508 16 SO4 SO4 . M 5 SO4 A 1 509 17 SO4 SO4 . N 6 CO A 1 510 1 CO CO . O 6 CO A 1 511 2 CO CO . P 3 GTP B 1 501 501 GTP GTP . Q 5 SO4 B 1 502 1 SO4 SO4 . R 5 SO4 B 1 503 2 SO4 SO4 . S 5 SO4 B 1 504 12 SO4 SO4 . T 5 SO4 B 1 505 18 SO4 SO4 . U 5 SO4 B 1 506 19 SO4 SO4 . V 6 CO B 1 507 3 CO CO . W 6 CO B 1 508 4 CO CO . X 7 HOH A 1 601 22 HOH HOH . X 7 HOH A 2 602 5 HOH HOH . X 7 HOH A 3 603 2 HOH HOH . X 7 HOH A 4 604 11 HOH HOH . X 7 HOH A 5 605 14 HOH HOH . X 7 HOH A 6 606 25 HOH HOH . Y 7 HOH B 1 601 13 HOH HOH . Y 7 HOH B 2 602 24 HOH HOH . Y 7 HOH B 3 603 4 HOH HOH . Y 7 HOH B 4 604 26 HOH HOH . Y 7 HOH B 5 605 21 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 PG GTP . . . E 3 17.497 8.28 33.456 0.52 61.94 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . E 3 17.79 6.83 33.721 0.87 49.99 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . E 3 16.033 8.54 33.202 0.91 67.86 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . E 3 17.978 9.135 34.594 1 59.18 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . E 3 18.317 8.615 32.127 0.9 67.22 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . E 3 19.727 9.336 32.291 0.75 60.4 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . E 3 19.474 10.651 32.997 1 56.43 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . E 3 20.74 8.514 33.066 0.67 76.37 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . E 3 20.176 9.395 30.744 0.55 65.42 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . E 3 19.352 10.263 29.661 0.69 60.12 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . E 3 18.613 9.369 28.695 1 63.55 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . E 3 18.461 11.244 30.363 1 52.29 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . E 3 20.498 11.044 28.875 0.61 66.66 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . E 3 20.162 12.259 28.274 0.92 69.23 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . E 3 21.227 12.547 27.242 0.44 65.37 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . E 3 22.32 13.212 27.831 0.83 67.33 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . E 3 21.866 11.307 26.653 1 62.51 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . E 3 21.085 10.682 25.662 0.61 66.98 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . E 3 23.146 11.885 26.07 0.89 70.13 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . E 3 22.948 12.276 24.737 0.93 70.09 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . E 3 23.376 13.143 26.88 0.94 68.92 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . E 3 24.679 13.087 27.547 0.58 70.51 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . E 3 25.251 11.999 28.148 0.74 72.83 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . E 3 26.449 12.379 28.648 1 73.8 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . E 3 26.645 13.685 28.363 0.95 72.94 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . E 3 27.686 14.559 28.637 0.31 70.46 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . E 3 28.679 14.171 29.247 0.96 69.43 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . E 3 27.602 15.869 28.222 0.78 69.75 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . E 3 26.493 16.307 27.532 1 69.58 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . E 3 26.43 17.572 27.13 0.75 67.47 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . E 3 25.459 15.434 27.258 0.55 68.61 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . E 3 25.538 14.145 27.669 0.75 70.71 ? C4 GTP 501 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #