data_6EGS # _model_server_result.job_id t3SK6Lyv04X80tUYohpXeg _model_server_result.datetime_utc '2024-11-14 04:50:05' _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 6egs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 6EGS # _exptl.entry_id 6EGS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 607.354 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE _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 6EGS _cell.length_a 154.036 _cell.length_b 154.036 _cell.length_c 109.823 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EGS _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # 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,D,G 1 1 B,E,F,H 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 D N N ? 3 F 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 disulf ? disulf1 A SG CYS 58 A CYS 126 1_555 A SG CYS 286 A CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf2 A SG CYS 277 A CYS 345 1_555 A SG CYS 355 A CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf3 A SG CYS 388 A CYS 456 1_555 A SG CYS 405 A CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 428 A CYS 496 1_555 A SG CYS 445 A CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf5 A SG CYS 471 A CYS 539 1_555 A SG CYS 487 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf6 B SG CYS 58 B CYS 126 1_555 B SG CYS 286 B CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf7 B SG CYS 277 B CYS 345 1_555 B SG CYS 355 B CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf8 B SG CYS 388 B CYS 456 1_555 B SG CYS 405 B CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf9 B SG CYS 428 B CYS 496 1_555 B SG CYS 445 B CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf10 B SG CYS 471 B CYS 539 1_555 B SG CYS 487 B CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc1 A OD2 ASP 156 A ASP 224 1_555 C MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc2 A NE2 HIS 158 A HIS 226 1_555 C MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc3 A NE2 HIS 291 A HIS 359 1_555 C MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc4 C MN MN . A MN 601 1_555 D O2B UD2 . A UD2 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc5 C MN MN . A MN 601 1_555 D O2A UD2 . A UD2 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc6 B OD2 ASP 156 B ASP 224 1_555 E MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc7 B NE2 HIS 158 B HIS 226 1_555 E MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc8 B NE2 HIS 291 B HIS 359 1_555 E MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc9 E MN MN . B MN 601 1_555 F O2A UD2 . B UD2 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc10 E MN MN . B MN 601 1_555 F O2B UD2 . B UD2 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? # _chem_comp.formula 'C17 H27 N3 O17 P2' _chem_comp.formula_weight 607.354 _chem_comp.id UD2 _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' # 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 O4 C4 UD2 doub 358 n n C4 N3 UD2 sing 359 n n C4 C5 UD2 sing 360 n n N3 C2 UD2 sing 361 n n C5 C6 UD2 doub 362 n n C2 O2 UD2 doub 363 n n C2 N1 UD2 sing 364 n n C6 N1 UD2 sing 365 n n N1 C1B UD2 sing 366 n n O2' C2B UD2 sing 367 n n C1B C2B UD2 sing 368 n n C1B O4B UD2 sing 369 n n C2B C3B UD2 sing 370 n n O2A PA UD2 doub 371 n n O4B C4B UD2 sing 372 n n O6' C6' UD2 sing 373 n n O5B PA UD2 sing 374 n n O5B C5B UD2 sing 375 n n C3B C4B UD2 sing 376 n n C3B O3B UD2 sing 377 n n PA O3A UD2 sing 378 n n PA O1A UD2 sing 379 n n C4B C5B UD2 sing 380 n n O3A PB UD2 sing 381 n n C6' C5' UD2 sing 382 n n O2B PB UD2 doub 383 n n C5' O5' UD2 sing 384 n n C5' C4' UD2 sing 385 n n PB O1B UD2 sing 386 n n PB O1' UD2 sing 387 n n O5' C1' UD2 sing 388 n n C4' O4' UD2 sing 389 n n C4' C3' UD2 sing 390 n n O1' C1' UD2 sing 391 n n C1' C2' UD2 sing 392 n n C3' C2' UD2 sing 393 n n C3' O3' UD2 sing 394 n n C2' N2' UD2 sing 395 n n N2' C7' UD2 sing 396 n n C7' O7' UD2 doub 397 n n C7' C8' UD2 sing 398 n n C1' H1' UD2 sing 399 n n C2' H2' UD2 sing 400 n n C3' H3' UD2 sing 401 n n C4' H4' UD2 sing 402 n n C5' H5' UD2 sing 403 n n C6' "H6'1" UD2 sing 404 n n C6' "H6'2" UD2 sing 405 n n C8' "H8'1" UD2 sing 406 n n C8' "H8'2" UD2 sing 407 n n C8' "H8'3" UD2 sing 408 n n N2' HN2' UD2 sing 409 n n O3' HO3' UD2 sing 410 n n O4' HO4' UD2 sing 411 n n O6' HO6' UD2 sing 412 n n N3 HN3 UD2 sing 413 n n C5 H5 UD2 sing 414 n n C6 H6 UD2 sing 415 n n C1B H1B UD2 sing 416 n n C2B H2B UD2 sing 417 n n O2' HO2' UD2 sing 418 n n C3B H3B UD2 sing 419 n n C4B H4B UD2 sing 420 n n O3B HO3A UD2 sing 421 n n C5B "H5'1" UD2 sing 422 n n C5B "H5'2" UD2 sing 423 n n O1A HOA2 UD2 sing 424 n n O1B HOB2 UD2 sing 425 n n # _atom_sites.entry_id 6EGS _atom_sites.fract_transf_matrix[1][1] 0.006492 _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] 0.006492 _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] 0.009106 _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 MN A 1 601 5600 MN MN . D 3 UD2 A 1 602 1573 UD2 UD2 . E 2 MN B 1 601 9600 MN MN . F 3 UD2 B 1 602 1573 UD2 UD2 . G 4 HOH A 1 701 180 HOH HOH . G 4 HOH A 2 702 187 HOH HOH . G 4 HOH A 3 703 117 HOH HOH . G 4 HOH A 4 704 82 HOH HOH . G 4 HOH A 5 705 135 HOH HOH . G 4 HOH A 6 706 124 HOH HOH . G 4 HOH A 7 707 30 HOH HOH . G 4 HOH A 8 708 181 HOH HOH . G 4 HOH A 9 709 24 HOH HOH . G 4 HOH A 10 710 52 HOH HOH . G 4 HOH A 11 711 104 HOH HOH . G 4 HOH A 12 712 16 HOH HOH . G 4 HOH A 13 713 119 HOH HOH . G 4 HOH A 14 714 89 HOH HOH . G 4 HOH A 15 715 31 HOH HOH . G 4 HOH A 16 716 29 HOH HOH . G 4 HOH A 17 717 27 HOH HOH . G 4 HOH A 18 718 53 HOH HOH . G 4 HOH A 19 719 116 HOH HOH . G 4 HOH A 20 720 110 HOH HOH . G 4 HOH A 21 721 28 HOH HOH . G 4 HOH A 22 722 127 HOH HOH . G 4 HOH A 23 723 108 HOH HOH . G 4 HOH A 24 724 81 HOH HOH . G 4 HOH A 25 725 179 HOH HOH . G 4 HOH A 26 726 178 HOH HOH . H 4 HOH B 1 701 130 HOH HOH . H 4 HOH B 2 702 102 HOH HOH . H 4 HOH B 3 703 14 HOH HOH . H 4 HOH B 4 704 34 HOH HOH . H 4 HOH B 5 705 137 HOH HOH . H 4 HOH B 6 706 57 HOH HOH . H 4 HOH B 7 707 40 HOH HOH . H 4 HOH B 8 708 168 HOH HOH . H 4 HOH B 9 709 101 HOH HOH . H 4 HOH B 10 710 182 HOH HOH . H 4 HOH B 11 711 49 HOH HOH . H 4 HOH B 12 712 79 HOH HOH . H 4 HOH B 13 713 39 HOH HOH . H 4 HOH B 14 714 56 HOH HOH . H 4 HOH B 15 715 91 HOH HOH . H 4 HOH B 16 716 177 HOH HOH . H 4 HOH B 17 717 97 HOH HOH . H 4 HOH B 18 718 96 HOH HOH . H 4 HOH B 19 719 44 HOH HOH . H 4 HOH B 20 720 185 HOH HOH . H 4 HOH B 21 721 19 HOH HOH . H 4 HOH B 22 722 8 HOH HOH . H 4 HOH B 23 723 3 HOH HOH . H 4 HOH B 24 724 10 HOH HOH . H 4 HOH B 25 725 184 HOH HOH . H 4 HOH B 26 726 65 HOH HOH . H 4 HOH B 27 727 33 HOH HOH . H 4 HOH B 28 728 