data_4AN4 # _model_server_result.job_id tRvAU9HkPUtAMuy19d5EEQ _model_server_result.datetime_utc '2025-02-20 15:42:10' _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 4an4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 4AN4 # _exptl.entry_id 4AN4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.162 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-DIPHOSPHATE" _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 91.71 _cell.angle_gamma 90 _cell.entry_id 4AN4 _cell.length_a 64.641 _cell.length_b 70.078 _cell.length_c 176.031 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AN4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E,G,H 1 1 C,D,F,I,J 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 ? 2 E N N ? 2 F 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 covale ? covale1 A C ALA 393 A ALA 383 1_555 A N MLY 394 A MLY 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale2 A C MLY 394 A MLY 384 1_555 A N LEU 395 A LEU 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 B C ALA 393 B ALA 383 1_555 B N MLY 394 B MLY 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale4 B C MLY 394 B MLY 384 1_555 B N LEU 395 B LEU 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 C C ALA 393 C ALA 383 1_555 C N MLY 394 C MLY 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 C C MLY 394 C MLY 384 1_555 C N LEU 395 C LEU 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 D C ALA 393 D ALA 383 1_555 D N MLY 394 D MLY 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale8 D C MLY 394 D MLY 384 1_555 D N LEU 395 D LEU 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C9 H14 N2 O11 P2' _chem_comp.formula_weight 388.162 _chem_comp.id DUD _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-DIPHOSPHATE" _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 N1 C2 DUD sing 83 n n N1 C6 DUD sing 84 n n N1 C1' DUD sing 85 n n C2 N3 DUD sing 86 n n C2 O2 DUD doub 87 n n N3 C4 DUD sing 88 n n N3 HN3 DUD sing 89 n n C4 C5 DUD sing 90 n n C4 O4 DUD doub 91 n n C5 C6 DUD doub 92 n n C5 H5 DUD sing 93 n n C6 H6 DUD sing 94 n n C1' C2' DUD sing 95 n n C1' O4' DUD sing 96 n n C1' H1' DUD sing 97 n n C2' C3' DUD sing 98 n n C2' "H2'1" DUD sing 99 n n C2' "H2'2" DUD sing 100 n n C3' C4' DUD sing 101 n n C3' O3' DUD sing 102 n n C3' H3' DUD sing 103 n n C4' O4' DUD sing 104 n n C4' C5' DUD sing 105 n n C4' H4' DUD sing 106 n n O3' HO3' DUD sing 107 n n C5' O5' DUD sing 108 n n C5' "H5'1" DUD sing 109 n n C5' "H5'2" DUD sing 110 n n O5' PA DUD sing 111 n n PA O1A DUD doub 112 n n PA O2A DUD sing 113 n n PA O3A DUD sing 114 n n O2A HOA2 DUD sing 115 n n O3A PB DUD sing 116 n n PB O1B DUD doub 117 n n PB O2B DUD sing 118 n n PB O3B DUD sing 119 n n O2B HOB2 DUD sing 120 n n O3B HOB3 DUD sing 121 n n # _atom_sites.entry_id 4AN4 _atom_sites.fract_transf_matrix[1][1] 0.01547 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000462 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01427 _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] 0.005683 _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 E 2 DUD B 1 401 401 DUD DUD . F 2 DUD D 1 401 401 DUD DUD . G 3 HOH A 1 2001 2001 HOH HOH . G 3 HOH A 2 2002 2002 HOH HOH . G 3 HOH A 3 2003 2003 HOH HOH . G 3 HOH A 4 2004 2004 HOH HOH . G 3 HOH A 5 2005 2005 HOH HOH . G 3 HOH A 6 2006 2006 HOH HOH . G 3 HOH A 7 2007 2007 HOH HOH . G 3 HOH A 8 2008 2008 HOH HOH . G 3 HOH A 9 2009 2009 HOH HOH . G 3 HOH A 10 2010 2010 HOH HOH . G 3 HOH A 11 2011 2011 HOH HOH . G 3 HOH A 12 2012 2012 HOH HOH . G 3 HOH A 13 2013 2013 HOH HOH . G 3 HOH A 14 2014 2014 HOH HOH . G 3 HOH A 15 2015 2015 HOH HOH . G 3 HOH A 16 2016 2016 HOH HOH . G 3 HOH A 17 2017 2017 HOH HOH . G 3 HOH A 18 2018 2018 HOH HOH . G 3 HOH A 19 2019 2019 HOH HOH . G 3 HOH A 20 2020 2020 HOH HOH . G 3 HOH A 21 2021 2021 HOH HOH . G 3 HOH A 22 2022 2022 HOH HOH . G 3 HOH A 23 2023 2023 HOH HOH . G 3 HOH A 24 2024 2024 HOH HOH . G 3 HOH A 25 2025 2025 HOH HOH . G 3 HOH A 26 2026 2026 HOH HOH . G 3 HOH A 27 2027 2027 HOH HOH . G 3 HOH A 28 2028 2028 HOH HOH . G 3 HOH A 29 2029 2029 HOH HOH . G 3 HOH A 30 2030 2030 HOH HOH . G 3 HOH A 31 2031 2031 HOH HOH . G 3 HOH A 32 2032 2032 HOH HOH . G 3 HOH A 33 2033 2033 HOH HOH . G 3 HOH A 34 2034 2034 HOH HOH . H 3 HOH B 1 2001 2001 HOH HOH . H 3 HOH B 2 2002 2002 HOH HOH . H 3 HOH B 3 2003 2003 HOH HOH . H 3 HOH B 4 2004 2004 HOH HOH . H 3 HOH B 5 2005 2005 HOH HOH . H 3 HOH B 6 2006 2006 HOH HOH . H 3 HOH B 7 2007 2007 HOH HOH . H 3 HOH B 8 2008 2008 HOH HOH . H 3 HOH B 9 2009 2009 HOH HOH . I 3 HOH C 1 2001 2001 HOH HOH . I 3 HOH C 2 2002 2002 HOH HOH . I 3 HOH C 3 2003 2003 HOH HOH . I 3 HOH C 4 2004 2004 HOH HOH . J 3 HOH D 1 2001 2001 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 DUD . . . E 2 -10.164 17.595 -31.766 1 73.15 ? N1 DUD 401 B 1 HETATM 2 C C2 DUD . . . E 2 -10.802 18.845 -31.6 1 70.57 ? C2 DUD 401 B 1 HETATM 3 N N3 DUD . . . E 2 -11.415 19.426 -32.631 1 74.48 ? N3 DUD 401 B 1 HETATM 4 C C4 DUD . . . E 2 -11.437 18.849 -33.847 1 77.8 ? C4 DUD 401 B 1 HETATM 5 C C5 DUD . . . E 2 -10.812 17.618 -34.047 1 77.7 ? C5 DUD 401 B 1 HETATM 6 C C6 DUD . . . E 2 -10.175 17 -32.971 1 77.9 ? C6 DUD 401 B 1 HETATM 7 O O2 DUD . . . E 2 -10.826 19.427 -30.499 1 65.34 ? O2 DUD 401 B 1 HETATM 8 O O4 DUD . . . E 2 -12.015 19.418 -34.799 1 80.52 ? O4 DUD 401 B 1 HETATM 9 C C1' DUD . . . E 2 -9.493 16.965 -30.624 1 77.09 ? C1' DUD 401 B 1 HETATM 10 C C2' DUD . . . E 2 -10.429 16.877 -29.424 1 74.44 ? C2' DUD 401 B 1 HETATM 11 C C3' DUD . . . E 2 -10.075 15.589 -28.722 1 77.17 ? C3' DUD 401 B 1 HETATM 12 C C4' DUD . . . E 2 -9.127 14.866 -29.668 1 81.58 ? C4' DUD 401 B 1 HETATM 13 O O4' DUD . . . E 2 -9.079 15.618 -30.883 1 80.45 ? O4' DUD 401 B 1 HETATM 14 O O3' DUD . . . E 2 -9.441 15.863 -27.465 1 77.74 ? O3' DUD 401 B 1 HETATM 15 C C5' DUD . . . E 2 -9.604 13.44 -29.915 1 87.19 ? C5' DUD 401 B 1 HETATM 16 O O5' DUD . . . E 2 -9.588 12.72 -28.67 1 87.86 ? O5' DUD 401 B 1 HETATM 17 P PA DUD . . . E 2 -9.087 11.192 -28.661 1 92.63 ? PA DUD 401 B 1 HETATM 18 O O1A DUD . . . E 2 -10.274 10.411 -29.158 1 89.08 ? O1A DUD 401 B 1 HETATM 19 O O2A DUD . . . E 2 -8.369 10.805 -27.387 1 76.88 ? O2A DUD 401 B 1 HETATM 20 O O3A DUD . . . E 2 -7.97 11.256 -29.82 1 90.67 ? O3A DUD 401 B 1 HETATM 21 P PB DUD . . . E 2 -7.445 9.95 -30.586 1 86.45 ? PB DUD 401 B 1 HETATM 22 O O1B DUD . . . E 2 -7.148 10.475 -31.97 1 92.36 ? O1B DUD 401 B 1 HETATM 23 O O2B DUD . . . E 2 -8.572 8.94 -30.515 1 87.7 ? O2B DUD 401 B 1 HETATM 24 O O3B DUD . . . E 2 -6.234 9.59 -29.758 1 86.47 ? O3B DUD 401 B 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #