data_2CCG # _model_server_result.job_id 7x5MuA6yZS32xgVd_LqsKg _model_server_result.datetime_utc '2024-11-24 04:35:25' _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 2ccg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1206}' # _entry.id 2CCG # _exptl.entry_id 2CCG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-PHOSPHATE" _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 103.63 _cell.angle_gamma 90 _cell.entry_id 2CCG _cell.length_a 54.54 _cell.length_b 51.27 _cell.length_c 72.94 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2CCG _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 D N N # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _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 P O1P TMP doub 306 n n P O2P TMP sing 307 n n P O3P TMP sing 308 n n P O5' TMP sing 309 n n O2P HOP2 TMP sing 310 n n O3P HOP3 TMP sing 311 n n O5' C5' TMP sing 312 n n C5' C4' TMP sing 313 n n C5' "H5'1" TMP sing 314 n n C5' "H5'2" TMP sing 315 n n C4' O4' TMP sing 316 n n C4' C3' TMP sing 317 n n C4' H4' TMP sing 318 n n O4' C1' TMP sing 319 n n C3' O3' TMP sing 320 n n C3' C2' TMP sing 321 n n C3' H3' TMP sing 322 n n O3' HO3' TMP sing 323 n n C2' C1' TMP sing 324 n n C2' "H2'1" TMP sing 325 n n C2' "H2'2" TMP sing 326 n n C1' N1 TMP sing 327 n n C1' H1' TMP sing 328 n n N1 C2 TMP sing 329 n n N1 C6 TMP sing 330 n n C2 O2 TMP doub 331 n n C2 N3 TMP sing 332 n n N3 C4 TMP sing 333 n n N3 HN3 TMP sing 334 n n C4 O4 TMP doub 335 n n C4 C5 TMP sing 336 n n C5 C5M TMP sing 337 n n C5 C6 TMP doub 338 n n C5M H51 TMP sing 339 n n C5M H52 TMP sing 340 n n C5M H53 TMP sing 341 n n C6 H6 TMP sing 342 n n # _atom_sites.entry_id 2CCG _atom_sites.fract_transf_matrix[1][1] 0.018335 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004446 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019505 _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] 0.014107 _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 TMP A 1 1205 1205 TMP TMP . D 2 TMP B 1 1206 1206 TMP TMP . E 3 HOH A 1 2001 2001 HOH HOH . E 3 HOH A 2 2002 2002 HOH HOH . E 3 HOH A 3 2003 2003 HOH HOH . E 3 HOH A 4 2004 2004 HOH HOH . E 3 HOH A 5 2005 2005 HOH HOH . E 3 HOH A 6 2006 2006 HOH HOH . E 3 HOH A 7 2007 2007 HOH HOH . E 3 HOH A 8 2008 2008 HOH HOH . E 3 HOH A 9 2009 2009 HOH HOH . E 3 HOH A 10 2010 2010 HOH HOH . E 3 HOH A 11 2011 2011 HOH HOH . E 3 HOH A 12 2012 2012 HOH HOH . E 3 HOH A 13 2013 2013 HOH HOH . E 3 HOH A 14 2014 2014 HOH HOH . E 3 HOH A 15 2015 2015 HOH HOH . E 3 HOH A 16 2016 2016 HOH HOH . E 3 HOH A 17 2017 2017 HOH HOH . E 3 HOH A 18 2018 2018 HOH HOH . E 3 HOH A 19 2019 2019 HOH HOH . E 3 HOH A 20 2020 2020 HOH HOH . E 3 HOH A 21 2021 2021 HOH HOH . E 3 HOH A 22 2022 2022 HOH HOH . E 3 HOH A 23 2023 2023 HOH HOH . E 3 HOH A 24 2024 2024 HOH HOH . E 3 HOH A 25 2025 2025 HOH HOH . E 3 HOH A 26 2026 2026 HOH HOH . E 3 HOH A 27 2027 2027 HOH HOH . E 3 HOH A 28 2028 2028 HOH HOH . E 3 HOH A 29 2029 2029 HOH HOH . E 3 HOH A 30 2030 2030 HOH HOH . E 3 HOH A 31 2031 2031 HOH HOH . E 3 HOH A 32 2032 2032 HOH HOH . E 3 HOH A 33 2033 2033 HOH HOH . E 3 HOH A 34 2034 2034 HOH HOH . E 3 HOH A 35 2035 2035 HOH HOH . E 3 HOH A 36 2036 2036 HOH HOH . E 3 HOH A 37 2037 2037 HOH HOH . E 3 HOH A 38 2038 2038 HOH HOH . E 3 HOH A 39 2039 2039 HOH HOH . E 3 HOH A 40 2040 2040 HOH HOH . E 3 HOH A 41 2041 2041 HOH HOH . E 3 HOH A 42 2042 2042 HOH HOH . E 3 HOH A 43 2043 2043 HOH HOH . F 3 HOH B 1 2001 2001 HOH HOH . F 3 HOH B 2 2002 2002 HOH HOH . F 3 HOH B 3 2003 2003 HOH HOH . F 3 HOH B 4 2004 2004 HOH HOH . F 3 HOH B 5 2005 2005 HOH HOH . F 3 HOH B 6 2006 2006 HOH HOH . F 3 HOH B 7 2007 2007 HOH HOH . F 3 HOH B 8 2008 2008 HOH HOH . F 3 HOH B 9 2009 2009 HOH HOH . F 3 HOH B 10 2010 2010 HOH HOH . F 3 HOH B 11 2011 2011 HOH HOH . F 3 HOH B 12 2012 2012 HOH HOH . F 3 HOH B 13 2013 2013 HOH HOH . F 3 HOH B 14 2014 2014 HOH HOH . F 3 HOH B 15 2015 2015 HOH HOH . F 3 HOH B 16 2016 2016 HOH HOH . F 3 HOH B 17 2017 2017 HOH HOH . F 3 HOH B 18 2018 2018 HOH HOH . F 3 HOH B 19 2019 2019 HOH HOH . F 3 HOH B 20 2020 2020 HOH HOH . F 3 HOH B 21 2021 2021 HOH HOH . F 3 HOH B 22 2022 2022 HOH HOH . F 3 HOH B 23 2023 2023 HOH HOH . F 3 HOH B 24 2024 2024 HOH HOH . F 3 HOH B 25 2025 2025 HOH HOH . F 3 HOH B 26 2026 2026 HOH HOH . F 3 HOH B 27 2027 2027 HOH HOH . F 3 HOH B 28 2028 2028 HOH HOH . F 3 HOH B 29 2029 2029 HOH HOH . F 3 HOH B 30 2030 2030 HOH HOH . F 3 HOH B 31 2031 2031 HOH HOH . F 3 HOH B 32 2032 2032 HOH HOH . F 3 HOH B 33 2033 2033 HOH HOH . F 3 HOH B 34 2034 2034 HOH HOH . F 3 HOH B 35 2035 2035 HOH HOH . F 3 HOH B 36 2036 2036 HOH HOH . F 3 HOH B 37 2037 2037 HOH HOH . F 3 HOH B 38 2038 2038 HOH HOH . F 3 HOH B 39 2039 2039 HOH HOH . F 3 HOH B 40 2040 2040 HOH HOH . F 3 HOH B 41 2041 2041 HOH HOH . F 3 HOH B 42 2042 2042 HOH HOH . F 3 HOH B 43 2043 2043 HOH HOH . F 3 HOH B 44 2044 2044 HOH HOH . F 3 HOH B 45 2045 2045 HOH HOH . F 3 HOH B 46 2046 2046 HOH HOH . F 3 HOH B 47 2047 2047 HOH HOH . F 3 HOH B 48 2048 2048 HOH HOH . F 3 HOH B 49 2049 2049 HOH HOH . F 3 HOH B 50 2050 2050 HOH HOH . F 3 HOH B 51 2051 2051 HOH HOH . F 3 HOH B 52 2052 2052 HOH HOH . F 3 HOH B 53 2053 2053 HOH HOH . F 3 HOH B 54 2054 2054 HOH HOH . F 3 HOH B 55 2055 2055 HOH HOH . F 3 HOH B 56 2056 2056 HOH HOH . F 3 HOH B 57 2057 2057 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 P TMP . . . D 2 0.66 6.614 82.227 1 66.43 ? P TMP 1206 B 1 HETATM 2 O O1P TMP . . . D 2 1.221 7.561 83.202 1 74.48 ? O1P TMP 1206 B 1 HETATM 3 O O2P TMP . . . D 2 1.599 6.427 81.052 1 63.48 ? O2P TMP 1206 B 1 HETATM 4 O O3P TMP . . . D 2 -0.683 7.031 81.771 1 62.51 ? O3P TMP 1206 B 1 HETATM 5 O O5' TMP . . . D 2 0.573 5.229 82.912 1 67.79 ? O5' TMP 1206 B 1 HETATM 6 C C5' TMP . . . D 2 -0.236 4.925 84.114 1 55.31 ? C5' TMP 1206 B 1 HETATM 7 C C4' TMP . . . D 2 -0.683 3.464 83.998 1 48.25 ? C4' TMP 1206 B 1 HETATM 8 O O4' TMP . . . D 2 -1.577 3.155 85.103 1 50.97 ? O4' TMP 1206 B 1 HETATM 9 C C3' TMP . . . D 2 -1.45 3.112 82.699 1 52.72 ? C3' TMP 1206 B 1 HETATM 10 O O3' TMP . . . D 2 -0.722 2.073 82.07 1 55.73 ? O3' TMP 1206 B 1 HETATM 11 C C2' TMP . . . D 2 -2.807 2.598 83.089 1 52.84 ? C2' TMP 1206 B 1 HETATM 12 C C1' TMP . . . D 2 -2.809 2.636 84.604 1 49.3 ? C1' TMP 1206 B 1 HETATM 13 N N1 TMP . . . D 2 -3.97 3.171 85.346 1 39.36 ? N1 TMP 1206 B 1 HETATM 14 C C2 TMP . . . D 2 -5.023 2.291 85.689 1 36.38 ? C2 TMP 1206 B 1 HETATM 15 O O2 TMP . . . D 2 -5.046 1.075 85.398 1 41.7 ? O2 TMP 1206 B 1 HETATM 16 N N3 TMP . . . D 2 -6.069 2.923 86.394 1 40.92 ? N3 TMP 1206 B 1 HETATM 17 C C4 TMP . . . D 2 -6.131 4.281 86.771 1 41.66 ? C4 TMP 1206 B 1 HETATM 18 O O4 TMP . . . D 2 -7.112 4.688 87.383 1 39.32 ? O4 TMP 1206 B 1 HETATM 19 C C5 TMP . . . D 2 -4.984 5.146 86.375 1 40.92 ? C5 TMP 1206 B 1 HETATM 20 C C5M TMP . . . D 2 -4.924 6.596 86.721 1 31.58 ? C5M TMP 1206 B 1 HETATM 21 C C6 TMP . . . D 2 -3.93 4.517 85.666 1 29.67 ? C6 TMP 1206 B 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 428 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #