data_8DCB # _model_server_result.job_id RrqlREsenrg_G7koRsrFVg _model_server_result.datetime_utc '2024-11-16 01:31:21' _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 8dcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 8DCB # _exptl.entry_id 8DCB _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 8DCB _cell.length_a 81.241 _cell.length_b 137.492 _cell.length_c 149.559 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DCB _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,Y 1 1 B,D,O,P,Q,R,S,T,U,V,W,X,Z 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 O 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 503 SUC 2 n C FRU 2 C 2 FRU A 503 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale2 D C1 GLC . D GLC 1 1_555 D O2 FRU . D FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? metalc ? metalc1 A OD2 ASP 115 A ASP 95 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc2 A SG CYS 118 A CYS 98 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc3 A SG CYS 118 A CYS 98 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc4 A NE2 HIS 223 A HIS 203 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc5 A NE2 HIS 254 A HIS 234 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc6 A NE2 HIS 349 A HIS 329 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc7 E O1B GTP . A GTP 501 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc8 E O2A GTP . A GTP 501 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc9 E O2G GTP . A GTP 501 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc10 E O1B GTP . A GTP 501 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc11 G NI NI . A NI 503 1_555 Y O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc12 B OD2 ASP 115 B ASP 95 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc13 B SG CYS 118 B CYS 98 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc14 B SG CYS 118 B CYS 98 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc15 B NE2 HIS 223 B HIS 203 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc16 B NE2 HIS 254 B HIS 234 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc17 B OE2 GLU 325 B GLU 305 1_555 R NI NI . B NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? metalc ? metalc18 B NE2 HIS 349 B HIS 329 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc19 O O2G GTP . B GTP 501 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc20 O O1B GTP . B GTP 501 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc21 O O1B GTP . B GTP 501 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc22 O O2A GTP . B GTP 501 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc23 Q NI NI . B NI 503 1_555 Z O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? # _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 8DCB _atom_sites.fract_transf_matrix[1][1] 0.012309 _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] 0.007273 _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] 0.006686 _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 1 502 502 GOL GOL . G 5 NI A 1 503 3 NI NI . H 5 NI A 1 504 4 NI NI . I 6 SO4 A 1 505 3 SO4 SO4 . J 6 SO4 A 1 506 4 SO4 SO4 . K 6 SO4 A 1 507 6 SO4 SO4 . L 6 SO4 A 1 508 8 SO4 SO4 . M 6 SO4 A 1 509 12 SO4 SO4 . N 7 CL A 1 510 2 CL CL . O 3 GTP B 1 501 501 GTP GTP . P 5 NI B 1 502 1 NI NI . Q 5 NI B 1 503 2 NI NI . R 5 NI B 1 504 5 NI NI . S 6 SO4 B 1 505 1 SO4 SO4 . T 6 SO4 B 1 506 2 SO4 SO4 . U 6 SO4 B 1 507 7 SO4 SO4 . V 6 SO4 B 1 508 15 SO4 SO4 . W 6 SO4 B 1 509 16 SO4 SO4 . X 7 CL B 1 510 3 CL CL . Y 8 HOH A 1 601 18 HOH HOH . Y 8 HOH A 2 602 5 HOH HOH . Y 8 HOH A 3 603 3 HOH HOH . Y 8 HOH A 4 604 2 HOH HOH . Y 8 HOH A 5 605 20 HOH HOH . Y 8 HOH A 6 606 22 HOH HOH . Y 8 HOH A 7 607 19 HOH HOH . Y 8 HOH A 8 608 15 HOH HOH . Z 8 HOH B 1 601 12 HOH HOH . Z 8 HOH B 2 602 1 HOH HOH . Z 8 HOH B 3 603 13 HOH HOH . Z 8 HOH B 4 604 14 HOH HOH . Z 8 HOH B 5 605 6 HOH HOH . Z 8 HOH B 6 606 21 HOH HOH . Z 8 HOH B 7 607 16 HOH HOH . Z 8 HOH B 8 608 23 HOH HOH . Z 8 HOH B 9 609 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 PG GTP . . . E 3 17.907 7.874 33.606 0.61 69.62 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . E 3 16.511 8.375 33.33 1 64.53 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . E 3 18.512 8.65 34.756 0.95 70.8 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . E 3 17.931 6.403 33.953 0.7 65.21 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . E 3 18.716 8.082 32.241 0 70.94 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . E 3 19.982 9.054 32.235 0.97 80.23 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . E 3 19.659 10.315 33.022 1 57.23 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . E 3 21.177 8.357 32.849 0.38 81.18 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . E 3 20.241 9.296 30.666 0 72.17 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . E 3 19.167 9.977 29.68 0.55 65.14 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . E 3 19.093 9.177 28.382 1 78.15 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . E 3 17.814 10.138 30.311 0.66 70.84 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . E 3 19.8 11.426 29.444 1 70.68 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . E 3 21.152 11.478 29.064 0 70.86 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . E 3 21.361 12.128 27.716 1 69.98 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . E 3 22.343 13.136 27.856 0.79 71.5 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . E 3 21.931 11.075 26.785 0.22 72.91 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . E 3 20.925 10.566 25.933 1 75.92 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . E 3 23.09 11.755 26.067 1 73.61 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . E 3 22.775 12.125 24.748 0.73 70.43 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . E 3 23.356 13.022 26.861 0.66 71.15 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . E 3 24.667 12.966 27.537 0.32 70.65 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . E 3 25.215 11.885 28.183 1 74.51 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . E 3 26.416 12.254 28.695 1 71.06 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . E 3 26.638 13.552 28.384 0.26 67.57 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . E 3 27.69 14.419 28.657 0.81 67.1 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . E 3 28.668 14.041 29.293 0.92 70.75 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . E 3 27.647 15.718 28.203 0.35 65.53 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . E 3 26.557 16.157 27.486 1 62.28 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . E 3 26.523 17.413 27.044 0.58 63.95 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . E 3 25.513 15.291 27.213 0.55 64.06 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . E 3 25.549 14.01 27.653 0.9 66.24 ? C4 GTP 501 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 32 #