data_1PNV # _model_server_result.job_id GaQwLSH6Fwm0FWJj-xQ1sw _model_server_result.datetime_utc '2024-11-23 09:23:33' _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 1pnv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":405}' # _entry.id 1PNV # _exptl.entry_id 1PNV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 1PNV _cell.length_a 153.17 _cell.length_b 153.17 _cell.length_c 100.64 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PNV _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 RER _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n D BGC 1 D 1 BGC C 8 BGC 3 n D RER 2 D 2 RER C 9 RER # 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 C C MLU 1 C MLU 1 1_555 C N OMZ 2 C OMZ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale2 C C OMZ 2 C OMZ 2 1_555 C N ASN 3 C ASN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale3 C OH OMZ 2 C OMZ 2 1_555 C C5 GHP 4 C GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale4 C C ASN 3 C ASN 3 1_555 C N GHP 4 C GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? covale ? covale5 C C GHP 4 C GHP 4 1_555 C N GHP 5 C GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale6 C C3 GHP 4 C GHP 4 1_555 C OCZ OMY 6 C OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale7 C O4 GHP 4 C GHP 4 1_555 D C1 BGC . D BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale8 C C GHP 5 C GHP 5 1_555 C N OMY 6 C OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale9 C C3 GHP 5 C GHP 5 1_555 C CG1 3FG 7 C 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.523 ? covale ? covale10 C C OMY 6 C OMY 6 1_555 C N 3FG 7 C 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale11 D O2 BGC . D BGC 1 1_555 D C1 RER . D RER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1PNV _atom_sites.fract_transf_matrix[1][1] 0.006529 _atom_sites.fract_transf_matrix[1][2] 0.003769 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007539 _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] 0.009936 _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 4 TYD A 1 405 405 TYD TYD . F 5 HOH A 1 2001 2001 HOH HOH . F 5 HOH A 2 2002 2002 HOH HOH . F 5 HOH A 3 2003 2003 HOH HOH . F 5 HOH A 4 2004 2004 HOH HOH . F 5 HOH A 5 2005 2005 HOH HOH . F 5 HOH A 6 2006 2006 HOH HOH . F 5 HOH A 7 2007 2007 HOH HOH . F 5 HOH A 8 2008 2008 HOH HOH . F 5 HOH A 9 2009 2009 HOH HOH . F 5 HOH A 10 2010 2010 HOH HOH . F 5 HOH A 11 2011 2011 HOH HOH . F 5 HOH A 12 2012 2012 HOH HOH . F 5 HOH A 13 2013 2013 HOH HOH . F 5 HOH A 14 2014 2014 HOH HOH . F 5 HOH A 15 2015 2015 HOH HOH . F 5 HOH A 16 2016 2016 HOH HOH . F 5 HOH A 17 2017 2017 HOH HOH . F 5 HOH A 18 2018 2018 HOH HOH . F 5 HOH A 19 2019 2019 HOH HOH . F 5 HOH A 20 2020 2020 HOH HOH . F 5 HOH A 21 2021 2021 HOH HOH . F 5 HOH A 22 2022 2022 HOH HOH . F 5 HOH A 23 2023 2023 HOH HOH . F 5 HOH A 24 2024 2024 HOH HOH . F 5 HOH A 25 2025 2025 HOH HOH . F 5 HOH A 26 2026 2026 HOH HOH . F 5 HOH A 27 2027 2027 HOH HOH . F 5 HOH A 28 2028 2028 HOH HOH . F 5 HOH A 29 2029 2029 HOH HOH . F 5 HOH A 30 2030 2030 HOH HOH . F 5 HOH A 31 2031 2031 HOH HOH . F 5 HOH A 32 2032 2032 HOH HOH . F 5 HOH A 33 2033 2033 HOH HOH . F 5 HOH A 34 2034 2034 HOH HOH . F 5 HOH A 35 2035 2035 HOH HOH . F 5 HOH A 36 2036 2036 HOH HOH . G 5 HOH B 1 2001 2001 HOH HOH . G 5 HOH B 2 2002 2002 HOH HOH . G 5 HOH B 3 2003 2003 HOH HOH . G 5 HOH B 4 2004 2004 HOH HOH . G 5 HOH B 5 2005 2005 HOH HOH . G 5 HOH B 6 