data_8G2J # _model_server_result.job_id tGYCWj0iGd69kfufLAAvfA _model_server_result.datetime_utc '2024-10-11 03:23:25' _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 8g2j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1001}' # _entry.id 8G2J # _exptl.entry_id 8G2J _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 566.302 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _entity.pdbx_number_of_molecules 3 _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 8G2J _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8G2J _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? _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 G N N ? 3 I N N ? 3 K N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 2 4 3 BGC BGC C1 O1 . O4 HO4 . sing 4 ? 2 5 4 BGC BGC C1 O1 . O4 HO4 . 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 D BGC 1 E 1 BGC E 1 BGC 2 n D BGC 2 E 2 BGC E 2 BGC 2 n D BGC 3 E 3 BGC E 3 BGC 2 n D BGC 4 E 4 BGC E 4 BGC 2 n D BGC 5 E 5 BGC E 5 BGC 2 n E BGC 1 A 1 BGC E 6 BGC 2 n E BGC 2 A 2 BGC E 7 BGC 2 n E BGC 3 A 3 BGC E 8 BGC 2 n E BGC 4 A 4 BGC E 9 BGC 2 n E BGC 5 A 5 BGC E 10 BGC 2 n F BGC 1 B 1 BGC E 11 BGC 2 n F BGC 2 B 2 BGC E 12 BGC 2 n F BGC 3 B 3 BGC E 13 BGC 2 n F BGC 4 B 4 BGC E 14 BGC 2 n F BGC 5 B 5 BGC E 15 BGC # 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 D O4 BGC . E BGC 1 1_555 D C1 BGC . E BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 D O4 BGC . E BGC 2 1_555 D C1 BGC . E BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 D O4 BGC . E BGC 3 1_555 D C1 BGC . E BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 D O4 BGC . E BGC 4 1_555 D C1 BGC . E BGC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 E O4 BGC . A BGC 1 1_555 E C1 BGC . A BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale6 E O4 BGC . A BGC 2 1_555 E C1 BGC . A BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale7 E O4 BGC . A BGC 3 1_555 E C1 BGC . A BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 E O4 BGC . A BGC 4 1_555 E C1 BGC . A BGC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 F O4 BGC . B BGC 1 1_555 F C1 BGC . B BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale10 F O4 BGC . B BGC 2 1_555 F C1 BGC . B BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale11 F O4 BGC . B BGC 3 1_555 F C1 BGC . B BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 F O4 BGC . B BGC 4 1_555 F C1 BGC . B BGC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 G O1B UPG . D UPG 1001 1_555 H MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc2 G O2B UPG . D UPG 1001 1_555 H MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc3 I O2B UPG . I UPG 1001 1_555 J MG MG . I MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc4 C OD2 ASP 475 C ASP 462 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 N1 C2 UPG sing 380 n n N1 C6 UPG sing 381 n n N1 C1C UPG sing 382 n n C2 N3 UPG sing 383 n n C2 O2 UPG doub 384 n n N3 C4 UPG sing 385 n n N3 HN3 UPG sing 386 n n C4 C5 UPG sing 387 n n C4 O4 UPG doub 388 n n C5 C6 UPG doub 389 n n C5 H5 UPG sing 390 n n C6 H6 UPG sing 391 n n C1C C2C UPG sing 392 n n C1C O4C UPG sing 393 n n C1C H1C UPG sing 394 n n C2C O2C UPG sing 395 n n C2C C3C UPG sing 396 n n C2C H2C UPG sing 397 n n O2C HO2C UPG sing 398 n n C3C C4C UPG sing 399 n n C3C O3C UPG sing 400 n n C3C H3C UPG sing 401 n n C4C O4C UPG sing 402 n n C4C C5C UPG sing 403 n n C4C H4C UPG sing 404 n n O3C HO3C UPG sing 405 n n C5C O5C UPG sing 406 n n C5C H5C1 UPG sing 407 n n C5C H5C2 UPG sing 408 n n O5C PA UPG sing 409 n n PA O1A UPG doub 410 n n PA O2A UPG sing 411 n n PA O3A UPG sing 412 n n O2A HOA2 UPG sing 413 n n O3A PB UPG sing 414 n n PB O1B UPG doub 415 n n PB O2B UPG sing 416 n n PB O3B UPG sing 417 n n O2B HOB2 UPG sing 418 n n O3B C1' UPG sing 419 n n C1' C2' UPG sing 420 n n C1' O5' UPG sing 421 n n C1' H1' UPG sing 422 n n C2' C3' UPG sing 423 n n C2' O2' UPG sing 424 n n C2' H2' UPG sing 425 n n C3' C4' UPG sing 426 n n C3' O3' UPG sing 427 n n C3' H3' UPG sing 428 n n C4' C5' UPG sing 429 n n C4' O4' UPG sing 430 n n C4' H4' UPG sing 431 n n C5' C6' UPG sing 432 n n C5' O5' UPG sing 433 n n C5' H5' UPG sing 434 n n C6' O6' UPG sing 435 n n C6' "H6'1" UPG sing 436 n n C6' "H6'2" UPG sing 437 n n O2' HO2' UPG sing 438 n n O3' HO3' UPG sing 439 n n O4' HO4' UPG sing 440 n n O6' HO6' UPG sing 441 n n # _atom_sites.entry_id 8G2J _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 3 UPG D 1 1001 1001 UPG UPG . H 4 MG D 1 1002 6 MG MG . I 3 UPG I 1 1001 1001 UPG UPG . J 4 MG I 1 1002 7 MG MG . K 3 UPG C 1 1001 1001 UPG UPG . L 4 MG C 1 1002 5 MG MG . # 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 N N1 UPG . . . I 3 166.912 131.297 110.575 1 76.66 ? N1 UPG 1001 I 1 HETATM 2 C C2 UPG . . . I 3 168.284 131.49 109.994 1 76.66 ? C2 UPG 1001 I 1 HETATM 3 N N3 UPG . . . I 3 169.319 130.412 110.132 1 76.66 ? N3 UPG 1001 I 1 HETATM 4 C C4 UPG . . . I 3 168.985 129.184 110.833 1 76.66 ? C4 UPG 1001 I 1 HETATM 5 C C5 UPG . . . I 3 167.616 129.003 111.411 1 76.66 ? C5 UPG 1001 I 1 HETATM 6 C C6 UPG . . . I 3 166.596 130.071 111.27 1 76.66 ? C6 UPG 1001 I 1 HETATM 7 O O2 UPG . . . I 3 168.564 132.516 109.408 1 76.66 ? O2 UPG 1001 I 1 HETATM 8 O O4 UPG . . . I 3 169.793 128.328 110.949 1 76.66 ? O4 UPG 1001 I 1 HETATM 9 C C1C UPG . . . I 3 165.989 132.255 110.456 1 76.66 ? C1C UPG 1001 I 1 HETATM 10 C C2C UPG . . . I 3 164.629 131.617 110.005 1 76.66 ? C2C UPG 1001 I 1 HETATM 11 O O2C UPG . . . I 3 163.795 131.88 108.838 1 76.66 ? O2C UPG 1001 I 1 HETATM 12 C C3C UPG . . . I 3 164.004 132.747 110.392 1 76.66 ? C3C UPG 1001 I 1 HETATM 13 C C4C UPG . . . I 3 164.492 133.112 111.916 1 76.66 ? C4C UPG 1001 I 1 HETATM 14 O O4C UPG . . . I 3 165.785 132.939 111.863 1 76.66 ? O4C UPG 1001 I 1 HETATM 15 O O3C UPG . . . I 3 164.295 133.835 109.51 1 76.66 ? O3C UPG 1001 I 1 HETATM 16 C C5C UPG . . . I 3 163.878 132.203 112.902 1 76.66 ? C5C UPG 1001 I 1 HETATM 17 O O5C UPG . . . I 3 164.79 131.984 113.97 1 76.66 ? O5C UPG 1001 I 1 HETATM 18 P PA UPG . . . I 3 164.451 130.744 115.07 1 76.66 ? PA UPG 1001 I 1 HETATM 19 O O1A UPG . . . I 3 165.31 130.921 116.31 1 76.66 ? O1A UPG 1001 I 1 HETATM 20 O O2A UPG . . . I 3 164.751 129.418 114.435 1 76.66 ? O2A UPG 1001 I 1 HETATM 21 O O3A UPG . . . I 3 162.842 130.791 115.495 1 76.66 ? O3A UPG 1001 I 1 HETATM 22 P PB UPG . . . I 3 162.114 132.127 116.226 1 76.66 ? PB UPG 1001 I 1 HETATM 23 O O1B UPG . . . I 3 161.806 131.806 117.652 1 76.66 ? O1B UPG 1001 I 1 HETATM 24 O O2B UPG . . . I 3 160.848 132.458 115.5 1 76.66 ? O2B UPG 1001 I 1 HETATM 25 O O3B UPG . . . I 3 163.149 133.422 116.151 1 76.66 ? O3B UPG 1001 I 1 HETATM 26 C C1' UPG . . . I 3 163.153 134.336 117.161 1 76.66 ? C1' UPG 1001 I 1 HETATM 27 C C2' UPG . . . I 3 162.104 135.406 116.875 1 76.66 ? C2' UPG 1001 I 1 HETATM 28 C C3' UPG . . . I 3 162.425 136.15 115.648 1 76.66 ? C3' UPG 1001 I 1 HETATM 29 C C4' UPG . . . I 3 163.806 136.732 115.689 1 76.66 ? C4' UPG 1001 I 1 HETATM 30 C C5' UPG . . . I 3 164.865 135.699 116.053 1 76.66 ? C5' UPG 1001 I 1 HETATM 31 C C6' UPG . . . I 3 166.189 136.422 116.305 1 76.66 ? C6' UPG 1001 I 1 HETATM 32 O O2' UPG . . . I 3 160.795 134.775 116.718 1 76.66 ? O2' UPG 1001 I 1 HETATM 33 O O3' UPG . . . I 3 161.445 137.248 115.479 1 76.66 ? O3' UPG 1001 I 1 HETATM 34 O O4' UPG . . . I 3 164.118 137.279 114.387 1 76.66 ? O4' UPG 1001 I 1 HETATM 35 O O5' UPG . . . I 3 164.517 134.931 117.258 1 76.66 ? O5' UPG 1001 I 1 HETATM 36 O O6' UPG . . . I 3 166.075 137.22 117.449 1 76.66 ? O6' UPG 1001 I 1 HETATM 37 H HN3 UPG . . . I 3 170.106 130.524 109.797 1 76.66 ? HN3 UPG 1001 I 1 HETATM 38 H H5 UPG . . . I 3 167.402 128.215 111.859 1 76.66 ? H5 UPG 1001 I 1 HETATM 39 H H6 UPG . . . I 3 165.746 129.951 111.632 1 76.66 ? H6 UPG 1001 I 1 HETATM 40 H H1C UPG . . . I 3 166.283 132.914 109.809 1 76.66 ? H1C UPG 1001 I 1 HETATM 41 H H2C UPG . . . I 3 165.189 131.377 109.251 1 76.66 ? H2C UPG 1001 I 1 HETATM 42 H HO2C UPG . . . I 3 163.297 131.207 108.688 1 76.66 ? HO2C UPG 1001 I 1 HETATM 43 H H3C UPG . . . I 3 163.048 132.582 110.399 1 76.66 ? H3C UPG 1001 I 1 HETATM 44 H H4C UPG . . . I 3 164.287 134.036 112.127 1 76.66 ? H4C UPG 1001 I 1 HETATM 45 H HO3C UPG . . . I 3 164.634 134.478 109.952 1 76.66 ? HO3C UPG 1001 I 1 HETATM 46 H H5C1 UPG . . . I 3 163.664 131.355 112.482 1 76.66 ? H5C1 UPG 1001 I 1 HETATM 47 H H5C2 UPG . . . I 3 163.066 132.606 113.247 1 76.66 ? H5C2 UPG 1001 I 1 HETATM 48 H H1' UPG . . . I 3 162.939 133.899 117.999 1 76.66 ? H1' UPG 1001 I 1 HETATM 49 H H2' UPG . . . I 3 162.075 136.024 117.622 1 76.66 ? H2' UPG 1001 I 1 HETATM 50 H H3' UPG . . . I 3 162.361 135.544 114.893 1 76.66 ? H3' UPG 1001 I 1 HETATM 51 H H4' UPG . . . I 3 163.828 137.444 116.347 1 76.66 ? H4' UPG 1001 I 1 HETATM 52 H H5' UPG . . . I 3 164.974 135.086 115.31 1 76.66 ? H5' UPG 1001 I 1 HETATM 53 H "H6'1" UPG . . . I 3 166.4 136.981 115.54 1 76.66 ? "H6'1" UPG 1001 I 1 HETATM 54 H "H6'2" UPG . . . I 3 166.895 135.769 116.431 1 76.66 ? "H6'2" UPG 1001 I 1 HETATM 55 H HO2' UPG . . . I 3 160.691 134.533 115.91 1 76.66 ? HO2' UPG 1001 I 1 HETATM 56 H HO3' UPG . . . I 3 161.626 137.875 116.024 1 76.66 ? HO3' UPG 1001 I 1 HETATM 57 H HO4' UPG . . . I 3 163.693 136.85 113.788 1 76.66 ? HO4' UPG 1001 I 1 HETATM 58 H HO6' UPG . . . I 3 165.671 136.788 118.059 1 76.66 ? HO6' UPG 1001 I 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 58 #