161 HOH HOH . H 4 HOH B 29 729 122 HOH HOH . H 4 HOH B 30 730 188 HOH HOH . H 4 HOH B 31 731 68 HOH HOH . H 4 HOH B 32 732 21 HOH HOH . H 4 HOH B 33 733 186 HOH HOH . H 4 HOH B 34 734 183 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 C C1' UD2 . . . D 3 -10.693 -45.066 19.87 1 114.4 ? C1' UD2 602 A 1 HETATM 2 C C2' UD2 . . . D 3 -9.875 -46.368 19.811 1 119.47 ? C2' UD2 602 A 1 HETATM 3 C C3' UD2 . . . D 3 -8.521 -46.045 20.484 1 124.75 ? C3' UD2 602 A 1 HETATM 4 C C4' UD2 . . . D 3 -7.845 -44.975 19.598 1 128.69 ? C4' UD2 602 A 1 HETATM 5 C C5' UD2 . . . D 3 -8.687 -43.692 19.747 1 129.63 ? C5' UD2 602 A 1 HETATM 6 C C6' UD2 . . . D 3 -8.032 -42.458 19.115 1 127.26 ? C6' UD2 602 A 1 HETATM 7 C C7' UD2 . . . D 3 -11.037 -48.543 19.781 1 100.22 ? C7' UD2 602 A 1 HETATM 8 C C8' UD2 . . . D 3 -11.907 -49.466 20.56 1 95.49 ? C8' UD2 602 A 1 HETATM 9 N N2' UD2 . . . D 3 -10.656 -47.443 20.433 1 113.32 ? N2' UD2 602 A 1 HETATM 10 O O1' UD2 . . . D 3 -10.919 -44.824 21.259 1 94.28 ? O1' UD2 602 A 1 HETATM 11 O O3' UD2 . . . D 3 -7.662 -47.154 20.813 1 106.53 ? O3' UD2 602 A 1 HETATM 12 O O4' UD2 . . . D 3 -7.731 -45.362 18.208 1 108.78 ? O4' UD2 602 A 1 HETATM 13 O O5' UD2 . . . D 3 -10.015 -43.947 19.241 1 120.85 ? O5' UD2 602 A 1 HETATM 14 O O6' UD2 . . . D 3 -7.66 -41.497 20.126 1 123.26 ? O6' UD2 602 A 1 HETATM 15 O O7' UD2 . . . D 3 -10.719 -48.8 18.631 1 93.44 ? O7' UD2 602 A 1 HETATM 16 N N1 UD2 . . . D 3 -6.838 -41.086 26.88 1 94.37 ? N1 UD2 602 A 1 HETATM 17 C C2 UD2 . . . D 3 -5.551 -40.543 27.176 1 87.77 ? C2 UD2 602 A 1 HETATM 18 N N3 UD2 . . . D 3 -4.568 -41.328 27.558 1 81.1 ? N3 UD2 602 A 1 HETATM 19 C C4 UD2 . . . D 3 -4.757 -42.63 27.657 1 78.02 ? C4 UD2 602 A 1 HETATM 20 C C5 UD2 . . . D 3 -5.983 -43.228 27.377 1 79.23 ? C5 UD2 602 A 1 HETATM 21 C C6 UD2 . . . D 3 -7.033 -42.421 26.985 1 84.55 ? C6 UD2 602 A 1 HETATM 22 O O2 UD2 . . . D 3 -5.274 -39.325 27.104 1 94.13 ? O2 UD2 602 A 1 HETATM 23 O O4 UD2 . . . D 3 -3.768 -43.272 28.004 1 72.29 ? O4 UD2 602 A 1 HETATM 24 C C1B UD2 . . . D 3 -7.944 -40.168 26.467 1 108.81 ? C1B UD2 602 A 1 HETATM 25 C C2B UD2 . . . D 3 -8.122 -40.172 24.949 1 112.88 ? C2B UD2 602 A 1 HETATM 26 O O2' UD2 . . . D 3 -7.364 -39.138 24.313 1 119.36 ? O2' UD2 602 A 1 HETATM 27 C C3B UD2 . . . D 3 -9.623 -40.029 24.723 1 116.84 ? C3B UD2 602 A 1 HETATM 28 C C4B UD2 . . . D 3 -10.25 -40.564 26.013 1 114.09 ? C4B UD2 602 A 1 HETATM 29 O O4B UD2 . . . D 3 -9.24 -40.477 27.039 1 107.41 ? O4B UD2 602 A 1 HETATM 30 O O3B UD2 . . . D 3 -10.022 -38.675 24.448 1 120.12 ? O3B UD2 602 A 1 HETATM 31 C C5B UD2 . . . D 3 -10.785 -42.002 25.821 1 109.28 ? C5B UD2 602 A 1 HETATM 32 O O5B UD2 . . . D 3 -9.825 -42.813 25.13 1 96.45 ? O5B UD2 602 A 1 HETATM 33 P PA UD2 . . . D 3 -10.159 -43.892 23.999 1 81.94 ? PA UD2 602 A 1 HETATM 34 O O1A UD2 . . . D 3 -8.819 -44.279 23.408 1 68.47 ? O1A UD2 602 A 1 HETATM 35 O O2A UD2 . . . D 3 -10.946 -45.017 24.615 1 91.78 ? O2A UD2 602 A 1 HETATM 36 O O3A UD2 . . . D 3 -11.228 -43.114 23.046 1 85.96 ? O3A UD2 602 A 1 HETATM 37 P PB UD2 . . . D 3 -12.033 -43.869 21.844 1 82.73 ? PB UD2 602 A 1 HETATM 38 O O1B UD2 . . . D 3 -12.403 -42.907 20.758 1 92.14 ? O1B UD2 602 A 1 HETATM 39 O O2B UD2 . . . D 3 -13.083 -44.756 22.456 1 96.65 ? O2B UD2 602 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #