data_3G2X # _model_server_result.job_id NT6W6zeCIZ4_qe0M_M7c_g _model_server_result.datetime_utc '2024-11-27 04:27:33' _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 3g2x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":201}' # _entry.id 3G2X # _exptl.entry_id 3G2X _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 3G2X _cell.length_a 84.371 _cell.length_b 151.492 _cell.length_c 181.723 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3G2X _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,B,C,G,H,I,J,K,L,S,T,U 1 1,2 D,E,F,M,N,O,P,Q,R,V,W,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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 84.371 0 90.8615 3 'crystal symmetry operation' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 151.492 0 # 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 # _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 3G2X _atom_sites.fract_transf_matrix[1][1] 0.011852 _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] 0.006601 _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] 0.005503 _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 1 202 202 MG MG . H 3 TYD A 1 201 201 TYD TYD . I 2 MG B 1 202 202 MG MG . J 3 TYD B 1 201 201 TYD TYD . K 2 MG C 1 202 202 MG MG . L 3 TYD C 1 201 201 TYD TYD . M 2 MG D 1 202 202 MG MG . N 3 TYD D 1 201 201 TYD TYD . O 2 MG E 1 202 202 MG MG . P 3 TYD E 1 201 201 TYD TYD . Q 2 MG F 1 202 202 MG MG . R 3 TYD F 1 201 201 TYD TYD . S 4 HOH A 1 142 5 HOH HOH . S 4 HOH A 2 143 6 HOH HOH . S 4 HOH A 3 144 14 HOH HOH . S 4 HOH A 4 145 19 HOH HOH . S 4 HOH A 5 146 32 HOH HOH . S 4 HOH A 6 147 45 HOH HOH . S 4 HOH A 7 148 57 HOH HOH . S 4 HOH A 8 149 59 HOH HOH . S 4 HOH A 9 150 60 HOH HOH . S 4 HOH A 10 151 64 HOH HOH . T 4 HOH B 1 142 12 HOH HOH . T 4 HOH B 2 143 25 HOH HOH . T 4 HOH B 3 144 36 HOH HOH . T 4 HOH B 4 145 39 HOH HOH . T 4 HOH B 5 146 43 HOH HOH . T 4 HOH B 6 147 62 HOH HOH . T 4 HOH B 7 148 70 HOH HOH . U 4 HOH C 1 142 8 HOH HOH . U 4 HOH C 2 143 22 HOH HOH . U 4 HOH C 3 144 23 HOH HOH . U 4 HOH C 4 145 29 HOH HOH . U 4 HOH C 5 146 35 HOH HOH . U 4 HOH C 6 147 41 HOH HOH . U 4 HOH C 7 148 47 HOH HOH . U 4 HOH C 8 149 49 HOH HOH . U 4 HOH C 9 150 58 HOH HOH . U 4 HOH C 10 151 63 HOH HOH . V 4 HOH D 1 142 13 HOH HOH . V 4 HOH D 2 143 17 HOH HOH . V 4 HOH D 3 144 18 HOH HOH . V 4 HOH D 4 145 26 HOH HOH . V 4 HOH D 5 146 30 HOH HOH . V 4 HOH D 6 147 33 HOH HOH . V 4 HOH D 7 148 40 HOH HOH . V 4 HOH D 8 149 44 HOH HOH . V 4 HOH D 9 150 51 HOH HOH . V 4 HOH D 10 151 52 HOH HOH . V 4 HOH D 11 152 54 HOH HOH . V 4 HOH D 12 153 55 HOH HOH . V 4 HOH D 13 154 56 HOH HOH . V 4 HOH D 14 155 65 HOH HOH . V 4 HOH D 15 156 67 HOH HOH . V 4 HOH D 16 157 68 HOH HOH . W 4 HOH E 1 142 3 HOH HOH . W 4 HOH E 2 143 16 HOH HOH . W 4 HOH E 3 144 31 HOH HOH . W 4 HOH E 4 145 37 HOH HOH . W 4 HOH E 5 146 38 HOH HOH . W 4 HOH E 6 147 42 HOH HOH . W 4 HOH E 7 148 46 HOH HOH . W 4 HOH E 8 149 48 HOH HOH . W 4 HOH E 9 150 61 HOH HOH . W 4 HOH E 10 151 66 HOH HOH . X 4 HOH F 1 142 24 HOH HOH . X 4 HOH F 2 143 34 HOH HOH . X 4 HOH F 3 144 50 HOH HOH . X 4 HOH F 4 145 69 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 . . . J 3 33.803 67.609 67.065 1 54.38 ? PA TYD 201 B 1 HETATM 2 O O1A TYD . . . J 3 33.087 66.955 68.221 1 54.44 ? O1A TYD 201 B 1 HETATM 3 O O2A TYD . . . J 3 33.149 68.706 66.259 1 52.65 ? O2A TYD 201 B 1 HETATM 4 O O3A TYD . . . J 3 34.289 66.394 66.118 1 55.96 ? O3A TYD 201 B 1 HETATM 5 P PB TYD . . . J 3 33.968 66.313 64.543 1 54.41 ? PB TYD 201 B 1 HETATM 6 O O1B TYD . . . J 3 35.33 66.543 63.943 1 44.62 ? O1B TYD 201 B 1 HETATM 7 O O2B TYD . . . J 3 33.032 67.464 64.244 1 59.76 ? O2B TYD 201 B 1 HETATM 8 O O3B TYD . . . J 3 33.335 64.943 64.41 1 47.4 ? O3B TYD 201 B 1 HETATM 9 O O5' TYD . . . J 3 35.236 68.103 67.555 1 46.67 ? O5' TYD 201 B 1 HETATM 10 C C5' TYD . . . J 3 35.944 69.051 66.779 1 49.15 ? C5' TYD 201 B 1 HETATM 11 C C4' TYD . . . J 3 37.395 68.584 66.707 1 51.65 ? C4' TYD 201 B 1 HETATM 12 O O4' TYD . . . J 3 38.021 68.727 67.984 1 50.46 ? O4' TYD 201 B 1 HETATM 13 C C3' TYD . . . J 3 37.503 67.103 66.377 1 49.69 ? C3' TYD 201 B 1 HETATM 14 O O3' TYD . . . J 3 37.593 66.9 64.978 1 51.08 ? O3' TYD 201 B 1 HETATM 15 C C2' TYD . . . J 3 38.794 66.677 67.036 1 49.57 ? C2' TYD 201 B 1 HETATM 16 C C1' TYD . . . J 3 38.905 67.628 68.223 1 50.43 ? C1' TYD 201 B 1 HETATM 17 N N1 TYD . . . J 3 38.573 66.95 69.483 1 46.57 ? N1 TYD 201 B 1 HETATM 18 C C2 TYD . . . J 3 39.616 66.648 70.385 1 49.11 ? C2 TYD 201 B 1 HETATM 19 O O2 TYD . . . J 3 40.808 66.944 70.105 1 48.58 ? O2 TYD 201 B 1 HETATM 20 N N3 TYD . . . J 3 39.356 66.042 71.551 1 51.75 ? N3 TYD 201 B 1 HETATM 21 C C4 TYD . . . J 3 38.113 65.705 71.899 1 51 ? C4 TYD 201 B 1 HETATM 22 O O4 TYD . . . J 3 37.923 65.136 72.991 1 51.03 ? O4 TYD 201 B 1 HETATM 23 C C5 TYD . . . J 3 36.992 66.014 70.972 1 51.85 ? C5 TYD 201 B 1 HETATM 24 C C5M TYD . . . J 3 35.568 65.651 71.315 1 46.3 ? C5M TYD 201 B 1 HETATM 25 C C6 TYD . . . J 3 37.301 66.652 69.775 1 49.72 ? C6 TYD 201 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #