data_6GFK # _model_server_result.job_id OidDKfp79WbfS-WDkB_6yQ _model_server_result.datetime_utc '2024-11-15 16:44:27' _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 6gfk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 6GFK # _exptl.entry_id 6GFK _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 3 _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 6GFK _cell.length_a 133.768 _cell.length_b 133.768 _cell.length_c 78.701 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GFK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 PISA hexameric 6 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,L 1 1 B,G,H,I,M 2 1 C,J,K,N 3 1 A,C,D,E,F,J,K,L,N 4 1,4 B,G,H,I,M 4 2,3 # 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_564 -x+y,-x+1,z-1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -66.884 115.846486 -26.233667 3 'crystal symmetry operation' 5_564 x-y,-y+1,-z-1/3 1 0 0 0 -1 0 0 0 -1 -66.884 115.846486 -26.233667 4 'crystal symmetry operation' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -52.467333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 G N N ? 2 J 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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 6GFK _atom_sites.fract_transf_matrix[1][1] 0.007476 _atom_sites.fract_transf_matrix[1][2] 0.004316 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008632 _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] 0.012706 _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 D 2 SAH A 1 301 300 SAH SAH . E 3 SO4 A 1 302 401 SO4 SO4 . F 3 SO4 A 1 303 402 SO4 SO4 . G 2 SAH B 1 301 300 SAH SAH . H 3 SO4 B 1 302 401 SO4 SO4 . I 3 SO4 B 1 303 402 SO4 SO4 . J 2 SAH C 1 301 300 SAH SAH . K 3 SO4 C 1 302 401 SO4 SO4 . L 4 HOH A 1 401 407 HOH HOH . L 4 HOH A 2 402 438 HOH HOH . L 4 HOH A 3 403 424 HOH HOH . L 4 HOH A 4 404 431 HOH HOH . L 4 HOH A 5 405 420 HOH HOH . L 4 HOH A 6 406 403 HOH HOH . L 4 HOH A 7 407 427 HOH HOH . L 4 HOH A 8 408 417 HOH HOH . L 4 HOH A 9 409 413 HOH HOH . L 4 HOH A 10 410 423 HOH HOH . L 4 HOH A 11 411 429 HOH HOH . L 4 HOH A 12 412 412 HOH HOH . L 4 HOH A 13 413 449 HOH HOH . L 4 HOH A 14 414 442 HOH HOH . L 4 HOH A 15 415 414 HOH HOH . L 4 HOH A 16 416 443 HOH HOH . L 4 HOH A 17 417 436 HOH HOH . L 4 HOH A 18 418 408 HOH HOH . L 4 HOH A 19 419 410 HOH HOH . L 4 HOH A 20 420 406 HOH HOH . L 4 HOH A 21 421 416 HOH HOH . L 4 HOH A 22 422 409 HOH HOH . L 4 HOH A 23 423 410 HOH HOH . L 4 HOH A 24 424 434 HOH HOH . L 4 HOH A 25 425 425 HOH HOH . L 4 HOH A 26 426 405 HOH HOH . L 4 HOH A 27 427 426 HOH HOH . L 4 HOH A 28 428 428 HOH HOH . L 4 HOH A 29 429 404 HOH HOH . L 4 HOH A 30 430 419 HOH HOH . L 4 HOH A 31 431 439 HOH HOH . L 4 HOH A 32 432 422 HOH HOH . L 4 HOH A 33 433 437 HOH HOH . L 4 HOH A 34 434 421 HOH HOH . L 4 HOH A 35 435 418 HOH HOH . L 4 HOH A 36 436 430 HOH HOH . L 4 HOH A 37 437 447 HOH HOH . L 4 HOH A 38 438 415 HOH HOH . L 4 HOH A 39 439 445 HOH HOH . L 4 HOH A 40 440 433 HOH HOH . L 4 HOH A 41 441 411 HOH HOH . L 4 HOH A 42 442 432 HOH HOH . L 4 HOH A 43 443 441 HOH HOH . L 4 HOH A 44 444 446 HOH HOH . L 4 HOH A 45 445 440 HOH HOH . L 4 HOH A 46 446 444 HOH HOH . L 4 HOH A 47 447 448 HOH HOH . M 4 HOH B 1 401 413 HOH HOH . M 4 HOH B 2 402 414 HOH HOH . M 4 HOH B 3 403 425 HOH HOH . M 4 HOH B 4 404 408 HOH HOH . M 4 HOH B 5 405 416 HOH HOH . M 4 HOH B 6 406 405 HOH HOH . M 4 HOH B 7 407 412 HOH HOH . M 4 HOH B 8 408 403 HOH HOH . M 4 HOH B 9 409 421 HOH HOH . M 4 HOH B 10 410 420 HOH HOH . M 4 HOH B 11 411 415 HOH HOH . M 4 HOH B 12 412 404 HOH HOH . M 4 HOH B 13 413 411 HOH HOH . M 4 HOH B 14 414 407 HOH HOH . M 4 HOH B 15 415 409 HOH HOH . M 4 HOH B 16 416 419 HOH HOH . M 4 HOH B 17 417 417 HOH HOH . M 4 HOH B 18 418 423 HOH HOH . M 4 HOH B 19 419 418 HOH HOH . M 4 HOH B 20 420 422 HOH HOH . M 4 HOH B 21 421 410 HOH HOH . M 4 HOH B 22 422 424 HOH HOH . M 4 HOH B 23 423 426 HOH HOH . M 4 HOH B 24 424 406 HOH HOH . M 4 HOH B 25 425 428 HOH HOH . M 4 HOH B 26 426 427 HOH HOH . N 4 HOH C 1 401 420 HOH HOH . N 4 HOH C 2 402 427 HOH HOH . N 4 HOH C 3 403 407 HOH HOH . N 4 HOH C 4 404 419 HOH HOH . N 4 HOH C 5 405 422 HOH HOH . N 4 HOH C 6 406 408 HOH HOH . N 4 HOH C 7 407 403 HOH HOH . N 4 HOH C 8 408 424 HOH HOH . N 4 HOH C 9 409 405 HOH HOH . N 4 HOH C 10 410 404 HOH HOH . N 4 HOH C 11 411 421 HOH HOH . N 4 HOH C 12 412 417 HOH HOH . N 4 HOH C 13 413 413 HOH HOH . N 4 HOH C 14 414 402 HOH HOH . N 4 HOH C 15 415 409 HOH HOH . N 4 HOH C 16 416 414 HOH HOH . N 4 HOH C 17 417 416 HOH HOH . N 4 HOH C 18 418 425 HOH HOH . N 4 HOH C 19 419 406 HOH HOH . N 4 HOH C 20 420 411 HOH HOH . N 4 HOH C 21 421 415 HOH HOH . N 4 HOH C 22 422 426 HOH HOH . N 4 HOH C 23 423 412 HOH HOH . N 4 HOH C 24 424 435 HOH HOH . N 4 HOH C 25 425 418 HOH HOH . N 4 HOH C 26 426 423 HOH HOH . N 4 HOH C 27 427 428 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 . . . D 2 -24.228 38.1 -11.813 1 50.64 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . D 2 -23.628 37.577 -13.061 1 50.33 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . D 2 -24.536 36.59 -13.898 1 49.45 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . D 2 -25.894 37.207 -14.219 1 51.35 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . D 2 -26.827 36.151 -15.36 1 48.57 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . D 2 -23.18 38.843 -13.881 1 50.46 ? C SAH 301 A 1 HETATM 7 O O SAH . . . D 2 -22.415 38.562 -14.897 1 48.61 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . D 2 -23.526 39.968 -13.596 1 53.19 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . D 2 -28.169 35.522 -14.317 1 48.8 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . D 2 -27.75 34.282 -13.554 1 49.08 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . D 2 -28.749 33.955 -12.569 1 49.11 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . D 2 -27.498 33.003 -14.366 1 50.43 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . D 2 -26.176 32.541 -14.107 1 54.92 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . D 2 -28.565 32.022 -13.855 1 47.91 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . D 2 -28.131 30.662 -13.834 1 45.92 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . D 2 -28.804 32.55 -12.444 1 50.76 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . D 2 -30.079 32.184 -11.821 1 52.5 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . D 2 -31.299 32.041 -12.43 1 50.99 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . D 2 -32.288 31.812 -11.6 1 51.77 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . D 2 -31.678 31.804 -10.355 1 52.16 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . D 2 -32.184 31.641 -9.045 1 53.46 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . D 2 -33.474 31.453 -8.765 1 53.98 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . D 2 -31.3 31.677 -8.02 1 53.14 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . D 2 -30.002 31.856 -8.292 1 48.41 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . D 2 -29.415 32.038 -9.479 1 50.19 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . D 2 -30.313 32.012 -10.476 1 51.78 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #