data_4FHE # _model_server_result.job_id 57oSlHBoDSACEbCXyztofA _model_server_result.datetime_utc '2024-11-20 11:23:44' _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 4fhe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":407}' # _entry.id 4FHE # _exptl.entry_id 4FHE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 446.34 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium' _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 4FHE _cell.length_a 54.02 _cell.length_b 63.03 _cell.length_c 143.62 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FHE _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 117 A CYS 90 1_555 B FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc2 A SG CYS 121 A CYS 94 1_555 B FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc3 A SG CYS 124 A CYS 97 1_555 B FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 B FE3 SF4 . A SF4 401 1_555 H N EEM . A EEM 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc5 B FE3 SF4 . A SF4 401 1_555 H O EEM . A EEM 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _chem_comp.formula 'C15 H23 N6 O5 Se 1' _chem_comp.formula_weight 446.34 _chem_comp.id EEM _chem_comp.mon_nstd_flag . _chem_comp.name '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Se-ADENOSYLSELENOMETHIONINE # 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 C2 EEM doub 92 n y C2 N3 EEM sing 93 n y C2 H2 EEM sing 94 n n C4 N3 EEM doub 95 n y C5 C4 EEM sing 96 n y N9 C4 EEM sing 97 n y N9 C1' EEM sing 98 n n C1' O4' EEM sing 99 n n C1' C2' EEM sing 100 n n C1' H1' EEM sing 101 n n O2' C2' EEM sing 102 n n C2' C3' EEM sing 103 n n C2' H2' EEM sing 104 n n C4' C3' EEM sing 105 n n O3' C3' EEM sing 106 n n C3' H3' EEM sing 107 n n O4' C4' EEM sing 108 n n C4' C5' EEM sing 109 n n C4' H4' EEM sing 110 n n C5' H5' EEM sing 111 n n C5' "H5'A" EEM sing 112 n n C5' SE EEM sing 113 n n C O EEM doub 114 n n CA C EEM sing 115 n n C OXT EEM sing 116 n n OXT HOXT EEM sing 117 n n CB CA EEM sing 118 n n N CA EEM sing 119 n n CA HA EEM sing 120 n n N HN EEM sing 121 n n N HNA EEM sing 122 n n CB CG EEM sing 123 n n CB HB EEM sing 124 n n CB HBA EEM sing 125 n n SE CG EEM sing 126 n n CG HG EEM sing 127 n n CG HGA EEM sing 128 n n SE CE EEM sing 129 n n CE HE EEM sing 130 n n CE HEA EEM sing 131 n n CE HEB EEM sing 132 n n O3' HO3' EEM sing 133 n n O2' HO2' EEM sing 134 n n C8 N9 EEM sing 135 n y N7 C8 EEM doub 136 n y C8 H8 EEM sing 137 n n N7 C5 EEM sing 138 n y C6 C5 EEM doub 139 n y C6 N1 EEM sing 140 n y N6 C6 EEM sing 141 n n N6 HN6 EEM sing 142 n n N6 HN6A EEM sing 143 n n # _atom_sites.entry_id 4FHE _atom_sites.fract_transf_matrix[1][1] 0.018512 _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] 0.015865 _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] 0.006963 _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 SF4 A 1 401 1 SF4 FS4 . C 3 SO4 A 1 402 1 SO4 SO4 . D 3 SO4 A 1 403 2 SO4 SO4 . E 3 SO4 A 1 404 3 SO4 SO4 . F 3 SO4 A 1 405 4 SO4 SO4 . G 4 EDO A 1 406 5 EDO EDO . H 5 EEM A 1 407 1 EEM SA2 . I 6 HOH A 1 501 1 HOH HOH . I 6 HOH A 2 502 2 HOH HOH . I 6 HOH A 3 503 3 HOH HOH . I 6 HOH A 4 504 4 HOH HOH . I 6 HOH A 5 505 8 HOH HOH . I 6 HOH A 6 506 11 HOH HOH . I 6 HOH A 7 507 12 HOH HOH . I 6 HOH A 8 508 13 HOH HOH . I 6 HOH A 9 509 16 HOH HOH . I 6 HOH A 10 510 17 HOH HOH . I 6 HOH A 11 511 21 HOH HOH . I 6 HOH A 12 512 25 HOH HOH . I 6 HOH A 13 513 26 HOH HOH . I 6 HOH A 14 514 27 HOH HOH . I 6 HOH A 15 515 28 HOH HOH . I 6 HOH A 16 516 29 HOH HOH . I 6 HOH A 17 517 30 HOH HOH . I 6 HOH A 18 518 31 HOH HOH . I 6 HOH A 19 519 32 HOH HOH . I 6 HOH A 20 520 33 HOH HOH . I 6 HOH A 21 521 35 HOH HOH . I 6 HOH A 22 522 36 HOH HOH . I 6 HOH A 23 523 38 HOH HOH . I 6 HOH A 24 524 39 HOH HOH . I 6 HOH A 25 525 41 HOH HOH . I 6 HOH A 26 526 42 HOH HOH . I 6 HOH A 27 527 43 HOH HOH . I 6 HOH A 28 528 44 HOH HOH . I 6 HOH A 29 529 45 HOH HOH . I 6 HOH A 30 530 46 HOH HOH . I 6 HOH A 31 531 47 HOH HOH . I 6 HOH A 32 532 48 HOH HOH . I 6 HOH A 33 533 50 HOH HOH . I 6 HOH A 34 534 51 HOH HOH . I 6 HOH A 35 535 53 HOH HOH . I 6 HOH A 36 536 54 HOH HOH . I 6 HOH A 37 537 55 HOH HOH . I 6 HOH A 38 538 57 HOH HOH . I 6 HOH A 39 539 58 HOH HOH . I 6 HOH A 40 540 59 HOH HOH . I 6 HOH A 41 541 60 HOH HOH . I 6 HOH A 42 542 61 HOH HOH . I 6 HOH A 43 543 65 HOH HOH . I 6 HOH A 44 544 67 HOH HOH . I 6 HOH A 45 545 68 HOH HOH . I 6 HOH A 46 546 70 HOH HOH . I 6 HOH A 47 547 72 HOH HOH . I 6 HOH A 48 548 74 HOH HOH . I 6 HOH A 49 549 75 HOH HOH . I 6 HOH A 50 550 79 HOH HOH . I 6 HOH A 51 551 80 HOH HOH . I 6 HOH A 52 552 81 HOH HOH . I 6 HOH A 53 553 82 HOH HOH . I 6 HOH A 54 554 84 HOH HOH . I 6 HOH A 55 555 86 HOH HOH . I 6 HOH A 56 556 87 HOH HOH . I 6 HOH A 57 557 88 HOH HOH . I 6 HOH A 58 558 90 HOH HOH . I 6 HOH A 59 559 91 HOH HOH . I 6 HOH A 60 560 93 HOH HOH . I 6 HOH A 61 561 94 HOH HOH . I 6 HOH A 62 562 95 HOH HOH . I 6 HOH A 63 563 103 HOH HOH . I 6 HOH A 64 564 105 HOH HOH . I 6 HOH A 65 565 113 HOH HOH . I 6 HOH A 66 566 115 HOH HOH . I 6 HOH A 67 567 117 HOH HOH . I 6 HOH A 68 568 122 HOH HOH . I 6 HOH A 69 569 127 HOH HOH . I 6 HOH A 70 570 134 HOH HOH . I 6 HOH A 71 571 135 HOH HOH . I 6 HOH A 72 572 136 HOH HOH . I 6 HOH A 73 573 146 HOH HOH . I 6 HOH A 74 574 147 HOH HOH . I 6 HOH A 75 575 148 HOH HOH . I 6 HOH A 76 576 153 HOH HOH . I 6 HOH A 77 577 156 HOH HOH . I 6 HOH A 78 578 164 HOH HOH . I 6 HOH A 79 579 176 HOH HOH . I 6 HOH A 80 580 178 HOH HOH . I 6 HOH A 81 581 181 HOH HOH . I 6 HOH A 82 582 206 HOH HOH . I 6 HOH A 83 583 229 HOH HOH . I 6 HOH A 84 584 230 HOH HOH . I 6 HOH A 85 585 233 HOH HOH . I 6 HOH A 86 586 238 HOH HOH . I 6 HOH A 87 587 243 HOH HOH . I 6 HOH A 88 588 262 HOH HOH . I 6 HOH A 89 589 263 HOH HOH . I 6 HOH A 90 590 264 HOH HOH . I 6 HOH A 91 591 266 HOH HOH . I 6 HOH A 92 592 267 HOH HOH . I 6 HOH A 93 593 268 HOH HOH . I 6 HOH A 94 594 271 HOH HOH . I 6 HOH A 95 595 273 HOH HOH . I 6 HOH A 96 596 275 HOH HOH . I 6 HOH A 97 597 276 HOH HOH . I 6 HOH A 98 598 277 HOH HOH . I 6 HOH A 99 599 281 HOH HOH . I 6 HOH A 100 600 282 HOH HOH . I 6 HOH A 101 601 283 HOH HOH . I 6 HOH A 102 602 284 HOH HOH . I 6 HOH A 103 603 285 HOH HOH . I 6 HOH A 104 604 289 HOH HOH . I 6 HOH A 105 605 290 HOH HOH . I 6 HOH A 106 606 291 HOH HOH . I 6 HOH A 107 607 295 HOH HOH . I 6 HOH A 108 608 297 HOH HOH . I 6 HOH A 109 609 298 HOH HOH . I 6 HOH A 110 610 299 HOH HOH . I 6 HOH A 111 611 303 HOH HOH . I 6 HOH A 112 612 306 HOH HOH . I 6 HOH A 113 613 307 HOH HOH . I 6 HOH A 114 614 316 HOH HOH . I 6 HOH A 115 615 317 HOH HOH . I 6 HOH A 116 616 318 HOH HOH . I 6 HOH A 117 617 319 HOH HOH . I 6 HOH A 118 618 320 HOH HOH . I 6 HOH A 119 619 321 HOH HOH . I 6 HOH A 120 620 322 HOH HOH . I 6 HOH A 121 621 323 HOH HOH . I 6 HOH A 122 622 324 HOH HOH . I 6 HOH A 123 623 326 HOH HOH . I 6 HOH A 124 624 327 HOH HOH . I 6 HOH A 125 625 328 HOH HOH . I 6 HOH A 126 626 329 HOH HOH . I 6 HOH A 127 627 330 HOH HOH . I 6 HOH A 128 628 331 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 C C2 EEM . . . H 5 -0.224 34.235 -44.435 1 22.95 ? C2 EEM 407 A 1 HETATM 2 N N3 EEM . . . H 5 -0.532 34.033 -45.763 1 22.96 ? N3 EEM 407 A 1 HETATM 3 C C4 EEM . . . H 5 0.183 33.149 -46.501 1 23.54 ? C4 EEM 407 A 1 HETATM 4 C C1' EEM . . . H 5 -0.924 33.322 -48.73 1 25.28 ? C1' EEM 407 A 1 HETATM 5 C C2' EEM . . . H 5 -0.405 33.553 -50.14 1 25.72 ? C2' EEM 407 A 1 HETATM 6 C C3' EEM . . . H 5 -1.678 33.426 -50.95 1 26.21 ? C3' EEM 407 A 1 HETATM 7 C C4' EEM . . . H 5 -2.588 32.517 -50.127 1 26.96 ? C4' EEM 407 A 1 HETATM 8 C C5' EEM . . . H 5 -2.769 31.111 -50.704 1 28.25 ? C5' EEM 407 A 1 HETATM 9 O O EEM . . . H 5 0.304 32.347 -53.776 1 29.22 ? O EEM 407 A 1 HETATM 10 C C EEM . . . H 5 -0.759 32.108 -54.354 1 29.34 ? C EEM 407 A 1 HETATM 11 O OXT EEM . . . H 5 -1.549 33.035 -54.515 1 29.13 ? OXT EEM 407 A 1 HETATM 12 C CA EEM . . . H 5 -1.092 30.706 -54.86 1 29.36 ? CA EEM 407 A 1 HETATM 13 N N EEM . . . H 5 0.137 29.868 -54.936 1 29.45 ? N EEM 407 A 1 HETATM 14 C CB EEM . . . H 5 -2.166 30.061 -53.98 1 29.48 ? CB EEM 407 A 1 HETATM 15 C CG EEM . . . H 5 -1.687 29.216 -52.799 1 29.62 ? CG EEM 407 A 1 HETATM 16 SE SE EEM . . . H 5 -1.104 30.244 -51.244 1 30.69 ? SE EEM 407 A 1 HETATM 17 C CE EEM . . . H 5 -0.915 28.804 -49.95 1 30.55 ? CE EEM 407 A 1 HETATM 18 O O4' EEM . . . H 5 -2.011 32.422 -48.841 1 25.67 ? O4' EEM 407 A 1 HETATM 19 O O3' EEM . . . H 5 -2.27 34.693 -51.115 1 26.52 ? O3' EEM 407 A 1 HETATM 20 O O2' EEM . . . H 5 0.224 34.809 -50.278 1 25.62 ? O2' EEM 407 A 1 HETATM 21 N N9 EEM . . . H 5 0.085 32.777 -47.81 1 24.26 ? N9 EEM 407 A 1 HETATM 22 C C8 EEM . . . H 5 1.053 31.838 -48.059 1 24.02 ? C8 EEM 407 A 1 HETATM 23 N N7 EEM . . . H 5 1.744 31.643 -46.912 1 23.59 ? N7 EEM 407 A 1 HETATM 24 C C5 EEM . . . H 5 1.231 32.432 -45.947 1 23.23 ? C5 EEM 407 A 1 HETATM 25 N N1 EEM . . . H 5 0.819 33.531 -43.866 1 22.87 ? N1 EEM 407 A 1 HETATM 26 C C6 EEM . . . H 5 1.554 32.626 -44.609 1 23.22 ? C6 EEM 407 A 1 HETATM 27 N N6 EEM . . . H 5 2.555 31.952 -44.05 1 22.75 ? N6 EEM 407 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #