data_8PB8 # _model_server_result.job_id Xnf-7BzZRlSP5OooW_1woQ _model_server_result.datetime_utc '2024-11-05 23:08:47' _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 8pb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8PB8 # _exptl.entry_id 8PB8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 90 _cell.entry_id 8PB8 _cell.length_a 62.2 _cell.length_b 62.2 _cell.length_c 154.83 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PB8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 F N N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 N CA SAH sing 321 n n N HN1 SAH sing 322 n n N HN2 SAH sing 323 n n CA CB SAH sing 324 n n CA C SAH sing 325 n n CA HA SAH sing 326 n n CB CG SAH sing 327 n n CB HB1 SAH sing 328 n n CB HB2 SAH sing 329 n n CG SD SAH sing 330 n n CG HG1 SAH sing 331 n n CG HG2 SAH sing 332 n n SD C5' SAH sing 333 n n C O SAH doub 334 n n C OXT SAH sing 335 n n OXT HXT SAH sing 336 n n C5' C4' SAH sing 337 n n C5' "H5'1" SAH sing 338 n n C5' "H5'2" SAH sing 339 n n C4' O4' SAH sing 340 n n C4' C3' SAH sing 341 n n C4' H4' SAH sing 342 n n O4' C1' SAH sing 343 n n C3' O3' SAH sing 344 n n C3' C2' SAH sing 345 n n C3' H3' SAH sing 346 n n O3' HO3' SAH sing 347 n n C2' O2' SAH sing 348 n n C2' C1' SAH sing 349 n n C2' H2' SAH sing 350 n n O2' HO2' SAH sing 351 n n C1' N9 SAH sing 352 n n C1' H1' SAH sing 353 n n N9 C8 SAH sing 354 n y N9 C4 SAH sing 355 n y C8 N7 SAH doub 356 n y C8 H8 SAH sing 357 n n N7 C5 SAH sing 358 n y C5 C6 SAH sing 359 n y C5 C4 SAH doub 360 n y C6 N6 SAH sing 361 n n C6 N1 SAH doub 362 n y N6 HN61 SAH sing 363 n n N6 HN62 SAH sing 364 n n N1 C2 SAH sing 365 n y C2 N3 SAH doub 366 n y C2 H2 SAH sing 367 n n N3 C4 SAH sing 368 n y # _atom_sites.entry_id 8PB8 _atom_sites.fract_transf_matrix[1][1] 0.016077 _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] 0.016077 _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] 0.006459 _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 SAH A 1 401 401 SAH SAH . D 3 P6G A 1 402 501 P6G P6G . E 4 CL A 1 403 1 CL CL . F 2 SAH B 1 401 401 SAH SAH . G 3 P6G B 1 402 501 P6G P6G . H 5 HOH A 1 501 5 HOH HOH . H 5 HOH A 2 502 3 HOH HOH . H 5 HOH A 3 503 2 HOH HOH . H 5 HOH A 4 504 14 HOH HOH . H 5 HOH A 5 505 15 HOH HOH . H 5 HOH A 6 506 7 HOH HOH . H 5 HOH A 7 507 4 HOH HOH . H 5 HOH A 8 508 13 HOH HOH . H 5 HOH A 9 509 17 HOH HOH . H 5 HOH A 10 510 6 HOH HOH . H 5 HOH A 11 511 16 HOH HOH . I 5 HOH B 1 501 21 HOH HOH . I 5 HOH B 2 502 8 HOH HOH . I 5 HOH B 3 503 9 HOH HOH . I 5 HOH B 4 504 18 HOH HOH . I 5 HOH B 5 505 10 HOH HOH . I 5 HOH B 6 506 19 HOH HOH . I 5 HOH B 7 507 20 HOH HOH . I 5 HOH B 8 508 11 HOH HOH . I 5 HOH B 9 509 1 HOH HOH . I 5 HOH B 10 510 12 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 N SAH . . . C 2 3.644 3.967 -4.937 1 43.99 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . C 2 4.749 4.782 -4.345 1 47.76 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . C 2 4.333 6.237 -4.066 1 43.81 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . C 2 3.134 6.401 -3.14 1 44.15 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . C 2 2.745 8.105 -2.65 1 52 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . C 2 5.305 4.193 -3.023 1 48.66 ? C SAH 401 A 1 HETATM 7 O O SAH . . . C 2 6.418 4.662 -2.597 1 50.75 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . C 2 4.65 3.309 -2.433 1 46.87 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . C 2 1.285 8.462 -3.665 1 41 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . C 2 1.69 8.657 -5.114 1 41.17 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . C 2 0.515 8.733 -5.951 1 37.49 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . C 2 2.465 9.967 -5.315 1 41.99 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . C 2 3.662 9.745 -6.052 1 36.56 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . C 2 1.484 10.848 -6.1 1 33.06 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . C 2 2.154 11.729 -6.997 1 43.48 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . C 2 0.683 9.799 -6.858 1 34.47 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . C 2 -0.64 10.248 -7.292 1 36.15 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . C 2 -1.443 11.167 -6.679 1 35.42 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . C 2 -2.582 11.375 -7.303 1 38.02 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . C 2 -2.514 10.536 -8.393 1 41.06 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . C 2 -3.409 10.278 -9.458 1 37.38 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . C 2 -4.593 10.88 -9.59 1 50.38 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . C 2 -3.04 9.375 -10.39 1 40.12 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . C 2 -1.854 8.771 -10.267 1 34.53 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . C 2 -0.93 8.929 -9.314 1 38.17 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . C 2 -1.321 9.824 -8.411 1 40.99 ? C4 SAH 401 A 1 HETATM 27 H H2 SAH . . . C 2 -1.637 8.125 -10.97 1 41.44 ? H2 SAH 401 A 1 HETATM 28 H HN1 SAH . . . C 2 3.034 4.441 -5.365 1 52.79 ? HN1 SAH 401 A 1 HETATM 29 H HN2 SAH . . . C 2 3.183 3.499 -4.347 1 52.79 ? HN2 SAH 401 A 1 HETATM 30 H HA SAH . . . C 2 5.432 4.683 -5.039 1 57.32 ? HA SAH 401 A 1 HETATM 31 H HB1 SAH . . . C 2 4.145 6.667 -4.925 1 52.57 ? HB1 SAH 401 A 1 HETATM 32 H HB2 SAH . . . C 2 5.105 6.705 -3.688 1 52.57 ? HB2 SAH 401 A 1 HETATM 33 H HG1 SAH . . . C 2 3.302 5.882 -2.327 1 52.98 ? HG1 SAH 401 A 1 HETATM 34 H HG2 SAH . . . C 2 2.348 6.028 -3.589 1 52.98 ? HG2 SAH 401 A 1 HETATM 35 H "H5'1" SAH . . . C 2 0.863 9.271 -3.309 1 49.2 ? "H5'1" SAH 401 A 1 HETATM 36 H "H5'2" SAH . . . C 2 0.665 7.709 -3.574 1 49.2 ? "H5'2" SAH 401 A 1 HETATM 37 H H4' SAH . . . C 2 2.214 7.898 -5.44 1 49.4 ? H4' SAH 401 A 1 HETATM 38 H H3' SAH . . . C 2 2.724 10.378 -4.465 1 50.38 ? H3' SAH 401 A 1 HETATM 39 H HO3' SAH . . . C 2 3.435 9.249 -6.704 1 43.88 ? HO3' SAH 401 A 1 HETATM 40 H H2' SAH . . . C 2 0.925 11.377 -5.494 1 39.67 ? H2' SAH 401 A 1 HETATM 41 H HO2' SAH . . . C 2 2.633 11.241 -7.501 1 52.18 ? HO2' SAH 401 A 1 HETATM 42 H H1' SAH . . . C 2 1.141 9.479 -7.662 1 41.37 ? H1' SAH 401 A 1 HETATM 43 H H8 SAH . . . C 2 -1.177 11.617 -5.851 1 42.51 ? H8 SAH 401 A 1 HETATM 44 H HN61 SAH . . . C 2 -4.836 11.473 -8.982 1 60.46 ? HN61 SAH 401 A 1 HETATM 45 H HN62 SAH . . . C 2 -5.1 10.669 -10.281 1 60.46 ? HN62 SAH 401 A 1 HETATM 46 H HN3 SAH . . . C 2 3.912 3.369 -5.529 1 52.79 ? HN3 SAH 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #