data_3EVW # _model_server_result.job_id IlZZEjPK27ZHpYaLLfirpw _model_server_result.datetime_utc '2024-11-28 02:04:06' _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 3evw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":138}' # _entry.id 3EVW # _exptl.entry_id 3EVW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 3EVW _cell.length_a 80.69 _cell.length_b 151.038 _cell.length_c 184.874 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EVW _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,H,K,L,O,P,S,U,W 1 1,2 B,D,F,I,J,M,N,Q,R,T,V,X 2 1,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 3_755 -x+2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 161.38 0 92.437 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R 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 H O2B TYD . A TYD 138 1_555 G MG MG . A MG 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc2 J O2B TYD . B TYD 138 1_555 I MG MG . B MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc3 L O1A TYD . C TYD 138 1_555 K MG MG . C MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc4 L O2B TYD . C TYD 138 1_555 K MG MG . C MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc5 N O2B TYD . D TYD 138 1_555 M MG MG . D MG 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc6 P O2B TYD . E TYD 138 1_555 O MG MG . E MG 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc7 P O1A TYD . E TYD 138 1_555 O MG MG . E MG 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc8 R O2B TYD . F TYD 138 1_555 Q MG MG . F MG 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? # _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 334 n n PA O2A TYD sing 335 n n PA O3A TYD sing 336 n n PA O5' TYD sing 337 n n O2A HOA2 TYD sing 338 n n O3A PB TYD sing 339 n n PB O1B TYD doub 340 n n PB O2B TYD sing 341 n n PB O3B TYD sing 342 n n O2B HOB2 TYD sing 343 n n O3B HOB3 TYD sing 344 n n O5' C5' TYD sing 345 n n C5' C4' TYD sing 346 n n C5' "H5'1" TYD sing 347 n n C5' "H5'2" TYD sing 348 n n C4' O4' TYD sing 349 n n C4' C3' TYD sing 350 n n C4' H4' TYD sing 351 n n O4' C1' TYD sing 352 n n C3' O3' TYD sing 353 n n C3' C2' TYD sing 354 n n C3' H3' TYD sing 355 n n O3' HO3' TYD sing 356 n n C2' C1' TYD sing 357 n n C2' "H2'1" TYD sing 358 n n C2' "H2'2" TYD sing 359 n n C1' N1 TYD sing 360 n n C1' H1' TYD sing 361 n n N1 C2 TYD sing 362 n y N1 C6 TYD sing 363 n y C2 O2 TYD doub 364 n n C2 N3 TYD sing 365 n y N3 C4 TYD sing 366 n y N3 HN3 TYD sing 367 n n C4 O4 TYD doub 368 n n C4 C5 TYD sing 369 n y C5 C5M TYD sing 370 n n C5 C6 TYD doub 371 n y C5M H51 TYD sing 372 n n C5M H52 TYD sing 373 n n C5M H53 TYD sing 374 n n C6 H6 TYD sing 375 n n # _atom_sites.entry_id 3EVW _atom_sites.fract_transf_matrix[1][1] 0.012393 _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] 0.006621 _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] 0.005409 _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 G 2 MG A 1 160 160 MG MG . H 3 TYD A 1 138 160 TYD TYD . I 2 MG B 1 161 161 MG MG . J 3 TYD B 1 138 161 TYD TYD . K 2 MG C 1 162 162 MG MG . L 3 TYD C 1 138 162 TYD TYD . M 2 MG D 1 163 163 MG MG . N 3 TYD D 1 138 163 TYD TYD . O 2 MG E 1 164 164 MG MG . P 3 TYD E 1 138 164 TYD TYD . Q 2 MG F 1 165 165 MG MG . R 3 TYD F 1 138 165 TYD TYD . S 4 HOH A 1 139 10 HOH HOH . S 4 HOH A 2 140 11 HOH HOH . S 4 HOH A 3 141 16 HOH HOH . S 4 HOH A 4 142 24 HOH HOH . S 4 HOH A 5 143 26 HOH HOH . T 4 HOH B 1 139 13 HOH HOH . T 4 HOH B 2 140 17 HOH HOH . T 4 HOH B 3 141 32 HOH HOH . T 4 HOH B 4 142 33 HOH HOH . U 4 HOH C 1 139 2 HOH HOH . U 4 HOH C 2 140 3 HOH HOH . U 4 HOH C 3 141 4 HOH HOH . U 4 HOH C 4 142 5 HOH HOH . U 4 HOH C 5 143 7 HOH HOH . U 4 HOH C 6 144 8 HOH HOH . U 4 HOH C 7 145 9 HOH HOH . U 4 HOH C 8 146 14 HOH HOH . U 4 HOH C 9 147 20 HOH HOH . U 4 HOH C 10 148 23 HOH HOH . V 4 HOH D 1 139 15 HOH HOH . V 4 HOH D 2 140 18 HOH HOH . V 4 HOH D 3 141 25 HOH HOH . V 4 HOH D 4 142 28 HOH HOH . V 4 HOH D 5 143 29 HOH HOH . V 4 HOH D 6 144 30 HOH HOH . V 4 HOH D 7 145 31 HOH HOH . W 4 HOH E 1 139 12 HOH HOH . W 4 HOH E 2 140 19 HOH HOH . W 4 HOH E 3 141 21 HOH HOH . W 4 HOH E 4 142 22 HOH HOH . W 4 HOH E 5 143 27 HOH HOH . X 4 HOH F 1 139 1 HOH HOH . X 4 HOH F 2 140 6 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 . . . N 3 71.686 31.843 68.454 1 58.63 ? PA TYD 138 D 1 HETATM 2 O O1A TYD . . . N 3 72.302 32.376 69.733 1 60.34 ? O1A TYD 138 D 1 HETATM 3 O O2A TYD . . . N 3 70.227 31.487 68.321 1 66.65 ? O2A TYD 138 D 1 HETATM 4 O O3A TYD . . . N 3 72.007 32.804 67.195 1 57.47 ? O3A TYD 138 D 1 HETATM 5 P PB TYD . . . N 3 73.033 34.046 67.307 1 57.01 ? PB TYD 138 D 1 HETATM 6 O O1B TYD . . . N 3 74.215 33.64 66.462 1 54.39 ? O1B TYD 138 D 1 HETATM 7 O O2B TYD . . . N 3 73.37 34.101 68.776 1 63.76 ? O2B TYD 138 D 1 HETATM 8 O O3B TYD . . . N 3 72.216 35.207 66.783 1 58.7 ? O3B TYD 138 D 1 HETATM 9 O O5' TYD . . . N 3 72.427 30.503 68.001 1 63.81 ? O5' TYD 138 D 1 HETATM 10 C C5' TYD . . . N 3 73.834 30.366 68.134 1 60.44 ? C5' TYD 138 D 1 HETATM 11 C C4' TYD . . . N 3 74.333 29.685 66.863 1 64.49 ? C4' TYD 138 D 1 HETATM 12 O O4' TYD . . . N 3 73.807 28.357 66.774 1 64.11 ? O4' TYD 138 D 1 HETATM 13 C C3' TYD . . . N 3 73.847 30.395 65.606 1 58.7 ? C3' TYD 138 D 1 HETATM 14 O O3' TYD . . . N 3 74.782 31.378 65.16 1 66.93 ? O3' TYD 138 D 1 HETATM 15 C C2' TYD . . . N 3 73.718 29.286 64.583 1 60.1 ? C2' TYD 138 D 1 HETATM 16 C C1' TYD . . . N 3 73.479 28.04 65.422 1 57.08 ? C1' TYD 138 D 1 HETATM 17 N N1 TYD . . . N 3 72.071 27.66 65.319 1 61.45 ? N1 TYD 138 D 1 HETATM 18 C C2 TYD . . . N 3 71.739 26.579 64.487 1 63.76 ? C2 TYD 138 D 1 HETATM 19 O O2 TYD . . . N 3 72.674 26.009 63.877 1 62.36 ? O2 TYD 138 D 1 HETATM 20 N N3 TYD . . . N 3 70.463 26.179 64.342 1 67.12 ? N3 TYD 138 D 1 HETATM 21 C C4 TYD . . . N 3 69.467 26.792 64.995 1 64 ? C4 TYD 138 D 1 HETATM 22 O O4 TYD . . . N 3 68.288 26.405 64.86 1 68.11 ? O4 TYD 138 D 1 HETATM 23 C C5 TYD . . . N 3 69.79 27.933 65.886 1 67.05 ? C5 TYD 138 D 1 HETATM 24 C C5M TYD . . . N 3 68.705 28.655 66.648 1 67.74 ? C5M TYD 138 D 1 HETATM 25 C C6 TYD . . . N 3 71.124 28.316 66.008 1 63.69 ? C6 TYD 138 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #