data_4L87 # _model_server_result.job_id fHfpKsVevUDu1G8QMWWudA _model_server_result.datetime_utc '2025-03-30 19:55:00' _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 4l87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4L87 # _exptl.entry_id 4L87 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 433.397 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE" _entity.pdbx_number_of_molecules 1 _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 4L87 _cell.length_a 167.074 _cell.length_b 167.074 _cell.length_c 65.156 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L87 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _pdbx_struct_assembly.method_details PISA _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C13 H19 N7 O8 S' _chem_comp.formula_weight 433.397 _chem_comp.id SSA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE" _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 N10 CA SSA sing 292 n n N10 HN11 SSA sing 293 n n N10 HN12 SSA sing 294 n n CA CB SSA sing 295 n n CA C9 SSA sing 296 n n CA HA SSA sing 297 n n CB OG SSA sing 298 n n CB HB1 SSA sing 299 n n CB HB2 SSA sing 300 n n OG HOG SSA sing 301 n n C9 O9 SSA doub 302 n n C9 N8 SSA sing 303 n n N8 S1 SSA sing 304 n n N8 HN8 SSA sing 305 n n S1 O1S SSA doub 306 n n S1 O2S SSA doub 307 n n S1 O5' SSA sing 308 n n O5' C5' SSA sing 309 n n C5' C4' SSA sing 310 n n C5' "H5'1" SSA sing 311 n n C5' "H5'2" SSA sing 312 n n C4' O4' SSA sing 313 n n C4' C3' SSA sing 314 n n C4' H4' SSA sing 315 n n O4' C1' SSA sing 316 n n C3' O3' SSA sing 317 n n C3' C2' SSA sing 318 n n C3' H3' SSA sing 319 n n O3' HO3' SSA sing 320 n n C2' O2' SSA sing 321 n n C2' C1' SSA sing 322 n n C2' H2' SSA sing 323 n n O2' HO2' SSA sing 324 n n C1' N9 SSA sing 325 n n C1' H1' SSA sing 326 n n N9 C8 SSA sing 327 n y N9 C4 SSA sing 328 n y C8 N7 SSA doub 329 n y C8 H8 SSA sing 330 n n N7 C5 SSA sing 331 n y C5 C6 SSA sing 332 n y C5 C4 SSA doub 333 n y C6 N6 SSA sing 334 n n C6 N1 SSA doub 335 n y N6 HN61 SSA sing 336 n n N6 HN62 SSA sing 337 n n N1 C2 SSA sing 338 n y C2 N3 SSA doub 339 n y C2 H2 SSA sing 340 n n N3 C4 SSA sing 341 n y # _atom_sites.entry_id 4L87 _atom_sites.fract_transf_matrix[1][1] 0.005985 _atom_sites.fract_transf_matrix[1][2] 0.003456 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006911 _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] 0.015348 _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 B 2 SSA A 1 501 1 SSA SSA . C 3 PO4 A 1 502 1 PO4 PO4 . D 4 MG A 1 503 1 MG MG . E 4 MG A 1 504 2 MG MG . # 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 N10 SSA . . . B 2 42.438 -41.392 5.389 1 57.33 ? N10 SSA 501 A 1 HETATM 2 C CA SSA . . . B 2 42.253 -41.125 6.803 1 57.66 ? CA SSA 501 A 1 HETATM 3 C CB SSA . . . B 2 41.115 -40.124 6.978 1 57.64 ? CB SSA 501 A 1 HETATM 4 O OG SSA . . . B 2 39.885 -40.69 6.512 1 57.72 ? OG SSA 501 A 1 HETATM 5 C C9 SSA . . . B 2 41.941 -42.396 7.541 1 57.61 ? C9 SSA 501 A 1 HETATM 6 O O9 SSA . . . B 2 41.404 -43.335 6.975 1 57.54 ? O9 SSA 501 A 1 HETATM 7 N N8 SSA . . . B 2 42.27 -42.435 8.831 1 57.39 ? N8 SSA 501 A 1 HETATM 8 S S1 SSA . . . B 2 41.139 -42.79 9.905 1 56.71 ? S1 SSA 501 A 1 HETATM 9 O O1S SSA . . . B 2 40.937 -44.209 9.914 1 56.37 ? O1S SSA 501 A 1 HETATM 10 O O2S SSA . . . B 2 41.548 -42.37 11.216 1 57.31 ? O2S SSA 501 A 1 HETATM 11 O O5' SSA . . . B 2 39.855 -42.047 9.509 1 56.69 ? O5' SSA 501 A 1 HETATM 12 C C5' SSA . . . B 2 38.617 -42.739 9.365 1 56.52 ? C5' SSA 501 A 1 HETATM 13 C C4' SSA . . . B 2 37.521 -42.016 10.137 1 56.28 ? C4' SSA 501 A 1 HETATM 14 O O4' SSA . . . B 2 36.345 -42.829 10.147 1 56.17 ? O4' SSA 501 A 1 HETATM 15 C C3' SSA . . . B 2 37.909 -41.759 11.586 1 56.22 ? C3' SSA 501 A 1 HETATM 16 O O3' SSA . . . B 2 38.236 -40.38 11.788 1 56.6 ? O3' SSA 501 A 1 HETATM 17 C C2' SSA . . . B 2 36.703 -42.179 12.402 1 56.05 ? C2' SSA 501 A 1 HETATM 18 O O2' SSA . . . B 2 35.921 -41.038 12.764 1 56.05 ? O2' SSA 501 A 1 HETATM 19 C C1' SSA . . . B 2 35.886 -43.072 11.48 1 55.77 ? C1' SSA 501 A 1 HETATM 20 N N9 SSA . . . B 2 36.055 -44.511 11.822 1 55.12 ? N9 SSA 501 A 1 HETATM 21 C C8 SSA . . . B 2 37.218 -45.192 11.879 1 55.06 ? C8 SSA 501 A 1 HETATM 22 N N7 SSA . . . B 2 37.016 -46.49 12.221 1 55.11 ? N7 SSA 501 A 1 HETATM 23 C C5 SSA . . . B 2 35.692 -46.659 12.385 1 54.85 ? C5 SSA 501 A 1 HETATM 24 C C6 SSA . . . B 2 34.795 -47.785 12.747 1 54.69 ? C6 SSA 501 A 1 HETATM 25 N N6 SSA . . . B 2 35.291 -49.018 13.006 1 54.67 ? N6 SSA 501 A 1 HETATM 26 N N1 SSA . . . B 2 33.464 -47.538 12.81 1 54.83 ? N1 SSA 501 A 1 HETATM 27 C C2 SSA . . . B 2 32.954 -46.315 12.553 1 54.98 ? C2 SSA 501 A 1 HETATM 28 N N3 SSA . . . B 2 33.71 -45.249 12.22 1 54.76 ? N3 SSA 501 A 1 HETATM 29 C C4 SSA . . . B 2 35.062 -45.354 12.121 1 54.88 ? C4 SSA 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 29 #