data_8DCB # _model_server_result.job_id SqrNaVP5b0plLFmR82CiMg _model_server_result.datetime_utc '2024-11-16 01:24:20' _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":"O","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 . . . O 3 41.629 -0.984 47.65 0.49 53.65 ? PG GTP 501 B 1 HETATM 2 O O1G GTP . . . O 3 41.586 -0.691 46.164 0.8 58.9 ? O1G GTP 501 B 1 HETATM 3 O O2G GTP . . . O 3 41.104 0.237 48.38 0.96 60.86 ? O2G GTP 501 B 1 HETATM 4 O O3G GTP . . . O 3 43.029 -1.272 48.106 0.74 55.59 ? O3G GTP 501 B 1 HETATM 5 O O3B GTP . . . O 3 40.764 -2.317 47.95 0.69 59.14 ? O3B GTP 501 B 1 HETATM 6 P PB GTP . . . O 3 39.616 -2.331 49.081 0.69 49.33 ? PB GTP 501 B 1 HETATM 7 O O1B GTP . . . O 3 40.14 -1.662 50.327 0.63 53.4 ? O1B GTP 501 B 1 HETATM 8 O O2B GTP . . . O 3 38.32 -1.684 48.636 0.7 66.13 ? O2B GTP 501 B 1 HETATM 9 O O3A GTP . . . O 3 39.401 -3.901 49.319 0.57 64.55 ? O3A GTP 501 B 1 HETATM 10 P PA GTP . . . O 3 40.612 -4.792 49.863 0.68 64.08 ? PA GTP 501 B 1 HETATM 11 O O1A GTP . . . O 3 40.952 -5.849 48.823 1 69.1 ? O1A GTP 501 B 1 HETATM 12 O O2A GTP . . . O 3 41.809 -3.962 50.258 0.16 61.45 ? O2A GTP 501 B 1 HETATM 13 O O5' GTP . . . O 3 39.96 -5.453 51.144 1 59.18 ? O5' GTP 501 B 1 HETATM 14 C C5' GTP . . . O 3 38.74 -6.099 50.904 0.37 69.57 ? C5' GTP 501 B 1 HETATM 15 C C4' GTP . . . O 3 38.566 -7.333 51.763 0.91 70.47 ? C4' GTP 501 B 1 HETATM 16 O O4' GTP . . . O 3 37.556 -7.064 52.716 0.82 66.31 ? O4' GTP 501 B 1 HETATM 17 C C3' GTP . . . O 3 38.049 -8.425 50.847 0.97 71.77 ? C3' GTP 501 B 1 HETATM 18 O O3' GTP . . . O 3 39.003 -9.448 50.676 0.8 79.76 ? O3' GTP 501 B 1 HETATM 19 C C2' GTP . . . O 3 36.802 -8.949 51.519 0 71.06 ? C2' GTP 501 B 1 HETATM 20 O O2' GTP . . . O 3 37.002 -10.253 51.967 0.96 60.54 ? O2' GTP 501 B 1 HETATM 21 C C1' GTP . . . O 3 36.6 -8.105 52.754 1 69.59 ? C1' GTP 501 B 1 HETATM 22 N N9 GTP . . . O 3 35.25 -7.535 52.74 0 72.57 ? N9 GTP 501 B 1 HETATM 23 C C8 GTP . . . O 3 34.573 -6.998 51.679 1 78.59 ? C8 GTP 501 B 1 HETATM 24 N N7 GTP . . . O 3 33.366 -6.584 52.115 0.94 79 ? N7 GTP 501 B 1 HETATM 25 C C5 GTP . . . O 3 33.26 -6.853 53.434 0.93 75.17 ? C5 GTP 501 B 1 HETATM 26 C C6 GTP . . . O 3 32.248 -6.631 54.356 0 74.04 ? C6 GTP 501 B 1 HETATM 27 O O6 GTP . . . O 3 31.189 -6.092 54.011 1 75.74 ? O6 GTP 501 B 1 HETATM 28 N N1 GTP . . . O 3 32.45 -7.033 55.662 1 63.66 ? N1 GTP 501 B 1 HETATM 29 C C2 GTP . . . O 3 33.642 -7.634 56.033 0 70.61 ? C2 GTP 501 B 1 HETATM 30 N N2 GTP . . . O 3 33.848 -8.013 57.288 0.97 64.07 ? N2 GTP 501 B 1 HETATM 31 N N3 GTP . . . O 3 34.642 -7.845 55.108 1 71.44 ? N3 GTP 501 B 1 HETATM 32 C C4 GTP . . . O 3 34.446 -7.458 53.832 1 73.11 ? C4 GTP 501 B 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 396 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 32 #