data_7VEK # _model_server_result.job_id VzmyNUH494_FjQbs-dF2sg _model_server_result.datetime_utc '2024-11-24 17:00:33' _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":"E","auth_seq_id":503}' # _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 . . . E 4 -17.861 1.04 -44.402 1 57.83 ? C1 U2F 503 A 1 HETATM 2 O O1 U2F . . . E 4 -18.626 1.186 -45.523 1 46.36 ? O1 U2F 503 A 1 HETATM 3 P PB U2F . . . E 4 -19.814 0.067 -45.836 1 48.86 ? PB U2F 503 A 1 HETATM 4 O O1B U2F . . . E 4 -21.166 0.725 -45.771 1 72.95 ? O1B U2F 503 A 1 HETATM 5 O O2B U2F . . . E 4 -19.789 -1.035 -44.801 1 76.6 ? O2B U2F 503 A 1 HETATM 6 O O3A U2F . . . E 4 -19.527 -0.589 -47.353 1 65.73 ? O3A U2F 503 A 1 HETATM 7 P PA U2F . . . E 4 -19.344 0.306 -48.759 1 71.38 ? PA U2F 503 A 1 HETATM 8 O O1A U2F . . . E 4 -17.952 0.886 -48.804 1 53.33 ? O1A U2F 503 A 1 HETATM 9 O O2A U2F . . . E 4 -20.346 1.433 -48.846 1 54.44 ? O2A U2F 503 A 1 HETATM 10 O O5' U2F . . . E 4 -19.643 -0.672 -50.07 1 67.41 ? O5' U2F 503 A 1 HETATM 11 C C5' U2F . . . E 4 -20.872 -1.377 -50.098 1 56.64 ? C5' U2F 503 A 1 HETATM 12 C C4' U2F . . . E 4 -20.567 -2.788 -50.584 1 72.44 ? C4' U2F 503 A 1 HETATM 13 O O4' U2F . . . E 4 -21.861 -3.725 -50.362 1 68.95 ? O4' U2F 503 A 1 HETATM 14 C C1' U2F . . . E 4 -22.295 -4.094 -51.531 1 74.96 ? C1' U2F 503 A 1 HETATM 15 C C2' U2F . . . E 4 -21.548 -3.256 -52.579 1 73.54 ? C2' U2F 503 A 1 HETATM 16 C C3' U2F . . . E 4 -20.286 -2.758 -51.852 1 65.01 ? C3' U2F 503 A 1 HETATM 17 O O3' U2F . . . E 4 -19.116 -3.657 -52.143 1 59.99 ? O3' U2F 503 A 1 HETATM 18 O O2' U2F . . . E 4 -21.196 -4.028 -53.655 1 69.39 ? O2' U2F 503 A 1 HETATM 19 N N1 U2F . . . E 4 -23.782 -3.891 -51.586 1 65.91 ? N1 U2F 503 A 1 HETATM 20 C C6' U2F . . . E 4 -24.589 -4.661 -52.581 1 69.56 ? C6' U2F 503 A 1 HETATM 21 O O6' U2F . . . E 4 -24.042 -5.41 -53.318 1 67.66 ? O6' U2F 503 A 1 HETATM 22 N N3 U2F . . . E 4 -26.084 -4.474 -52.631 1 67.07 ? N3 U2F 503 A 1 HETATM 23 C C7' U2F . . . E 4 -26.738 -3.553 -51.708 1 68.16 ? C7' U2F 503 A 1 HETATM 24 O O7' U2F . . . E 4 -27.922 -3.404 -51.747 1 73.81 ? O7' U2F 503 A 1 HETATM 25 C C8' U2F . . . E 4 -25.917 -2.797 -50.721 1 72.94 ? C8' U2F 503 A 1 HETATM 26 C C9' U2F . . . E 4 -24.441 -2.977 -50.669 1 67.51 ? C9' U2F 503 A 1 HETATM 27 C C2 U2F . . . E 4 -17.539 2.428 -43.88 1 47.01 ? C2 U2F 503 A 1 HETATM 28 F F1 U2F . . . E 4 -18.718 3.142 -43.589 1 54.6 ? F1 U2F 503 A 1 HETATM 29 C C3 U2F . . . E 4 -16.797 3.186 -44.899 1 40.83 ? C3 U2F 503 A 1 HETATM 30 O O3 U2F . . . E 4 -16.592 4.495 -44.304 1 41.06 ? O3 U2F 503 A 1 HETATM 31 C C4 U2F . . . E 4 -15.511 2.469 -45.256 1 46.17 ? C4 U2F 503 A 1 HETATM 32 O O4 U2F . . . E 4 -14.761 3.159 -46.265 1 33.37 ? O4 U2F 503 A 1 HETATM 33 C C5 U2F . . . E 4 -15.796 1.043 -45.745 1 44.19 ? C5 U2F 503 A 1 HETATM 34 C C6 U2F . . . E 4 -14.496 0.307 -45.975 1 37.38 ? C6 U2F 503 A 1 HETATM 35 O O6 U2F . . . E 4 -13.51 0.893 -45.155 1 40.01 ? O6 U2F 503 A 1 HETATM 36 O O5 U2F . . . E 4 -16.595 0.302 -44.755 1 49.18 ? O5 U2F 503 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 389 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #