data_4M28 # _model_server_result.job_id mk4BPq35Fs_yRmmJQAMusw _model_server_result.datetime_utc '2024-12-16 18:41:23' _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 4m28 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 4M28 # _exptl.entry_id 4M28 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 466.169 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine" _entity.pdbx_number_of_molecules 1 _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 4M28 _cell.length_a 72.25 _cell.length_b 108.47 _cell.length_c 152.59 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M28 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 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,B,C 1 1 A,B,C 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -76.295 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 92 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 92 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 92 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 92 _struct_conn.ptnr2_symmetry 3_554 _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 2.335 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H17 N2 O13 P3' _chem_comp.formula_weight 466.169 _chem_comp.id UPC _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine" _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' N1 UPC sing 358 n n N1 C6 UPC sing 359 n n N1 C2 UPC sing 360 n n O2 C2 UPC doub 361 n n C2 N3 UPC sing 362 n n N3 C4 UPC sing 363 n n C5 C4 UPC sing 364 n n C4 O4 UPC doub 365 n n C6 C5 UPC doub 366 n n C5 H5 UPC sing 367 n n C6 H6 UPC sing 368 n n O2A PA UPC doub 369 n n PA C3A UPC sing 370 n n PA O5' UPC sing 371 n n PA O1A UPC sing 372 n n O2B PB UPC doub 373 n n O3B PB UPC sing 374 n n PB O1B UPC sing 375 n n PB C3A UPC sing 376 n n O2G PG UPC doub 377 n n O1G PG UPC sing 378 n n PG O3B UPC sing 379 n n PG O3G UPC sing 380 n n O4' C1' UPC sing 381 n n C2' C1' UPC sing 382 n n C1' H1' UPC sing 383 n n O1A HO1A UPC sing 384 n n O1B HO1B UPC sing 385 n n O1G HO1G UPC sing 386 n n C3' C2' UPC sing 387 n n C2' H2' UPC sing 388 n n C2' "H2'A" UPC sing 389 n n O3' C3' UPC sing 390 n n C4' C3' UPC sing 391 n n C3' H3' UPC sing 392 n n O3' HO3' UPC sing 393 n n C3A H3A UPC sing 394 n n C3A H3AA UPC sing 395 n n O3G HO3G UPC sing 396 n n C5' C4' UPC sing 397 n n C4' O4' UPC sing 398 n n C4' H4' UPC sing 399 n n C5' O5' UPC sing 400 n n C5' H5' UPC sing 401 n n C5' "H5'A" UPC sing 402 n n N3 HN3 UPC sing 403 n n # _atom_sites.entry_id 4M28 _atom_sites.fract_transf_matrix[1][1] 0.013841 _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] 0.009219 _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] 0.006554 _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 B 2 UPC A 1 1001 1001 UPC UPC . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2005 HOH HOH . C 3 HOH A 3 2003 2006 HOH HOH . C 3 HOH A 4 2004 2010 HOH HOH . C 3 HOH A 5 2005 2011 HOH HOH . C 3 HOH A 6 2006 2012 HOH HOH . C 3 HOH A 7 2007 2013 HOH HOH . C 3 HOH A 8 2008 2014 HOH HOH . C 3 HOH A 9 2009 2015 HOH HOH . C 3 HOH A 10 2010 2016 HOH HOH . C 3 HOH A 11 2011 2018 HOH HOH . C 3 HOH A 12 2012 2019 HOH HOH . C 3 HOH A 13 2013 2020 HOH HOH . C 3 HOH A 14 2014 2021 HOH HOH . C 3 HOH A 15 2015 2022 HOH HOH . C 3 HOH A 16 2016 2023 HOH HOH . C 3 HOH A 17 2017 2025 HOH HOH . C 3 HOH A 18 2018 2026 HOH HOH . C 3 HOH A 19 2019 2027 HOH HOH . C 3 HOH A 20 2020 2028 HOH HOH . C 3 HOH A 21 2021 2030 HOH HOH . C 3 HOH A 22 2022 2031 HOH HOH . C 3 HOH A 23 2023 2032 HOH HOH . C 3 HOH A 24 2024 2033 HOH HOH . C 3 HOH A 25 2025 2034 HOH HOH . C 3 HOH A 26 2026 2035 HOH HOH . C 3 HOH A 27 2027 2036 HOH HOH . C 3 HOH A 28 2028 2037 HOH HOH . C 3 HOH A 29 2029 2038 HOH HOH . C 3 HOH A 30 2030 2039 HOH HOH . C 3 HOH A 31 2031 2040 HOH HOH . C 3 HOH A 32 2032 2042 HOH HOH . C 3 HOH A 33 2033 2043 HOH HOH . C 3 HOH A 34 2034 2044 HOH HOH . C 3 HOH A 35 2035 2045 HOH HOH . C 3 HOH A 36 2036 2046 HOH HOH . C 3 HOH A 37 2037 2047 HOH HOH . C 3 HOH A 38 2038 2048 HOH HOH . C 3 HOH A 39 2039 2049 HOH HOH . C 3 HOH A 40 2040 2050 HOH HOH . C 3 HOH A 41 2041 2051 HOH HOH . C 3 HOH A 42 2042 2052 HOH HOH . C 3 HOH A 43 2043 2053 HOH HOH . C 3 HOH A 44 2044 2054 HOH HOH . C 3 HOH A 45 2045 2055 HOH HOH . C 3 HOH A 46 2046 2056 HOH HOH . C 3 HOH A 47 2047 2057 HOH HOH . C 3 HOH A 48 2048 2058 HOH HOH . C 3 HOH A 49 2049 2059 HOH HOH . C 3 HOH A 50 2050 2060 HOH HOH . C 3 HOH A 51 2051 2061 HOH HOH . C 3 HOH A 52 2052 2062 HOH HOH . C 3 HOH A 53 2053 2063 HOH HOH . C 3 HOH A 54 2054 2064 HOH HOH . C 3 HOH A 55 2055 2065 HOH HOH . C 3 HOH A 56 2056 2066 HOH HOH . C 3 HOH A 57 2057 2067 HOH HOH . C 3 HOH A 58 2058 2068 HOH HOH . C 3 HOH A 59 2059 2069 HOH HOH . C 3 HOH A 60 2060 2070 HOH HOH . C 3 HOH A 61 2061 2071 HOH HOH . C 3 HOH A 62 2062 2072 HOH HOH . C 3 HOH A 63 2063 2073 HOH HOH . C 3 HOH A 64 2064 2074 HOH HOH . C 3 HOH A 65 2065 2076 HOH HOH . C 3 HOH A 66 2066 2078 HOH HOH . C 3 HOH A 67 2067 2079 HOH HOH . C 3 HOH A 68 2068 2081 HOH HOH . C 3 HOH A 69 2069 2082 HOH HOH . C 3 HOH A 70 2070 2083 HOH HOH . C 3 HOH A 71 2071 2084 HOH HOH . C 3 HOH A 72 2072 2085 HOH HOH . C 3 HOH A 73 2073 2086 HOH HOH . C 3 HOH A 74 2074 2087 HOH HOH . C 3 HOH A 75 2075 2088 HOH HOH . C 3 HOH A 76 2076 2089 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 N N1 UPC . . . B 2 3.966 20.475 -22.843 1 161.88 ? N1 UPC 1001 A 1 HETATM 2 C C2 UPC . . . B 2 3.762 19.069 -22.546 1 147 ? C2 UPC 1001 A 1 HETATM 3 O O2 UPC . . . B 2 4.664 18.204 -22.619 1 131.53 ? O2 UPC 1001 A 1 HETATM 4 N N3 UPC . . . B 2 2.546 18.604 -22.179 1 138.62 ? N3 UPC 1001 A 1 HETATM 5 C C4 UPC . . . B 2 1.486 19.425 -22.065 1 135.45 ? C4 UPC 1001 A 1 HETATM 6 O O4 UPC . . . B 2 0.352 19.013 -21.731 1 117.5 ? O4 UPC 1001 A 1 HETATM 7 C C5 UPC . . . B 2 1.641 20.773 -22.324 1 143 ? C5 UPC 1001 A 1 HETATM 8 C C6 UPC . . . B 2 2.885 21.268 -22.702 1 154.7 ? C6 UPC 1001 A 1 HETATM 9 P PA UPC . . . B 2 1.781 25.007 -23.313 1 182.21 ? PA UPC 1001 A 1 HETATM 10 P PB UPC . . . B 2 0.611 24.023 -25.802 1 183.29 ? PB UPC 1001 A 1 HETATM 11 P PG UPC . . . B 2 1.022 23.475 -28.65 1 165.68 ? PG UPC 1001 A 1 HETATM 12 C C1' UPC . . . B 2 5.269 21.143 -23.24 1 165.37 ? C1' UPC 1001 A 1 HETATM 13 O O1A UPC . . . B 2 1.005 23.919 -22.609 1 184.67 ? O1A UPC 1001 A 1 HETATM 14 O O1B UPC . . . B 2 -0.861 24.348 -25.966 1 177.38 ? O1B UPC 1001 A 1 HETATM 15 O O1G UPC . . . B 2 1.214 21.995 -28.408 1 144.31 ? O1G UPC 1001 A 1 HETATM 16 C C2' UPC . . . B 2 5.389 21.76 -24.665 1 152.04 ? C2' UPC 1001 A 1 HETATM 17 O O2A UPC . . . B 2 1.829 26.384 -22.698 1 181.99 ? O2A UPC 1001 A 1 HETATM 18 O O2B UPC . . . B 2 1.047 22.668 -25.288 1 182.92 ? O2B UPC 1001 A 1 HETATM 19 O O2G UPC . . . B 2 2.056 24.103 -29.556 1 171.8 ? O2G UPC 1001 A 1 HETATM 20 C C3' UPC . . . B 2 5.438 23.272 -24.506 1 151.41 ? C3' UPC 1001 A 1 HETATM 21 O O3' UPC . . . B 2 6.586 23.816 -25.169 1 130.99 ? O3' UPC 1001 A 1 HETATM 22 C C3A UPC . . . B 2 1.261 25.175 -24.848 1 180.74 ? C3A UPC 1001 A 1 HETATM 23 O O3B UPC . . . B 2 1.326 24.247 -27.247 1 183.53 ? O3B UPC 1001 A 1 HETATM 24 O O3G UPC . . . B 2 -0.389 23.853 -29.032 1 159.72 ? O3G UPC 1001 A 1 HETATM 25 C C4' UPC . . . B 2 5.472 23.543 -22.997 1 167.43 ? C4' UPC 1001 A 1 HETATM 26 O O4' UPC . . . B 2 5.494 22.257 -22.339 1 177.64 ? O4' UPC 1001 A 1 HETATM 27 C C5' UPC . . . B 2 4.302 24.407 -22.491 1 168.83 ? C5' UPC 1001 A 1 HETATM 28 O O5' UPC . . . B 2 3.306 24.518 -23.516 1 179.48 ? O5' UPC 1001 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #