data_8RDM # _model_server_result.job_id LZcR3thHMxxPXmOz-sVw5A _model_server_result.datetime_utc '2024-10-23 01:37:16' _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 8rdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8RDM # _exptl.entry_id 8RDM _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 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 90 _cell.entry_id 8RDM _cell.length_a 53.21 _cell.length_b 53.21 _cell.length_c 207.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # _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' 8_665 -y+1,-x+1,-z+1/4 0 -1 0 -1 0 0 0 0 -1 53.21 53.21 51.9875 # _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 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _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 N CA SAH sing 290 n n N HN1 SAH sing 291 n n N HN2 SAH sing 292 n n CA CB SAH sing 293 n n CA C SAH sing 294 n n CA HA SAH sing 295 n n CB CG SAH sing 296 n n CB HB1 SAH sing 297 n n CB HB2 SAH sing 298 n n CG SD SAH sing 299 n n CG HG1 SAH sing 300 n n CG HG2 SAH sing 301 n n SD C5' SAH sing 302 n n C O SAH doub 303 n n C OXT SAH sing 304 n n OXT HXT SAH sing 305 n n C5' C4' SAH sing 306 n n C5' "H5'1" SAH sing 307 n n C5' "H5'2" SAH sing 308 n n C4' O4' SAH sing 309 n n C4' C3' SAH sing 310 n n C4' H4' SAH sing 311 n n O4' C1' SAH sing 312 n n C3' O3' SAH sing 313 n n C3' C2' SAH sing 314 n n C3' H3' SAH sing 315 n n O3' HO3' SAH sing 316 n n C2' O2' SAH sing 317 n n C2' C1' SAH sing 318 n n C2' H2' SAH sing 319 n n O2' HO2' SAH sing 320 n n C1' N9 SAH sing 321 n n C1' H1' SAH sing 322 n n N9 C8 SAH sing 323 n y N9 C4 SAH sing 324 n y C8 N7 SAH doub 325 n y C8 H8 SAH sing 326 n n N7 C5 SAH sing 327 n y C5 C6 SAH sing 328 n y C5 C4 SAH doub 329 n y C6 N6 SAH sing 330 n n C6 N1 SAH doub 331 n y N6 HN61 SAH sing 332 n n N6 HN62 SAH sing 333 n n N1 C2 SAH sing 334 n y C2 N3 SAH doub 335 n y C2 H2 SAH sing 336 n n N3 C4 SAH sing 337 n y # _atom_sites.entry_id 8RDM _atom_sites.fract_transf_matrix[1][1] 0.018793 _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] 0.018793 _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] 0.004809 _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 SAH A 1 401 998 SAH SAH . C 3 GOL A 1 402 1 GOL GOL . D 3 GOL A 1 403 2 GOL GOL . E 4 HOH A 1 501 93 HOH HOH . E 4 HOH A 2 502 10 HOH HOH . E 4 HOH A 3 503 67 HOH HOH . E 4 HOH A 4 504 30 HOH HOH . E 4 HOH A 5 505 17 HOH HOH . E 4 HOH A 6 506 15 HOH HOH . E 4 HOH A 7 507 47 HOH HOH . E 4 HOH A 8 508 50 HOH HOH . E 4 HOH A 9 509 11 HOH HOH . E 4 HOH A 10 510 86 HOH HOH . E 4 HOH A 11 511 35 HOH HOH . E 4 HOH A 12 512 51 HOH HOH . E 4 HOH A 13 513 13 HOH HOH . E 4 HOH A 14 514 6 HOH HOH . E 4 HOH A 15 515 54 HOH HOH . E 4 HOH A 16 516 68 HOH HOH . E 4 HOH A 17 517 49 HOH HOH . E 4 HOH A 18 518 87 HOH HOH . E 4 HOH A 19 519 19 HOH HOH . E 4 HOH A 20 520 52 HOH HOH . E 4 HOH A 21 521 45 HOH HOH . E 4 HOH A 22 522 23 HOH HOH . E 4 HOH A 23 523 84 HOH HOH . E 4 HOH A 24 524 85 HOH HOH . E 4 HOH A 25 525 44 HOH HOH . E 4 HOH A 26 526 37 HOH HOH . E 4 HOH A 27 527 41 HOH HOH . E 4 HOH A 28 528 66 HOH HOH . E 4 HOH A 29 529 60 HOH HOH . E 4 HOH A 30 530 72 HOH HOH . E 4 HOH A 31 531 14 HOH HOH . E 4 HOH A 32 532 70 HOH HOH . E 4 HOH A 33 533 3 HOH HOH . E 4 HOH A 34 534 65 HOH HOH . E 4 HOH A 35 535 48 HOH HOH . E 4 HOH A 36 536 64 HOH HOH . E 4 HOH A 37 537 33 HOH HOH . E 4 HOH A 38 538 26 HOH HOH . E 4 HOH A 39 539 27 HOH HOH . E 4 HOH A 40 540 77 HOH HOH . E 4 HOH A 41 541 25 HOH HOH . E 4 HOH A 42 542 46 HOH HOH . E 4 HOH A 43 543 12 HOH HOH . E 4 HOH A 44 544 62 HOH HOH . E 4 HOH A 45 545 69 HOH HOH . E 4 HOH A 46 546 80 HOH HOH . E 4 HOH A 47 547 40 HOH HOH . E 4 HOH A 48 548 7 HOH HOH . E 4 HOH A 49 549 71 HOH HOH . E 4 HOH A 50 550 32 HOH HOH . E 4 HOH A 51 551 53 HOH HOH . E 4 HOH A 52 552 78 HOH HOH . E 4 HOH A 53 553 36 HOH HOH . E 4 HOH A 54 554 82 HOH HOH . E 4 HOH A 55 555 9 HOH HOH . E 4 HOH A 56 556 83 HOH HOH . E 4 HOH A 57 557 75 HOH HOH . E 4 HOH A 58 558 20 HOH HOH . E 4 HOH A 59 559 57 HOH HOH . E 4 HOH A 60 560 24 HOH HOH . E 4 HOH A 61 561 29 HOH HOH . E 4 HOH A 62 562 21 HOH HOH . E 4 HOH A 63 563 96 HOH HOH . E 4 HOH A 64 564 39 HOH HOH . E 4 HOH A 65 565 8 HOH HOH . E 4 HOH A 66 566 22 HOH HOH . E 4 HOH A 67 567 4 HOH HOH . E 4 HOH A 68 568 16 HOH HOH . E 4 HOH A 69 569 5 HOH HOH . E 4 HOH A 70 570 58 HOH HOH . E 4 HOH A 71 571 18 HOH HOH . E 4 HOH A 72 572 81 HOH HOH . E 4 HOH A 73 573 73 HOH HOH . E 4 HOH A 74 574 43 HOH HOH . E 4 HOH A 75 575 28 HOH HOH . E 4 HOH A 76 576 61 HOH HOH . E 4 HOH A 77 577 76 HOH HOH . E 4 HOH A 78 578 59 HOH HOH . E 4 HOH A 79 579 31 HOH HOH . E 4 HOH A 80 580 63 HOH HOH . E 4 HOH A 81 581 42 HOH HOH . E 4 HOH A 82 582 88 HOH HOH . E 4 HOH A 83 583 95 HOH HOH . E 4 HOH A 84 584 92 HOH HOH . E 4 HOH A 85 585 94 HOH HOH . E 4 HOH A 86 586 38 HOH HOH . E 4 HOH A 87 587 89 HOH HOH . E 4 HOH A 88 588 56 HOH HOH . E 4 HOH A 89 589 79 HOH HOH . E 4 HOH A 90 590 91 HOH HOH . E 4 HOH A 91 591 74 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 . . . B 2 14.553 66.748 42.646 1 26.49 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . B 2 13.258 66.096 42.988 1 25.69 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . B 2 12.07 66.888 42.432 1 26.02 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . B 2 12.125 67.113 40.927 1 26.01 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . B 2 10.663 67.97 40.292 1 27.3 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . B 2 13.235 64.675 42.414 1 26.19 ? C SAH 401 A 1 HETATM 7 O O SAH . . . B 2 14.008 64.347 41.512 1 26.23 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . B 2 12.441 63.835 42.84 1 26.71 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . B 2 11.241 69.688 40.234 1 27.52 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . B 2 11.118 70.445 41.538 1 27.95 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . B 2 11.419 71.839 41.308 1 28.95 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . B 2 9.723 70.413 42.178 1 27.37 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . B 2 9.773 69.75 43.435 1 26.16 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . B 2 9.323 71.891 42.31 1 27.62 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . B 2 8.676 72.192 43.528 1 27.22 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . B 2 10.67 72.596 42.226 1 28.35 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . B 2 10.608 73.973 41.75 1 29.32 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . B 2 9.887 74.447 40.682 1 30.11 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . B 2 10.04 75.731 40.479 1 30.41 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . B 2 10.923 76.133 41.471 1 30.39 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . B 2 11.486 77.385 41.788 1 30.88 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . B 2 11.239 78.5 41.106 1 32.54 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . B 2 12.342 77.438 42.837 1 29.75 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . B 2 12.591 76.311 43.517 1 29.38 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . B 2 12.121 75.083 43.31 1 28.92 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . B 2 11.282 75.057 42.261 1 29.3 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #