data_3TYD # _model_server_result.job_id LIDyCGZCdk1OCN8WB7ni5w _model_server_result.datetime_utc '2024-11-07 21:38:51' _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 3tyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":801}' # _entry.id 3TYD # _exptl.entry_id 3TYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 177.163 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one _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 120 _cell.entry_id 3TYD _cell.length_a 99.44 _cell.length_b 99.44 _cell.length_c 262.13 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_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,D,E,F,G,H,I,J,S 1 1,2 B,K,L,M,N,O,P,Q,R,T 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_475 -x-1,-y+2,z -1 0 0 0 -1 0 0 0 1 -198.88 172.235132 0 3 'crystal symmetry operation' 4_465 -x-1,-y+1,z -1 0 0 0 -1 0 0 0 1 -149.16 86.117566 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 L N N # _chem_comp.formula 'C7 H7 N5 O' _chem_comp.formula_weight 177.163 _chem_comp.id XHP _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one _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 N1 C9 XHP sing 390 n n C2 N1 XHP doub 391 n n N2 C2 XHP sing 392 n n N2 HN2 XHP sing 393 n n N2 HN2A XHP sing 394 n n N3 C2 XHP sing 395 n n N3 C4 XHP sing 396 n n N3 HN3 XHP sing 397 n n C4 C10 XHP sing 398 n n O4 C4 XHP doub 399 n n N5 C6 XHP sing 400 n n C6 C7 XHP sing 401 n n C6 C6A XHP doub 402 n n C7 H7 XHP sing 403 n n C7 H5 XHP sing 404 n n N8 C7 XHP sing 405 n n C9 N8 XHP doub 406 n n C10 N5 XHP doub 407 n n C10 C9 XHP sing 408 n n C6A H6A XHP sing 409 n n C6A H6AA XHP sing 410 n n # _atom_sites.entry_id 3TYD _atom_sites.fract_transf_matrix[1][1] 0.010056 _atom_sites.fract_transf_matrix[1][2] 0.005806 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011612 _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] 0.003815 _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 POP A 1 701 701 POP POP . D 3 XHP A 1 801 801 XHP XHP . E 4 SO4 A 1 278 1 SO4 SO4 . F 4 SO4 A 1 279 2 SO4 SO4 . G 4 SO4 A 1 280 3 SO4 SO4 . H 4 SO4 A 1 281 4 SO4 SO4 . I 4 SO4 A 1 282 5 SO4 SO4 . J 4 SO4 A 1 283 12 SO4 SO4 . K 2 POP B 1 702 702 POP POP . L 3 XHP B 1 802 802 XHP XHP . M 4 SO4 B 1 278 6 SO4 SO4 . N 4 SO4 B 1 279 7 SO4 SO4 . O 4 SO4 B 1 280 8 SO4 SO4 . P 4 SO4 B 1 281 9 SO4 SO4 . Q 4 SO4 B 1 282 10 SO4 SO4 . R 4 SO4 B 1 283 11 SO4 SO4 . S 5 HOH A 1 284 1 HOH HOH . S 5 HOH A 2 285 4 HOH HOH . S 5 HOH A 3 286 9 HOH HOH . S 5 HOH A 4 287 10 HOH HOH . S 5 HOH A 5 288 11 HOH HOH . S 5 HOH A 6 289 12 HOH HOH . S 5 HOH A 7 290 13 HOH HOH . S 5 HOH A 8 291 14 HOH HOH . S 5 HOH A 9 292 15 HOH HOH . S 5 HOH A 10 293 16 HOH HOH . S 5 HOH A 11 294 17 HOH HOH . S 5 HOH A 12 295 19 HOH HOH . S 5 HOH A 13 296 20 HOH HOH . S 5 HOH A 14 297 26 HOH HOH . S 5 HOH A 15 298 28 HOH HOH . T 5 HOH B 1 284 2 HOH HOH . T 5 HOH B 2 285 3 HOH HOH . T 5 HOH B 3 286 5 HOH HOH . T 5 HOH B 4 287 6 HOH HOH . T 5 HOH B 5 288 7 HOH HOH . T 5 HOH B 6 289 8 HOH HOH . T 5 HOH B 7 290 18 HOH HOH . T 5 HOH B 8 291 21 HOH HOH . T 5 HOH B 9 292 22 HOH HOH . T 5 HOH B 10 293 23 HOH HOH . T 5 HOH B 11 294 24 HOH HOH . T 5 HOH B 12 295 25 HOH HOH . T 5 HOH B 13 296 27 HOH HOH . T 5 HOH B 14 297 29 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 N N1 XHP . . . D 3 -78.659 85.15 92.24 1 69.76 ? N1 XHP 801 A 1 HETATM 2 C C2 XHP . . . D 3 -79.459 84.992 91.238 1 70.63 ? C2 XHP 801 A 1 HETATM 3 N N2 XHP . . . D 3 -79.245 84.005 90.419 1 70.4 ? N2 XHP 801 A 1 HETATM 4 N N3 XHP . . . D 3 -80.524 85.82 90.979 1 69.83 ? N3 XHP 801 A 1 HETATM 5 C C4 XHP . . . D 3 -80.833 86.87 91.767 1 68.51 ? C4 XHP 801 A 1 HETATM 6 O O4 XHP . . . D 3 -81.799 87.565 91.496 1 67.64 ? O4 XHP 801 A 1 HETATM 7 N N5 XHP . . . D 3 -80.238 88.072 93.762 1 67.75 ? N5 XHP 801 A 1 HETATM 8 C C6 XHP . . . D 3 -79.386 88.309 94.887 1 66.31 ? C6 XHP 801 A 1 HETATM 9 C C7 XHP . . . D 3 -78.199 87.439 95.179 1 66.84 ? C7 XHP 801 A 1 HETATM 10 N N8 XHP . . . D 3 -78.067 86.375 94.186 1 68.58 ? N8 XHP 801 A 1 HETATM 11 C C9 XHP . . . D 3 -78.863 86.222 93.191 1 69.53 ? C9 XHP 801 A 1 HETATM 12 C C10 XHP . . . D 3 -79.995 87.125 92.957 1 69.18 ? C10 XHP 801 A 1 HETATM 13 C C6A XHP . . . D 3 -79.661 89.331 95.68 1 66.63 ? C6A XHP 801 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 13 #