data_6SVP # _model_server_result.job_id Y03aHSQR97kwUydshipU4A _model_server_result.datetime_utc '2024-11-24 06:22:36' _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":"C","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 . . . C 2 50.85 21.988 -19.065 1 59.83 ? C1' UD1 701 A 1 HETATM 2 C C2' UD1 . . . C 2 51.604 20.894 -19.803 1 63.05 ? C2' UD1 701 A 1 HETATM 3 C C3' UD1 . . . C 2 53.05 20.938 -19.479 1 69.89 ? C3' UD1 701 A 1 HETATM 4 C C4' UD1 . . . C 2 53.649 22.294 -19.706 1 72.33 ? C4' UD1 701 A 1 HETATM 5 C C5' UD1 . . . C 2 52.808 23.446 -19.136 1 69.51 ? C5' UD1 701 A 1 HETATM 6 C C6' UD1 . . . C 2 53.315 24.734 -19.703 1 69.78 ? C6' UD1 701 A 1 HETATM 7 C C7' UD1 . . . C 2 50.9 18.52 -20.398 1 67.09 ? C7' UD1 701 A 1 HETATM 8 C C8' UD1 . . . C 2 50.339 17.166 -19.992 1 70.08 ? C8' UD1 701 A 1 HETATM 9 N N2' UD1 . . . C 2 51.055 19.567 -19.409 1 64.51 ? N2' UD1 701 A 1 HETATM 10 O O1' UD1 . . . C 2 51.035 21.825 -17.726 1 53.86 ? O1' UD1 701 A 1 HETATM 11 O O3' UD1 . . . C 2 53.747 19.97 -20.314 1 74.27 ? O3' UD1 701 A 1 HETATM 12 O O4' UD1 . . . C 2 54.935 22.319 -19.079 1 74.97 ? O4' UD1 701 A 1 HETATM 13 O O5' UD1 . . . C 2 51.374 23.333 -19.455 1 64.97 ? O5' UD1 701 A 1 HETATM 14 O O6' UD1 . . . C 2 53.016 25.779 -18.817 1 70.02 ? O6' UD1 701 A 1 HETATM 15 O O7' UD1 . . . C 2 51.21 18.716 -21.525 1 67.26 ? O7' UD1 701 A 1 HETATM 16 N N1 UD1 . . . C 2 44.508 16.858 -16.366 1 55.62 ? N1 UD1 701 A 1 HETATM 17 C C2 UD1 . . . C 2 43.293 16.113 -15.922 1 53.8 ? C2 UD1 701 A 1 HETATM 18 N N3 UD1 . . . C 2 43.395 15.135 -14.794 1 53.58 ? N3 UD1 701 A 1 HETATM 19 C C4 UD1 . . . C 2 44.677 14.911 -14.142 1 54.35 ? C4 UD1 701 A 1 HETATM 20 C C5 UD1 . . . C 2 45.877 15.657 -14.598 1 56.48 ? C5 UD1 701 A 1 HETATM 21 C C6 UD1 . . . C 2 45.776 16.624 -15.712 1 55.81 ? C6 UD1 701 A 1 HETATM 22 O O2 UD1 . . . C 2 42.251 16.297 -16.455 1 54.38 ? O2 UD1 701 A 1 HETATM 23 O O4 UD1 . . . C 2 44.759 14.135 -13.248 1 53.17 ? O4 UD1 701 A 1 HETATM 24 C C1B UD1 . . . C 2 44.429 17.795 -17.459 1 54.14 ? C1B UD1 701 A 1 HETATM 25 C C2B UD1 . . . C 2 44.547 19.327 -16.941 1 56.11 ? C2B UD1 701 A 1 HETATM 26 O O2' UD1 . . . C 2 43.234 19.834 -16.557 1 54.11 ? O2' UD1 701 A 1 HETATM 27 C C3B UD1 . . . C 2 45.017 19.986 -17.962 1 53.25 ? C3B UD1 701 A 1 HETATM 28 C C4B UD1 . . . C 2 45.935 18.988 -18.692 1 48.37 ? C4B UD1 701 A 1 HETATM 29 O O4B UD1 . . . C 2 45.445 17.595 -18.244 1 54.33 ? O4B UD1 701 A 1 HETATM 30 O O3B UD1 . . . C 2 43.906 20.399 -18.876 1 55.71 ? O3B UD1 701 A 1 HETATM 31 C C5B UD1 . . . C 2 47.276 19.174 -18.316 1 50.25 ? C5B UD1 701 A 1 HETATM 32 O O5B UD1 . . . C 2 47.403 19.073 -16.923 1 54.41 ? O5B UD1 701 A 1 HETATM 33 P PA UD1 . . . C 2 48.7 19.802 -16.218 1 48.04 ? PA UD1 701 A 1 HETATM 34 O O1A UD1 . . . C 2 48.642 19.64 -14.72 1 53.79 ? O1A UD1 701 A 1 HETATM 35 O O2A UD1 . . . C 2 49.962 19.173 -16.745 1 56.35 ? O2A UD1 701 A 1 HETATM 36 O O3A UD1 . . . C 2 48.627 21.41 -16.592 1 52.88 ? O3A UD1 701 A 1 HETATM 37 P PB UD1 . . . C 2 49.92 22.437 -16.668 1 50.58 ? PB UD1 701 A 1 HETATM 38 O O1B UD1 . . . C 2 49.431 23.784 -17.143 1 52.97 ? O1B UD1 701 A 1 HETATM 39 O O2B UD1 . . . C 2 50.532 22.591 -15.295 1 54.16 ? O2B UD1 701 A 1 HETATM 40 H H1' UD1 . . . C 2 49.905 21.933 -19.278 1 71.82 ? H1' UD1 701 A 1 HETATM 41 H H2' UD1 . . . C 2 51.489 21.02 -20.758 1 75.69 ? H2' UD1 701 A 1 HETATM 42 H H3' UD1 . . . C 2 53.168 20.697 -18.547 1 83.9 ? H3' UD1 701 A 1 HETATM 43 H H4' UD1 . . . C 2 53.758 22.431 -20.66 1 86.83 ? H4' UD1 701 A 1 HETATM 44 H H5' UD1 . . . C 2 52.912 23.46 -18.172 1 83.44 ? H5' UD1 701 A 1 HETATM 45 H "H6'1" UD1 . . . C 2 52.887 24.903 -20.558 1 83.77 ? "H6'1" UD1 701 A 1 HETATM 46 H "H6'2" UD1 . . . C 2 54.275 24.679 -19.827 1 83.77 ? "H6'2" UD1 701 A 1 HETATM 47 H "H8'1" UD1 . . . C 2 50.782 16.86 -19.186 1 84.12 ? "H8'1" UD1 701 A 1 HETATM 48 H "H8'2" UD1 . . . C 2 49.387 17.247 -19.827 1 84.12 ? "H8'2" UD1 701 A 1 HETATM 49 H "H8'3" UD1 . . . C 2 50.49 16.526 -20.706 1 84.12 ? "H8'3" UD1 701 A 1 HETATM 50 H HN2' UD1 . . . C 2 50.829 19.421 -18.592 1 77.44 ? HN2' UD1 701 A 1 HETATM 51 H HO4' UD1 . . . C 2 54.986 22.992 -18.562 1 89.99 ? HO4' UD1 701 A 1 HETATM 52 H HO6' UD1 . . . C 2 53.281 25.572 -18.036 1 84.05 ? HO6' UD1 701 A 1 HETATM 53 H HN3 UD1 . . . C 2 42.698 14.705 -14.532 1 64.33 ? HN3 UD1 701 A 1 HETATM 54 H H5 UD1 . . . C 2 46.697 15.515 -14.182 1 67.8 ? H5 UD1 701 A 1 HETATM 55 H H6 UD1 . . . C 2 46.533 17.085 -15.993 1 67 ? H6 UD1 701 A 1 HETATM 56 H H1B UD1 . . . C 2 43.601 17.674 -17.95 1 65 ? H1B UD1 701 A 1 HETATM 57 H H2B UD1 . . . C 2 45.165 19.38 -16.195 1 67.36 ? H2B UD1 701 A 1 HETATM 58 H HO2' UD1 . . . C 2 42.823 19.243 -16.105 1 64.96 ? HO2' UD1 701 A 1 HETATM 59 H H3B UD1 . . . C 2 45.524 20.757 -17.663 1 63.93 ? H3B UD1 701 A 1 HETATM 60 H H4B UD1 . . . C 2 45.835 19.084 -19.652 1 58.08 ? H4B UD1 701 A 1 HETATM 61 H HO3A UD1 . . . C 2 44.232 20.671 -19.612 1 66.88 ? HO3A UD1 701 A 1 HETATM 62 H "H5'1" UD1 . . . C 2 47.564 20.056 -18.601 1 60.33 ? "H5'1" UD1 701 A 1 HETATM 63 H "H5'2" UD1 . . . C 2 47.829 18.5 -18.742 1 60.33 ? "H5'2" UD1 701 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 63 #