data_6SVP # _model_server_result.job_id '_KS3VaSACZJuPZyv9NKhpw' _model_server_result.datetime_utc '2024-11-07 18:52:04' _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 6svp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":701}' # _entry.id 6SVP # _exptl.entry_id 6SVP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 607.354 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _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 6SVP _cell.length_a 152.628 _cell.length_b 152.628 _cell.length_c 166.526 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SVP _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 _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 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 ? 2 C N N ? 2 G 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 metalc ? metalc1 A O SER 461 A SER 455 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc2 A O ARG 462 A ARG 456 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc3 A O THR 464 A THR 458 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc4 C O2 UD1 . A UD1 701 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc5 B O SER 461 B SER 455 1_555 H MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc6 B O ARG 462 B ARG 456 1_555 H MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc7 B O THR 464 B THR 458 1_555 H MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc8 G O2 UD1 . B UD1 701 1_555 H MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? # _chem_comp.formula 'C17 H27 N3 O17 P2' _chem_comp.formula_weight 607.354 _chem_comp.id UD1 _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _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 C1' C2' UD1 sing 386 n n C1' O1' UD1 sing 387 n n C1' O5' UD1 sing 388 n n C1' H1' UD1 sing 389 n n C2' C3' UD1 sing 390 n n C2' N2' UD1 sing 391 n n C2' H2' UD1 sing 392 n n C3' C4' UD1 sing 393 n n C3' O3' UD1 sing 394 n n C3' H3' UD1 sing 395 n n C4' C5' UD1 sing 396 n n C4' O4' UD1 sing 397 n n C4' H4' UD1 sing 398 n n C5' C6' UD1 sing 399 n n C5' O5' UD1 sing 400 n n C5' H5' UD1 sing 401 n n C6' O6' UD1 sing 402 n n C6' "H6'1" UD1 sing 403 n n C6' "H6'2" UD1 sing 404 n n C7' C8' UD1 sing 405 n n C7' N2' UD1 sing 406 n n C7' O7' UD1 doub 407 n n C8' "H8'1" UD1 sing 408 n n C8' "H8'2" UD1 sing 409 n n C8' "H8'3" UD1 sing 410 n n N2' HN2' UD1 sing 411 n n O1' PB UD1 sing 412 n n O3' HO3' UD1 sing 413 n n O4' HO4' UD1 sing 414 n n O6' HO6' UD1 sing 415 n n N1 C2 UD1 sing 416 n n N1 C6 UD1 sing 417 n n N1 C1B UD1 sing 418 n n C2 N3 UD1 sing 419 n n C2 O2 UD1 doub 420 n n N3 C4 UD1 sing 421 n n N3 HN3 UD1 sing 422 n n C4 C5 UD1 sing 423 n n C4 O4 UD1 doub 424 n n C5 C6 UD1 doub 425 n n C5 H5 UD1 sing 426 n n C6 H6 UD1 sing 427 n n C1B C2B UD1 sing 428 n n C1B O4B UD1 sing 429 n n C1B H1B UD1 sing 430 n n C2B O2' UD1 sing 431 n n C2B C3B UD1 sing 432 n n C2B H2B UD1 sing 433 n n O2' HO2' UD1 sing 434 n n C3B C4B UD1 sing 435 n n C3B O3B UD1 sing 436 n n C3B H3B UD1 sing 437 n n C4B O4B UD1 sing 438 n n C4B C5B UD1 sing 439 n n C4B H4B UD1 sing 440 n n O3B HO3A UD1 sing 441 n n C5B O5B UD1 sing 442 n n C5B "H5'1" UD1 sing 443 n n C5B "H5'2" UD1 sing 444 n n O5B PA UD1 sing 445 n n PA O1A UD1 doub 446 n n PA O2A UD1 sing 447 n n PA O3A UD1 sing 448 n n O2A HOA2 UD1 sing 449 n n O3A PB UD1 sing 450 n n PB O1B UD1 doub 451 n n PB O2B UD1 sing 452 n n O2B HOB2 UD1 sing 453 n n # _atom_sites.entry_id 6SVP _atom_sites.fract_transf_matrix[1][1] 0.006552 _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] 0.006552 _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] 0.006005 _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 UD1 A 1 701 1 UD1 UD1 . D 3 MG A 1 702 2 MG MG . E 4 G6Q A 1 703 1 G6Q G6Q . F 5 GLU A 1 704 1 GLU GLU . G 2 UD1 B 1 701 3 UD1 UD1 . H 3 MG B 1 702 4 MG MG . I 4 G6Q B 1 703 2 G6Q G6Q . J 6 HOH A 1 801 59 HOH HOH . J 6 HOH A 2 802 1 HOH HOH . J 6 HOH A 3 803 55 HOH HOH . J 6 HOH A 4 804 39 HOH HOH . J 6 HOH A 5 805 2 HOH HOH . J 6 HOH A 6 806 109 HOH HOH . J 6 HOH A 7 807 4 HOH HOH . J 6 HOH A 8 808 8 HOH HOH . J 6 HOH A 9 809 60 HOH HOH . J 6 HOH A 10 810 17 HOH HOH . J 6 HOH A 11 811 73 HOH HOH . J 6 HOH A 12 812 58 HOH HOH . J 6 HOH A 13 813 36 HOH HOH . J 6 HOH A 14 814 54 HOH HOH . J 6 HOH A 15 815 52 HOH HOH . J 6 HOH A 16 816 13 HOH HOH . J 6 HOH A 17 817 21 HOH HOH . J 6 HOH A 18 818 50 HOH HOH . J 6 HOH A 19 819 47 HOH HOH . J 6 HOH A 20 820 27 HOH HOH . J 6 HOH A 21 821 37 HOH HOH . J 6 HOH A 22 822 15 HOH HOH . J 6 HOH A 23 823 33 HOH HOH . J 6 HOH A 24 824 83 HOH HOH . J 6 HOH A 25 825 44 HOH HOH . J 6 HOH A 26 826 6 HOH HOH . J 6 HOH A 27 827 139 HOH HOH . J 6 HOH A 28 828 49 HOH HOH . J 6 HOH A 29 829 11 HOH HOH . J 6 HOH A 30 830 5 HOH HOH . J 6 HOH A 31 831 61 HOH HOH . J 6 HOH A 32 832 32 HOH HOH . J 6 HOH A 33 833 56 HOH HOH . J 6 HOH A 34 834 31 HOH HOH . J 6 HOH A 35 835 70 HOH HOH . J 6 HOH A 36 836 121 HOH HOH . J 6 HOH A 37 837 3 HOH HOH . J 6 HOH A 38 838 101 HOH HOH . J 6 HOH A 39 839 81 HOH HOH . J 6 HOH A 40 840 23 HOH HOH . J 6 HOH A 41 841 67 HOH HOH . J 6 HOH A 42 842 76 HOH HOH . J 6 HOH A 43 843 66 HOH HOH . J 6 HOH A 44 844 20 HOH HOH . J 6 HOH A 45 845 92 HOH HOH . J 6 HOH A 46 846 79 HOH HOH . K 6 HOH B 1 801 34 HOH HOH . K 6 HOH B 2 802 18 HOH HOH . K 6 HOH B 3 803 120 HOH HOH . K 6 HOH B 4 804 38 HOH HOH . K 6 HOH B 5 805 7 HOH HOH . K 6 HOH B 6 806 118 HOH HOH . K 6 HOH B 7 807 14 HOH HOH . K 6 HOH B 8 808 29 HOH HOH . K 6 HOH B 9 809 110 HOH HOH . K 6 HOH B 10 810 63 HOH HOH . K 6 HOH B 11 811 22 HOH HOH . K 6 HOH B 12 812 19 HOH HOH . K 6 HOH B 13 813 74 HOH HOH . K 6 HOH B 14 814 71 HOH HOH . K 6 HOH B 15 815 46 HOH HOH . K 6 HOH B 16 816 41 HOH HOH . K 6 HOH B 17 817 62 HOH HOH . K 6 HOH B 18 818 85 HOH HOH . K 6 HOH B 19 819 43 HOH HOH . K 6 HOH B 20 820 107 HOH HOH . K 6 HOH B 21 821 132 HOH HOH . K 6 HOH B 22 822 12 HOH HOH . K 6 HOH B 23 823 48 HOH HOH . K 6 HOH B 24 824 129 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' UD1 . . . G 2 10.499 6.848 27.533 1 84.75 ? C1' UD1 701 B 1 HETATM 2 C C2' UD1 . . . G 2 10.884 6.646 28.99 1 88.99 ? C2' UD1 701 B 1 HETATM 3 C C3' UD1 . . . G 2 10.763 5.219 29.38 1 90.77 ? C3' UD1 701 B 1 HETATM 4 C C4' UD1 . . . G 2 9.419 4.645 29.053 1 90.53 ? C4' UD1 701 B 1 HETATM 5 C C5' UD1 . . . G 2 8.979 4.939 27.615 1 90.67 ? C5' UD1 701 B 1 HETATM 6 C C6' UD1 . . . G 2 7.552 4.524 27.442 1 92.74 ? C6' UD1 701 B 1 HETATM 7 C C7' UD1 . . . G 2 12.67 7.853 30.346 1 94.35 ? C7' UD1 701 B 1 HETATM 8 C C8' UD1 . . . G 2 14.111 8.301 30.535 1 94.33 ? C8' UD1 701 B 1 HETATM 9 N N2' UD1 . . . G 2 12.296 7.087 29.177 1 91.03 ? N2' UD1 701 B 1 HETATM 10 O O1' UD1 . . . G 2 11.361 6.135 26.759 1 75.84 ? O1' UD1 701 B 1 HETATM 11 O O3' UD1 . . . G 2 10.981 5.101 30.812 1 91.65 ? O3' UD1 701 B 1 HETATM 12 O O4' UD1 . . . G 2 9.482 3.228 29.224 1 91.48 ? O4' UD1 701 B 1 HETATM 13 O O5' UD1 . . . G 2 9.105 6.366 27.275 1 88.72 ? O5' UD1 701 B 1 HETATM 14 O O6' UD1 . . . G 2 7.328 4.181 26.099 1 94.44 ? O6' UD1 701 B 1 HETATM 15 O O7' UD1 . . . G 2 11.854 8.134 31.157 1 97.33 ? O7' UD1 701 B 1 HETATM 16 N N1 UD1 . . . G 2 17.261 11.988 25.188 1 73.76 ? N1 UD1 701 B 1 HETATM 17 C C2 UD1 . . . G 2 18.289 12.962 24.717 1 71.23 ? C2 UD1 701 B 1 HETATM 18 N N3 UD1 . . . G 2 19.673 12.477 24.399 1 73.09 ? N3 UD1 701 B 1 HETATM 19 C C4 UD1 . . . G 2 20.005 11.066 24.555 1 71.52 ? C4 UD1 701 B 1 HETATM 20 C C5 UD1 . . . G 2 18.969 10.114 25.026 1 73.45 ? C5 UD1 701 B 1 HETATM 21 C C6 UD1 . . . G 2 17.607 10.592 25.339 1 74.47 ? C6 UD1 701 B 1 HETATM 22 O O2 UD1 . . . G 2 18.013 14.109 24.593 1 65.96 ? O2 UD1 701 B 1 HETATM 23 O O4 UD1 . . . G 2 21.099 10.675 24.306 1 69.02 ? O4 UD1 701 B 1 HETATM 24 C C1B UD1 . . . G 2 15.925 12.43 25.508 1 73.98 ? C1B UD1 701 B 1 HETATM 25 C C2B UD1 . . . G 2 14.845 11.818 24.463 1 73.58 ? C2B UD1 701 B 1 HETATM 26 O O2' UD1 . . . G 2 14.689 12.723 23.33 1 70.81 ? O2' UD1 701 B 1 HETATM 27 C C3B UD1 . . . G 2 13.731 11.727 25.132 1 75.66 ? C3B UD1 701 B 1 HETATM 28 C C4B UD1 . . . G 2 14.152 11.481 26.593 1 72.34 ? C4B UD1 701 B 1 HETATM 29 O O4B UD1 . . . G 2 15.612 11.977 26.686 1 72.98 ? O4B UD1 701 B 1 HETATM 30 O O3B UD1 . . . G 2 12.966 13.01 25.042 1 79.14 ? O3B UD1 701 B 1 HETATM 31 C C5B UD1 . . . G 2 14.068 10.114 26.924 1 70.61 ? C5B UD1 701 B 1 HETATM 32 O O5B UD1 . . . G 2 14.753 9.318 25.989 1 67.93 ? O5B UD1 701 B 1 HETATM 33 P PA UD1 . . . G 2 14.207 7.779 25.732 1 67.94 ? PA UD1 701 B 1 HETATM 34 O O1A UD1 . . . G 2 15.079 7.07 24.721 1 67.55 ? O1A UD1 701 B 1 HETATM 35 O O2A UD1 . . . G 2 14.234 7.017 27.034 1 71.2 ? O2A UD1 701 B 1 HETATM 36 O O3A UD1 . . . G 2 12.658 7.861 25.149 1 69.89 ? O3A UD1 701 B 1 HETATM 37 P PB UD1 . . . G 2 11.584 6.6 25.192 1 72.52 ? PB UD1 701 B 1 HETATM 38 O O1B UD1 . . . G 2 10.266 7.041 24.602 1 72.29 ? O1B UD1 701 B 1 HETATM 39 O O2B UD1 . . . G 2 12.125 5.44 24.39 1 75.66 ? O2B UD1 701 B 1 HETATM 40 H H1' UD1 . . . G 2 10.56 7.79 27.311 1 101.72 ? H1' UD1 701 B 1 HETATM 41 H H2' UD1 . . . G 2 10.3 7.18 29.551 1 106.81 ? H2' UD1 701 B 1 HETATM 42 H H3' UD1 . . . G 2 11.442 4.709 28.912 1 108.96 ? H3' UD1 701 B 1 HETATM 43 H H4' UD1 . . . G 2 8.762 5.014 29.664 1 108.66 ? H4' UD1 701 B 1 HETATM 44 H H5' UD1 . . . G 2 9.535 4.424 27.009 1 108.83 ? H5' UD1 701 B 1 HETATM 45 H "H6'1" UD1 . . . G 2 6.969 5.259 27.69 1 111.32 ? "H6'1" UD1 701 B 1 HETATM 46 H "H6'2" UD1 . . . G 2 7.366 3.758 28.007 1 111.32 ? "H6'2" UD1 701 B 1 HETATM 47 H "H8'1" UD1 . . . G 2 14.707 7.553 30.368 1 113.22 ? "H8'1" UD1 701 B 1 HETATM 48 H "H8'2" UD1 . . . G 2 14.312 9.018 29.915 1 113.22 ? "H8'2" UD1 701 B 1 HETATM 49 H "H8'3" UD1 . . . G 2 14.235 8.615 31.445 1 113.22 ? "H8'3" UD1 701 B 1 HETATM 50 H HN2' UD1 . . . G 2 12.89 6.884 28.589 1 109.26 ? HN2' UD1 701 B 1 HETATM 51 H HO4' UD1 . . . G 2 9.981 2.892 28.624 1 109.81 ? HO4' UD1 701 B 1 HETATM 52 H HO6' UD1 . . . G 2 7.484 4.854 25.604 1 113.36 ? HO6' UD1 701 B 1 HETATM 53 H HN3 UD1 . . . G 2 20.27 13.032 24.126 1 87.73 ? HN3 UD1 701 B 1 HETATM 54 H H5 UD1 . . . G 2 19.179 9.214 25.126 1 88.17 ? H5 UD1 701 B 1 HETATM 55 H H6 UD1 . . . G 2 16.964 9.988 25.635 1 89.4 ? H6 UD1 701 B 1 HETATM 56 H H1B UD1 . . . G 2 15.879 13.399 25.503 1 88.81 ? H1B UD1 701 B 1 HETATM 57 H H2B UD1 . . . G 2 15.129 10.94 24.164 1 88.32 ? H2B UD1 701 B 1 HETATM 58 H HO2' UD1 . . . G 2 13.999 12.503 22.884 1 85 ? HO2' UD1 701 B 1 HETATM 59 H H3B UD1 . . . G 2 13.2 10.985 24.803 1 90.82 ? H3B UD1 701 B 1 HETATM 60 H H4B UD1 . . . G 2 13.591 12.003 27.188 1 86.83 ? H4B UD1 701 B 1 HETATM 61 H HO3A UD1 . . . G 2 13.334 13.594 25.539 1 94.99 ? HO3A UD1 701 B 1 HETATM 62 H "H5'1" UD1 . . . G 2 13.133 9.853 26.935 1 84.76 ? "H5'1" UD1 701 B 1 HETATM 63 H "H5'2" UD1 . . . G 2 14.45 9.973 27.804 1 84.76 ? "H5'2" UD1 701 B 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 63 #