data_4V31 # _model_server_result.job_id 6Lckkl8s0bTBM1dFtTDHKw _model_server_result.datetime_utc '2024-11-28 20:37:59' _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 4v31 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":151}' # _entry.id 4V31 # _exptl.entry_id 4V31 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.202 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE" _entity.pdbx_number_of_molecules 3 _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 4V31 _cell.length_a 56.809 _cell.length_b 59.993 _cell.length_c 88.37 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4V31 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _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 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,K 1 1 B,F,G,H,L 2 1 C,I,J,M 3 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 ? 3 E N N ? 3 G N N ? 3 J 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 SG CYS 25 A CYS 24 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc2 A SG CYS 28 A CYS 27 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc3 A SG CYS 91 A CYS 90 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc4 A SG CYS 94 A CYS 93 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc5 B SG CYS 25 B CYS 24 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc6 B SG CYS 28 B CYS 27 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc7 B SG CYS 91 B CYS 90 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc8 B SG CYS 94 B CYS 93 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc9 C SG CYS 25 C CYS 24 1_555 I ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc10 C SG CYS 28 C CYS 27 1_555 I ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc11 C SG CYS 91 C CYS 90 1_555 I ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc12 C SG CYS 94 C CYS 93 1_555 I ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? # _chem_comp.formula 'C9 H12 N2 O5' _chem_comp.formula_weight 228.202 _chem_comp.id DUR _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE" _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 DUR sing 83 n n N1 C6 DUR sing 84 n n N1 C1' DUR sing 85 n n C2 N3 DUR sing 86 n n C2 O2 DUR doub 87 n n N3 C4 DUR sing 88 n n N3 HN3 DUR sing 89 n n C4 C5 DUR sing 90 n n C4 O4 DUR doub 91 n n C5 C6 DUR doub 92 n n C5 H5 DUR sing 93 n n C6 H6 DUR sing 94 n n C1' C2' DUR sing 95 n n C1' O4' DUR sing 96 n n C1' H1' DUR sing 97 n n C2' C3' DUR sing 98 n n C2' "H2'1" DUR sing 99 n n C2' "H2'2" DUR sing 100 n n C3' C4' DUR sing 101 n n C3' O3' DUR sing 102 n n C3' H3' DUR sing 103 n n C4' O4' DUR sing 104 n n C4' C5' DUR sing 105 n n C4' H4' DUR sing 106 n n O3' HO3' DUR sing 107 n n C5' O5' DUR sing 108 n n C5' "H5'1" DUR sing 109 n n C5' "H5'2" DUR sing 110 n n O5' HO5' DUR sing 111 n n # _atom_sites.entry_id 4V31 _atom_sites.fract_transf_matrix[1][1] 0.017603 _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] 0.016669 _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] 0.011316 _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 D 2 ZN A 1 150 150 ZN ZN . E 3 DUR A 1 151 151 DUR DUR . F 2 ZN B 1 150 150 ZN ZN . G 3 DUR B 1 151 151 DUR DUR . H 4 FLC B 1 1124 1124 FLC FLC . I 2 ZN C 1 150 150 ZN ZN . J 3 DUR C 1 151 151 DUR DUR . K 5 HOH A 1 2001 2001 HOH HOH . K 5 HOH A 2 2002 2002 HOH HOH . K 5 HOH A 3 2003 2003 HOH HOH . K 5 HOH A 4 2004 2004 HOH HOH . K 5 HOH A 5 2005 2005 HOH HOH . K 5 HOH A 6 2006 2006 HOH HOH . K 5 HOH A 7 2007 2007 HOH HOH . K 5 HOH A 8 2008 2008 HOH HOH . K 5 HOH A 9 2009 2009 HOH HOH . K 5 HOH A 10 2010 2010 HOH HOH . K 5 HOH A 11 2011 2011 HOH HOH . K 5 HOH A 12 2012 2012 HOH HOH . K 5 HOH A 13 2013 2013 HOH HOH . K 5 HOH A 14 2014 2014 HOH HOH . K 5 HOH A 15 2015 2015 HOH HOH . K 5 HOH A 16 2016 2016 HOH HOH . K 5 HOH A 17 2017 2017 HOH HOH . K 5 HOH A 18 2018 2018 HOH HOH . K 5 HOH A 19 2019 2019 HOH HOH . K 5 HOH A 20 2020 2020 HOH HOH . K 5 HOH A 21 2021 2021 HOH HOH . K 5 HOH A 22 2022 2022 HOH HOH . K 5 HOH A 23 2023 2023 HOH HOH . K 5 HOH A 24 2024 2024 HOH HOH . K 5 HOH A 25 2025 2025 HOH HOH . K 5 HOH A 26 2026 2026 HOH HOH . K 5 HOH A 27 2027 2027 HOH HOH . K 5 HOH A 28 2028 2028 HOH HOH . K 5 HOH A 29 2029 2029 HOH HOH . K 5 HOH A 30 2030 2030 HOH HOH . K 5 HOH A 31 2031 2031 HOH HOH . K 5 HOH A 32 2032 2032 HOH HOH . K 5 HOH A 33 2033 2033 HOH HOH . K 5 HOH A 34 2034 2034 HOH HOH . K 5 HOH A 35 2035 2035 HOH HOH . K 5 HOH A 36 2036 2036 HOH HOH . K 5 HOH A 37 2037 2037 HOH HOH . K 5 HOH A 38 2038 2038 HOH HOH . K 5 HOH A 39 2039 2039 HOH HOH . K 5 HOH A 40 2040 2040 HOH HOH . K 5 HOH A 41 2041 2041 HOH HOH . K 5 HOH A 42 2042 2042 HOH HOH . K 5 HOH A 43 2043 2043 HOH HOH . K 5 HOH A 44 2044 2044 HOH HOH . K 5 HOH A 45 2045 2045 HOH HOH . K 5 HOH A 46 2046 2046 HOH HOH . K 5 HOH A 47 2047 2047 HOH HOH . K 5 HOH A 48 2048 2048 HOH HOH . K 5 HOH A 49 2049 2049 HOH HOH . K 5 HOH A 50 2050 2050 HOH HOH . K 5 HOH A 51 2051 2051 HOH HOH . K 5 HOH A 52 2052 2052 HOH HOH . K 5 HOH A 53 2053 2053 HOH HOH . K 5 HOH A 54 2054 2054 HOH HOH . K 5 HOH A 55 2055 2055 HOH HOH . K 5 HOH A 56 2056 2056 HOH HOH . K 5 HOH A 57 2057 2057 HOH HOH . K 5 HOH A 58 2058 2058 HOH HOH . K 5 HOH A 59 2059 2059 HOH HOH . K 5 HOH A 60 2060 2060 HOH HOH . K 5 HOH A 61 2061 2061 HOH HOH . K 5 HOH A 62 2062 2062 HOH HOH . K 5 HOH A 63 2063 2063 HOH HOH . K 5 HOH A 64 2064 2064 HOH HOH . K 5 HOH A 65 2065 2065 HOH HOH . K 5 HOH A 66 2066 2066 HOH HOH . K 5 HOH A 67 2067 2067 HOH HOH . K 5 HOH A 68 2068 2068 HOH HOH . K 5 HOH A 69 2069 2069 HOH HOH . K 5 HOH A 70 2070 2070 HOH HOH . K 5 HOH A 71 2071 2071 HOH HOH . K 5 HOH A 72 2072 2072 HOH HOH . K 5 HOH A 73 2073 2073 HOH HOH . K 5 HOH A 74 2074 2074 HOH HOH . K 5 HOH A 75 2075 2075 HOH HOH . K 5 HOH A 76 2076 2076 HOH HOH . K 5 HOH A 77 2077 2077 HOH HOH . L 5 HOH B 1 2001 2001 HOH HOH . L 5 HOH B 2 2002 2002 HOH HOH . L 5 HOH B 3 2003 2003 HOH HOH . L 5 HOH B 4 2004 2004 HOH HOH . L 5 HOH B 5 2005 2005 HOH HOH . L 5 HOH B 6 2006 2006 HOH HOH . L 5 HOH B 7 2007 2007 HOH HOH . L 5 HOH B 8 2008 2008 HOH HOH . L 5 HOH B 9 2009 2009 HOH HOH . L 5 HOH B 10 2010 2010 HOH HOH . L 5 HOH B 11 2011 2011 HOH HOH . L 5 HOH B 12 2012 2012 HOH HOH . L 5 HOH B 13 2013 2013 HOH HOH . L 5 HOH B 14 2014 2014 HOH HOH . L 5 HOH B 15 2015 2015 HOH HOH . L 5 HOH B 16 2016 2016 HOH HOH . L 5 HOH B 17 2017 2017 HOH HOH . L 5 HOH B 18 2018 2018 HOH HOH . L 5 HOH B 19 2019 2019 HOH HOH . L 5 HOH B 20 2020 2020 HOH HOH . L 5 HOH B 21 2021 2021 HOH HOH . L 5 HOH B 22 2022 2022 HOH HOH . L 5 HOH B 23 2023 2023 HOH HOH . L 5 HOH B 24 2024 2024 HOH HOH . L 5 HOH B 25 2025 2025 HOH HOH . L 5 HOH B 26 2026 2026 HOH HOH . L 5 HOH B 27 2027 2027 HOH HOH . L 5 HOH B 28 2028 2028 HOH HOH . L 5 HOH B 29 2029 2029 HOH HOH . L 5 HOH B 30 2030 2030 HOH HOH . L 5 HOH B 31 2031 2031 HOH HOH . L 5 HOH B 32 2032 2032 HOH HOH . L 5 HOH B 33 2033 2033 HOH HOH . L 5 HOH B 34 2034 2034 HOH HOH . L 5 HOH B 35 2035 2035 HOH HOH . L 5 HOH B 36 2036 2036 HOH HOH . L 5 HOH B 37 2037 2037 HOH HOH . L 5 HOH B 38 2038 2038 HOH HOH . L 5 HOH B 39 2039 2039 HOH HOH . L 5 HOH B 40 2040 2040 HOH HOH . L 5 HOH B 41 2041 2041 HOH HOH . L 5 HOH B 42 2042 2042 HOH HOH . L 5 HOH B 43 2043 2043 HOH HOH . L 5 HOH B 44 2044 2044 HOH HOH . L 5 HOH B 45 2045 2045 HOH HOH . L 5 HOH B 46 2046 2046 HOH HOH . L 5 HOH B 47 2047 2047 HOH HOH . L 5 HOH B 48 2048 2048 HOH HOH . L 5 HOH B 49 2049 2049 HOH HOH . L 5 HOH B 50 2050 2050 HOH HOH . L 5 HOH B 51 2051 2051 HOH HOH . L 5 HOH B 52 2052 2052 HOH HOH . M 5 HOH C 1 2001 2001 HOH HOH . M 5 HOH C 2 2002 2002 HOH HOH . M 5 HOH C 3 2003 2003 HOH HOH . M 5 HOH C 4 2004 2004 HOH HOH . M 5 HOH C 5 2005 2005 HOH HOH . M 5 HOH C 6 2006 2006 HOH HOH . M 5 HOH C 7 2007 2007 HOH HOH . M 5 HOH C 8 2008 2008 HOH HOH . M 5 HOH C 9 2009 2009 HOH HOH . M 5 HOH C 10 2010 2010 HOH HOH . M 5 HOH C 11 2011 2011 HOH HOH . M 5 HOH C 12 2012 2012 HOH HOH . M 5 HOH C 13 2013 2013 HOH HOH . M 5 HOH C 14 2014 2014 HOH HOH . M 5 HOH C 15 2015 2015 HOH HOH . M 5 HOH C 16 2016 2016 HOH HOH . M 5 HOH C 17 2017 2017 HOH HOH . M 5 HOH C 18 2018 2018 HOH HOH . M 5 HOH C 19 2019 2019 HOH HOH . M 5 HOH C 20 2020 2020 HOH HOH . M 5 HOH C 21 2021 2021 HOH HOH . M 5 HOH C 22 2022 2022 HOH HOH . M 5 HOH C 23 2023 2023 HOH HOH . M 5 HOH C 24 2024 2024 HOH HOH . M 5 HOH C 25 2025 2025 HOH HOH . M 5 HOH C 26 2026 2026 HOH HOH . M 5 HOH C 27 2027 2027 HOH HOH . M 5 HOH C 28 2028 2028 HOH HOH . M 5 HOH C 29 2029 2029 HOH HOH . M 5 HOH C 30 2030 2030 HOH HOH . M 5 HOH C 31 2031 2031 HOH HOH . M 5 HOH C 32 2032 2032 HOH HOH . M 5 HOH C 33 2033 2033 HOH HOH . M 5 HOH C 34 2034 2034 HOH HOH . M 5 HOH C 35 2035 2035 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 DUR . . . J 3 25.361 -14.73 0.184 1 42.27 ? N1 DUR 151 C 1 HETATM 2 C C2 DUR . . . J 3 24.086 -15.195 -0.196 1 42.73 ? C2 DUR 151 C 1 HETATM 3 N N3 DUR . . . J 3 23.837 -15.306 -1.485 1 43.43 ? N3 DUR 151 C 1 HETATM 4 C C4 DUR . . . J 3 24.723 -15.001 -2.438 1 38.69 ? C4 DUR 151 C 1 HETATM 5 C C5 DUR . . . J 3 26 -14.524 -2.097 1 36.29 ? C5 DUR 151 C 1 HETATM 6 C C6 DUR . . . J 3 26.3 -14.387 -0.756 1 37.41 ? C6 DUR 151 C 1 HETATM 7 O O2 DUR . . . J 3 23.17 -15.486 0.615 1 44.22 ? O2 DUR 151 C 1 HETATM 8 O O4 DUR . . . J 3 24.355 -15.175 -3.636 1 37.75 ? O4 DUR 151 C 1 HETATM 9 C C1' DUR . . . J 3 25.636 -14.581 1.623 1 44.83 ? C1' DUR 151 C 1 HETATM 10 C C2' DUR . . . J 3 25.946 -15.947 2.209 1 47.73 ? C2' DUR 151 C 1 HETATM 11 C C3' DUR . . . J 3 27.321 -15.836 2.813 1 46.76 ? C3' DUR 151 C 1 HETATM 12 C C4' DUR . . . J 3 27.798 -14.41 2.611 1 42.46 ? C4' DUR 151 C 1 HETATM 13 O O3' DUR . . . J 3 27.178 -16.121 4.201 1 51.87 ? O3' DUR 151 C 1 HETATM 14 O O4' DUR . . . J 3 26.768 -13.727 1.868 1 40.7 ? O4' DUR 151 C 1 HETATM 15 C C5' DUR . . . J 3 29.104 -14.338 1.842 1 39.88 ? C5' DUR 151 C 1 HETATM 16 O O5' DUR . . . J 3 29.438 -12.994 1.573 1 35.52 ? O5' DUR 151 C 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 421 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 16 #