data_7VEK # _model_server_result.job_id kdoEw-JV5QXGMHjjcBFA0Q _model_server_result.datetime_utc '2024-11-08 04:08:20' _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 7vek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":502}' # _entry.id 7VEK # _exptl.entry_id 7VEK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 568.293 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE" _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 7VEK _cell.length_a 94.276 _cell.length_b 103.022 _cell.length_c 109.648 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VEK _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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,E 1 1 B,F,G 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 ? 4 E N N ? 4 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 GLU 258 A GLU 238 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc2 C OAM O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc3 C OAO O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc4 C OAQ O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? metalc ? metalc5 C OAR O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? metalc ? metalc6 C OAP O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc7 C OAN O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? metalc ? metalc8 D K K . A K 502 1_555 B O GLU 258 B GLU 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? # _chem_comp.formula 'C15 H23 F N2 O16 P2' _chem_comp.formula_weight 568.293 _chem_comp.id U2F _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE" _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 O1 U2F sing 447 n n C1 C2 U2F sing 448 n n C1 O5 U2F sing 449 n n C1 H1 U2F sing 450 n n O1 PB U2F sing 451 n n PB O1B U2F doub 452 n n PB O2B U2F sing 453 n n PB O3A U2F sing 454 n n O3A PA U2F sing 455 n n PA O1A U2F doub 456 n n PA O2A U2F sing 457 n n PA O5' U2F sing 458 n n O5' C5' U2F sing 459 n n C5' C4' U2F sing 460 n n C5' "H5'1" U2F sing 461 n n C5' "H5'2" U2F sing 462 n n C4' O4' U2F sing 463 n n C4' C3' U2F sing 464 n n C4' H4' U2F sing 465 n n O4' C1' U2F sing 466 n n C1' C2' U2F sing 467 n n C1' N1 U2F sing 468 n n C1' H1' U2F sing 469 n n C2' C3' U2F sing 470 n n C2' O2' U2F sing 471 n n C2' H2' U2F sing 472 n n C3' O3' U2F sing 473 n n C3' H3' U2F sing 474 n n O3' HB U2F sing 475 n n O2' HA U2F sing 476 n n N1 C6' U2F sing 477 n n N1 C9' U2F sing 478 n n C6' O6' U2F doub 479 n n C6' N3 U2F sing 480 n n N3 C7' U2F sing 481 n n N3 H3 U2F sing 482 n n C7' O7' U2F doub 483 n n C7' C8' U2F sing 484 n n C8' C9' U2F doub 485 n n C8' H8' U2F sing 486 n n C9' H9' U2F sing 487 n n C2 F1 U2F sing 488 n n C2 C3 U2F sing 489 n n C2 H2 U2F sing 490 n n C3 O3 U2F sing 491 n n C3 C4 U2F sing 492 n n C3 HC U2F sing 493 n n O3 HD U2F sing 494 n n C4 O4 U2F sing 495 n n C4 C5 U2F sing 496 n n C4 H4 U2F sing 497 n n O4 HE U2F sing 498 n n C5 C6 U2F sing 499 n n C5 O5 U2F sing 500 n n C5 H5 U2F sing 501 n n C6 O6 U2F sing 502 n n C6 H6C1 U2F sing 503 n n C6 H6C2 U2F sing 504 n n O6 H6 U2F sing 505 n n HO1 O2A U2F sing 506 n n HO2 O2B U2F sing 507 n n # _atom_sites.entry_id 7VEK _atom_sites.fract_transf_matrix[1][1] 0.010607 _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] 0.009707 _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] 0.00912 _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 O4B A 1 501 1 O4B O4B . D 3 K A 1 502 1 K K . E 4 U2F A 1 503 1 U2F U2F . F 5 4DY B 1 501 501 4DY 4DY . G 4 U2F B 1 502 2 U2F U2F . # 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 U2F . . . G 4 31.682 8.653 -29.03 1 54.65 ? C1 U2F 502 B 1 HETATM 2 O O1 U2F . . . G 4 32.288 9.708 -28.429 1 54.44 ? O1 U2F 502 B 1 HETATM 3 P PB U2F . . . G 4 33.726 9.524 -27.628 1 55.22 ? PB U2F 502 B 1 HETATM 4 O O1B U2F . . . G 4 33.558 8.602 -26.447 1 47.77 ? O1B U2F 502 B 1 HETATM 5 O O2B U2F . . . G 4 34.776 9.05 -28.605 1 72.95 ? O2B U2F 502 B 1 HETATM 6 O O3A U2F . . . G 4 34.176 11.021 -27.069 1 61.01 ? O3A U2F 502 B 1 HETATM 7 P PA U2F . . . G 4 33.137 11.942 -26.155 1 51.16 ? PA U2F 502 B 1 HETATM 8 O O1A U2F . . . G 4 31.719 11.844 -26.644 1 46.2 ? O1A U2F 502 B 1 HETATM 9 O O2A U2F . . . G 4 33.603 13.362 -26.271 1 53.43 ? O2A U2F 502 B 1 HETATM 10 O O5' U2F . . . G 4 33.216 11.41 -24.581 1 55.76 ? O5' U2F 502 B 1 HETATM 11 C C5' U2F . . . G 4 34.364 11.761 -23.826 1 45.22 ? C5' U2F 502 B 1 HETATM 12 C C4' U2F . . . G 4 34.012 11.702 -22.346 1 45.47 ? C4' U2F 502 B 1 HETATM 13 O O4' U2F . . . G 4 35.317 11.218 -21.543 1 47.04 ? O4' U2F 502 B 1 HETATM 14 C C1' U2F . . . G 4 35.686 12.209 -20.785 1 54.58 ? C1' U2F 502 B 1 HETATM 15 C C2' U2F . . . G 4 35 13.451 -21.349 1 51.4 ? C2' U2F 502 B 1 HETATM 16 C C3' U2F . . . G 4 33.688 12.874 -21.891 1 49.95 ? C3' U2F 502 B 1 HETATM 17 O O3' U2F . . . G 4 32.709 12.72 -20.764 1 41.71 ? O3' U2F 502 B 1 HETATM 18 O O2' U2F . . . G 4 34.767 14.333 -20.333 1 51.01 ? O2' U2F 502 B 1 HETATM 19 N N1 U2F . . . G 4 37.174 12.359 -20.815 1 50.85 ? N1 U2F 502 B 1 HETATM 20 C C6' U2F . . . G 4 37.91 12.607 -19.534 1 51.49 ? C6' U2F 502 B 1 HETATM 21 O O6' U2F . . . G 4 37.328 12.685 -18.508 1 56.03 ? O6' U2F 502 B 1 HETATM 22 N N3 U2F . . . G 4 39.401 12.75 -19.552 1 51.38 ? N3 U2F 502 B 1 HETATM 23 C C7' U2F . . . G 4 40.119 12.644 -20.814 1 56.76 ? C7' U2F 502 B 1 HETATM 24 O O7' U2F . . . G 4 41.305 12.758 -20.815 1 62.12 ? O7' U2F 502 B 1 HETATM 25 C C8' U2F . . . G 4 39.375 12.398 -22.084 1 49.35 ? C8' U2F 502 B 1 HETATM 26 C C9' U2F . . . G 4 37.897 12.254 -22.072 1 45.15 ? C9' U2F 502 B 1 HETATM 27 C C2 U2F . . . G 4 31.57 9.004 -30.5 1 47.37 ? C2 U2F 502 B 1 HETATM 28 F F1 U2F . . . G 4 32.869 9.108 -31.026 1 48.47 ? F1 U2F 502 B 1 HETATM 29 C C3 U2F . . . G 4 30.894 10.313 -30.631 1 50.23 ? C3 U2F 502 B 1 HETATM 30 O O3 U2F . . . G 4 30.829 10.695 -32.038 1 42.36 ? O3 U2F 502 B 1 HETATM 31 C C4 U2F . . . G 4 29.524 10.3 -29.997 1 45.11 ? C4 U2F 502 B 1 HETATM 32 O O4 U2F . . . G 4 29.007 11.637 -29.989 1 38.08 ? O4 U2F 502 B 1 HETATM 33 C C5 U2F . . . G 4 29.549 9.777 -28.551 1 42.48 ? C5 U2F 502 B 1 HETATM 34 C C6 U2F . . . G 4 28.138 9.514 -28.058 1 50.45 ? C6 U2F 502 B 1 HETATM 35 O O6 U2F . . . G 4 27.613 8.318 -28.609 1 53.32 ? O6 U2F 502 B 1 HETATM 36 O O5 U2F . . . G 4 30.328 8.535 -28.402 1 52.56 ? O5 U2F 502 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 36 #