2006 2006 HOH HOH . G 5 HOH B 7 2007 2007 HOH HOH . G 5 HOH B 8 2008 2008 HOH HOH . G 5 HOH B 9 2009 2009 HOH HOH . G 5 HOH B 10 2010 2010 HOH HOH . G 5 HOH B 11 2011 2011 HOH HOH . G 5 HOH B 12 2012 2012 HOH HOH . G 5 HOH B 13 2013 2013 HOH HOH . G 5 HOH B 14 2014 2014 HOH HOH . G 5 HOH B 15 2015 2015 HOH HOH . G 5 HOH B 16 2016 2016 HOH HOH . G 5 HOH B 17 2017 2017 HOH HOH . G 5 HOH B 18 2018 2018 HOH HOH . G 5 HOH B 19 2019 2019 HOH HOH . G 5 HOH B 20 2020 2020 HOH HOH . G 5 HOH B 21 2021 2021 HOH HOH . G 5 HOH B 22 2022 2022 HOH HOH . G 5 HOH B 23 2023 2023 HOH HOH . G 5 HOH B 24 2024 2024 HOH HOH . G 5 HOH B 25 2025 2025 HOH HOH . G 5 HOH B 26 2026 2026 HOH HOH . G 5 HOH B 27 2027 2027 HOH HOH . G 5 HOH B 28 2028 2028 HOH HOH . G 5 HOH B 29 2029 2029 HOH HOH . G 5 HOH B 30 2030 2030 HOH HOH . G 5 HOH B 31 2031 2031 HOH HOH . G 5 HOH B 32 2032 2032 HOH HOH . G 5 HOH B 33 2033 2033 HOH HOH . G 5 HOH B 34 2034 2034 HOH HOH . G 5 HOH B 35 2035 2035 HOH HOH . G 5 HOH B 36 2036 2036 HOH HOH . G 5 HOH B 37 2037 2037 HOH HOH . G 5 HOH B 38 2038 2038 HOH HOH . G 5 HOH B 39 2039 2039 HOH HOH . G 5 HOH B 40 2040 2040 HOH HOH . G 5 HOH B 41 2041 2041 HOH HOH . G 5 HOH B 42 2042 2042 HOH HOH . G 5 HOH B 43 2043 2043 HOH HOH . H 5 HOH C 1 2001 2001 HOH HOH . H 5 HOH C 2 2002 2002 HOH HOH . H 5 HOH C 3 2003 2003 HOH HOH . H 5 HOH C 4 2004 2004 HOH HOH . H 5 HOH C 5 2005 2005 HOH HOH . H 5 HOH C 6 2006 2006 HOH HOH . H 5 HOH C 7 2007 2007 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 P PA TYD . . . E 4 42.426 79.145 28.361 1 78.15 ? PA TYD 405 A 1 HETATM 2 O O1A TYD . . . E 4 41.73 79.918 29.422 1 77.04 ? O1A TYD 405 A 1 HETATM 3 O O2A TYD . . . E 4 43.357 78.059 28.76 1 77.44 ? O2A TYD 405 A 1 HETATM 4 O O3A TYD . . . E 4 43.326 80.23 27.543 1 72.98 ? O3A TYD 405 A 1 HETATM 5 P PB TYD . . . E 4 44.66 80.16 26.617 1 68.77 ? PB TYD 405 A 1 HETATM 6 O O1B TYD . . . E 4 44.579 81.286 25.601 1 66.15 ? O1B TYD 405 A 1 HETATM 7 O O2B TYD . . . E 4 44.584 78.775 25.999 1 69.81 ? O2B TYD 405 A 1 HETATM 8 O O3B TYD . . . E 4 45.822 80.32 27.582 1 68.98 ? O3B TYD 405 A 1 HETATM 9 O O5' TYD . . . E 4 41.323 78.505 27.389 1 76.45 ? O5' TYD 405 A 1 HETATM 10 C C5' TYD . . . E 4 40.305 79.316 26.801 1 74.88 ? C5' TYD 405 A 1 HETATM 11 C C4' TYD . . . E 4 39.117 78.48 26.359 1 74.86 ? C4' TYD 405 A 1 HETATM 12 O O4' TYD . . . E 4 39.389 77.671 25.195 1 74.62 ? O4' TYD 405 A 1 HETATM 13 C C3' TYD . . . E 4 38.6 77.441 27.34 1 74.86 ? C3' TYD 405 A 1 HETATM 14 O O3' TYD . . . E 4 37.738 78.037 28.301 1 77.6 ? O3' TYD 405 A 1 HETATM 15 C C2' TYD . . . E 4 37.798 76.477 26.459 1 74.83 ? C2' TYD 405 A 1 HETATM 16 C C1' TYD . . . E 4 38.302 76.782 25.043 1 74.53 ? C1' TYD 405 A 1 HETATM 17 N N1 TYD . . . E 4 38.712 75.598 24.252 1 74.47 ? N1 TYD 405 A 1 HETATM 18 C C2 TYD . . . E 4 37.695 74.876 23.653 1 75.25 ? C2 TYD 405 A 1 HETATM 19 O O2 TYD . . . E 4 36.514 75.052 23.905 1 76.4 ? O2 TYD 405 A 1 HETATM 20 N N3 TYD . . . E 4 38.115 73.928 22.753 1 74.61 ? N3 TYD 405 A 1 HETATM 21 C C4 TYD . . . E 4 39.414 73.627 22.401 1 72.91 ? C4 TYD 405 A 1 HETATM 22 O O4 TYD . . . E 4 39.629 72.758 21.568 1 72.41 ? O4 TYD 405 A 1 HETATM 23 C C5 TYD . . . E 4 40.434 74.403 23.076 1 72.72 ? C5 TYD 405 A 1 HETATM 24 C C5M TYD . . . E 4 41.873 74.124 22.774 1 69.99 ? C5M TYD 405 A 1 HETATM 25 C C6 TYD . . . E 4 40.037 75.342 23.954 1 73.46 ? C6 TYD 405 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #