data_2V54 # _model_server_result.job_id GKpnmkvBOprI_OMQCYruwA _model_server_result.datetime_utc '2024-12-04 02:32:29' _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 2v54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1207}' # _entry.id 2V54 # _exptl.entry_id 2V54 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 90 _cell.angle_gamma 90 _cell.entry_id 2V54 _cell.length_a 56.77 _cell.length_b 55.59 _cell.length_c 161.17 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2V54 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C 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 metalc ? metalc1 B OD1 ASP 13 B ASP 13 1_555 D MG MG . B MG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc2 B OE2 GLU 145 B GLU 145 1_555 D MG MG . B MG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc3 D MG MG . B MG 1205 1_555 E O4 POP . B POP 1206 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.26 ? metalc ? metalc4 D MG MG . B MG 1205 1_555 F O2B TYD . B TYD 1207 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.036 ? metalc ? metalc5 D MG MG . B MG 1205 1_555 H O HOH . B HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? # _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 ? # 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 PA O1A TYD doub 344 n n PA O2A TYD sing 345 n n PA O3A TYD sing 346 n n PA O5' TYD sing 347 n n O2A HOA2 TYD sing 348 n n O3A PB TYD sing 349 n n PB O1B TYD doub 350 n n PB O2B TYD sing 351 n n PB O3B TYD sing 352 n n O2B HOB2 TYD sing 353 n n O3B HOB3 TYD sing 354 n n O5' C5' TYD sing 355 n n C5' C4' TYD sing 356 n n C5' "H5'1" TYD sing 357 n n C5' "H5'2" TYD sing 358 n n C4' O4' TYD sing 359 n n C4' C3' TYD sing 360 n n C4' H4' TYD sing 361 n n O4' C1' TYD sing 362 n n C3' O3' TYD sing 363 n n C3' C2' TYD sing 364 n n C3' H3' TYD sing 365 n n O3' HO3' TYD sing 366 n n C2' C1' TYD sing 367 n n C2' "H2'1" TYD sing 368 n n C2' "H2'2" TYD sing 369 n n C1' N1 TYD sing 370 n n C1' H1' TYD sing 371 n n N1 C2 TYD sing 372 n y N1 C6 TYD sing 373 n y C2 O2 TYD doub 374 n n C2 N3 TYD sing 375 n y N3 C4 TYD sing 376 n y N3 HN3 TYD sing 377 n n C4 O4 TYD doub 378 n n C4 C5 TYD sing 379 n y C5 C5M TYD sing 380 n n C5 C6 TYD doub 381 n y C5M H51 TYD sing 382 n n C5M H52 TYD sing 383 n n C5M H53 TYD sing 384 n n C6 H6 TYD sing 385 n n # _atom_sites.entry_id 2V54 _atom_sites.fract_transf_matrix[1][1] 0.017615 _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] 0.017989 _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] 0.006205 _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 TYD A 1 1205 1205 TYD TYD . D 3 MG B 1 1205 1205 MG MG . E 4 POP B 1 1206 1206 POP POP . F 2 TYD B 1 1207 1207 TYD TYD . G 5 HOH A 1 2001 2001 HOH HOH . G 5 HOH A 2 2002 2002 HOH HOH . G 5 HOH A 3 2003 2003 HOH HOH . G 5 HOH A 4 2004 2004 HOH HOH . G 5 HOH A 5 2005 2005 HOH HOH . G 5 HOH A 6 2006 2006 HOH HOH . G 5 HOH A 7 2007 2007 HOH HOH . G 5 HOH A 8 2008 2008 HOH HOH . G 5 HOH A 9 2009 2009 HOH HOH . G 5 HOH A 10 2010 2010 HOH HOH . G 5 HOH A 11 2011 2011 HOH HOH . G 5 HOH A 12 2012 2012 HOH HOH . G 5 HOH A 13 2013 2013 HOH HOH . G 5 HOH A 14 2014 2014 HOH HOH . G 5 HOH A 15 2015 2015 HOH HOH . G 5 HOH A 16 2016 2016 HOH HOH . G 5 HOH A 17 2017 2017 HOH HOH . G 5 HOH A 18 2018 2018 HOH HOH . G 5 HOH A 19 2019 2019 HOH HOH . G 5 HOH A 20 2020 2020 HOH HOH . G 5 HOH A 21 2021 2021 HOH HOH . G 5 HOH A 22 2022 2022 HOH HOH . G 5 HOH A 23 2023 2023 HOH HOH . G 5 HOH A 24 2024 2024 HOH HOH . G 5 HOH A 25 2025 2025 HOH HOH . G 5 HOH A 26 2026 2026 HOH HOH . G 5 HOH A 27 2027 2027 HOH HOH . G 5 HOH A 28 2028 2028 HOH HOH . G 5 HOH A 29 2029 2029 HOH HOH . G 5 HOH A 30 2030 2030 HOH HOH . G 5 HOH A 31 2031 2031 HOH HOH . G 5 HOH A 32 2032 2032 HOH HOH . G 5 HOH A 33 2033 2033 HOH HOH . G 5 HOH A 34 2034 2034 HOH HOH . G 5 HOH A 35 2035 2035 HOH HOH . G 5 HOH A 36 2036 2036 HOH HOH . G 5 HOH A 37 2037 2037 HOH HOH . G 5 HOH A 38 2038 2038 HOH HOH . G 5 HOH A 39 2039 2039 HOH HOH . G 5 HOH A 40 2040 2040 HOH HOH . G 5 HOH A 41 2041 2041 HOH HOH . G 5 HOH A 42 2042 2042 HOH HOH . G 5 HOH A 43 2043 2043 HOH HOH . G 5 HOH A 44 2044 2044 HOH HOH . G 5 HOH A 45 2045 2045 HOH HOH . G 5 HOH A 46 2046 2046 HOH HOH . H 5 HOH B 1 2001 2001 HOH HOH . H 5 HOH B 2 2002 2002 HOH HOH . H 5 HOH B 3 2003 2003 HOH HOH . H 5 HOH B 4 2004 2004 HOH HOH . H 5 HOH B 5 2005 2005 HOH HOH . H 5 HOH B 6 2006 2006 HOH HOH . H 5 HOH B 7 2007 2007 HOH HOH . H 5 HOH B 8 2008 2008 HOH HOH . H 5 HOH B 9 2009 2009 HOH HOH . H 5 HOH B 10 2010 2010 HOH HOH . H 5 HOH B 11 2011 2011 HOH HOH . H 5 HOH B 12 2012 2012 HOH HOH . H 5 HOH B 13 2013 2013 HOH HOH . H 5 HOH B 14 2014 2014 HOH HOH . H 5 HOH B 15 2015 2015 HOH HOH . H 5 HOH B 16 2016 2016 HOH HOH . H 5 HOH B 17 2017 2017 HOH HOH . H 5 HOH B 18 2018 2018 HOH HOH . H 5 HOH B 19 2019 2019 HOH HOH . H 5 HOH B 20 2020 2020 HOH HOH . H 5 HOH B 21 2021 2021 HOH HOH . H 5 HOH B 22 2022 2022 HOH HOH . H 5 HOH B 23 2023 2023 HOH HOH . H 5 HOH B 24 2024 2024 HOH HOH . H 5 HOH B 25 2025 2025 HOH HOH . H 5 HOH B 26 2026 2026 HOH HOH . H 5 HOH B 27 2027 2027 HOH HOH . H 5 HOH B 28 2028 2028 HOH HOH . H 5 HOH B 29 2029 2029 HOH HOH . H 5 HOH B 30 2030 2030 HOH HOH . H 5 HOH B 31 2031 2031 HOH HOH . H 5 HOH B 32 2032 2032 HOH HOH . H 5 HOH B 33 2033 2033 HOH HOH . H 5 HOH B 34 2034 2034 HOH HOH . H 5 HOH B 35 2035 2035 HOH HOH . H 5 HOH B 36 2036 2036 HOH HOH . H 5 HOH B 37 2037 2037 HOH HOH . H 5 HOH B 38 2038 2038 HOH HOH . H 5 HOH B 39 2039 2039 HOH HOH . H 5 HOH B 40 2040 2040 HOH HOH . H 5 HOH B 41 2041 2041 HOH HOH . H 5 HOH B 42 2042 2042 HOH HOH . H 5 HOH B 43 2043 2043 HOH HOH . H 5 HOH B 44 2044 2044 HOH HOH . H 5 HOH B 45 2045 2045 HOH HOH . H 5 HOH B 46 2046 2046 HOH HOH . H 5 HOH B 47 2047 2047 HOH HOH . H 5 HOH B 48 2048 2048 HOH HOH . H 5 HOH B 49 2049 2049 HOH HOH . H 5 HOH B 50 2050 2050 HOH HOH . H 5 HOH B 51 2051 2051 HOH HOH . H 5 HOH B 52 2052 2052 HOH HOH . H 5 HOH B 53 2053 2053 HOH HOH . H 5 HOH B 54 2054 2054 HOH HOH . H 5 HOH B 55 2055 2055 HOH HOH . H 5 HOH B 56 2056 2056 HOH HOH . H 5 HOH B 57 2057 2057 HOH HOH . H 5 HOH B 58 2058 2058 HOH HOH . H 5 HOH B 59 2059 2059 HOH HOH . H 5 HOH B 60 2060 2060 HOH HOH . H 5 HOH B 61 2061 2061 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 . A . F 2 7.012 19.297 -32.387 0.59 33.65 ? PA TYD 1207 B 1 HETATM 2 P PA TYD . B . F 2 6.993 19.123 -32.435 0.4 40.81 ? PA TYD 1207 B 1 HETATM 3 O O1A TYD . A . F 2 7.787 18.331 -31.573 0.59 33.72 ? O1A TYD 1207 B 1 HETATM 4 O O1A TYD . B . F 2 6.44 18.839 -33.92 0.4 39.8 ? O1A TYD 1207 B 1 HETATM 5 O O2A TYD . A . F 2 7.629 20.606 -32.699 0.59 30.81 ? O2A TYD 1207 B 1 HETATM 6 O O2A TYD . B . F 2 7.603 17.87 -31.937 0.4 40.46 ? O2A TYD 1207 B 1 HETATM 7 O O3A TYD . A . F 2 6.664 18.563 -33.777 0.59 30.21 ? O3A TYD 1207 B 1 HETATM 8 O O3A TYD . B . F 2 7.827 20.344 -32.471 0.4 39.69 ? O3A TYD 1207 B 1 HETATM 9 P PB TYD . A . F 2 5.744 19.283 -34.887 0.59 26.44 ? PB TYD 1207 B 1 HETATM 10 O O1B TYD . A . F 2 5.843 20.872 -34.641 0.59 26.62 ? O1B TYD 1207 B 1 HETATM 11 O O2B TYD . A . F 2 4.234 18.867 -34.517 0.59 25.12 ? O2B TYD 1207 B 1 HETATM 12 O O3B TYD . A . F 2 6.124 18.89 -36.262 0.59 29.63 ? O3B TYD 1207 B 1 HETATM 13 O O5' TYD . A . F 2 5.567 19.537 -31.714 0.59 31.45 ? O5' TYD 1207 B 1 HETATM 14 O O5' TYD . B . F 2 5.643 19.429 -31.61 0.4 38.28 ? O5' TYD 1207 B 1 HETATM 15 C C5' TYD . A . F 2 4.74 18.432 -31.335 0.59 29.76 ? C5' TYD 1207 B 1 HETATM 16 C C5' TYD . B . F 2 4.73 18.371 -31.306 0.4 35.59 ? C5' TYD 1207 B 1 HETATM 17 C C4' TYD . A . F 2 3.419 18.896 -30.715 0.59 29 ? C4' TYD 1207 B 1 HETATM 18 C C4' TYD . B . F 2 3.435 18.907 -30.693 0.4 33.99 ? C4' TYD 1207 B 1 HETATM 19 O O4' TYD . A . F 2 3.66 19.583 -29.473 0.59 29.54 ? O4' TYD 1207 B 1 HETATM 20 O O4' TYD . B . F 2 3.712 19.608 -29.467 0.4 33.7 ? O4' TYD 1207 B 1 HETATM 21 C C3' TYD . A . F 2 2.689 19.889 -31.626 0.59 28.2 ? C3' TYD 1207 B 1 HETATM 22 C C3' TYD . B . F 2 2.757 19.919 -31.622 0.4 33.07 ? C3' TYD 1207 B 1 HETATM 23 O O3' TYD . A . F 2 1.301 19.54 -31.691 0.59 31.02 ? O3' TYD 1207 B 1 HETATM 24 O O3' TYD . B . F 2 1.377 19.573 -31.783 0.4 34.61 ? O3' TYD 1207 B 1 HETATM 25 C C2' TYD . A . F 2 2.879 21.208 -30.875 0.59 28.38 ? C2' TYD 1207 B 1 HETATM 26 C C2' TYD . B . F 2 2.892 21.228 -30.841 0.4 32.76 ? C2' TYD 1207 B 1 HETATM 27 C C1' TYD . A . F 2 2.732 20.681 -29.447 0.59 26.08 ? C1' TYD 1207 B 1 HETATM 28 C C1' TYD . B . F 2 2.754 20.678 -29.422 0.4 30.97 ? C1' TYD 1207 B 1 HETATM 29 N N1 TYD . A . F 2 3.135 21.699 -28.446 0.59 22.7 ? N1 TYD 1207 B 1 HETATM 30 N N1 TYD . B . F 2 3.152 21.685 -28.411 0.4 28.24 ? N1 TYD 1207 B 1 HETATM 31 C C2 TYD . A . F 2 2.223 22.166 -27.489 0.59 20.09 ? C2 TYD 1207 B 1 HETATM 32 C C2 TYD . B . F 2 2.231 22.168 -27.472 0.4 26.3 ? C2 TYD 1207 B 1 HETATM 33 O O2 TYD . A . F 2 1.053 21.787 -27.507 0.59 19.23 ? O2 TYD 1207 B 1 HETATM 34 O O2 TYD . B . F 2 1.061 21.789 -27.495 0.4 25.62 ? O2 TYD 1207 B 1 HETATM 35 N N3 TYD . A . F 2 2.646 23.067 -26.504 0.59 18.73 ? N3 TYD 1207 B 1 HETATM 36 N N3 TYD . B . F 2 2.646 23.087 -26.501 0.4 25.21 ? N3 TYD 1207 B 1 HETATM 37 C C4 TYD . A . F 2 3.976 23.502 -26.476 0.59 18.8 ? C4 TYD 1207 B 1 HETATM 38 C C4 TYD . B . F 2 3.977 23.524 -26.472 0.4 25.16 ? C4 TYD 1207 B 1 HETATM 39 O O4 TYD . A . F 2 4.36 24.249 -25.576 0.59 18.75 ? O4 TYD 1207 B 1 HETATM 40 O O4 TYD . B . F 2 4.346 24.311 -25.603 0.4 25.2 ? O4 TYD 1207 B 1 HETATM 41 C C5 TYD . A . F 2 4.876 23.047 -27.433 0.59 19.57 ? C5 TYD 1207 B 1 HETATM 42 C C5 TYD . B . F 2 4.886 23.048 -27.409 0.4 25.66 ? C5 TYD 1207 B 1 HETATM 43 C C5M TYD . A . F 2 6.327 23.531 -27.409 0.59 15.63 ? C5M TYD 1207 B 1 HETATM 44 C C5M TYD . B . F 2 6.335 23.539 -27.392 0.4 23.31 ? C5M TYD 1207 B 1 HETATM 45 C C6 TYD . A . F 2 4.459 22.151 -28.412 0.59 20.86 ? C6 TYD 1207 B 1 HETATM 46 C C6 TYD . B . F 2 4.478 22.132 -28.373 0.4 26.72 ? C6 TYD 1207 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #