data_4FHG # _model_server_result.job_id tKj0mLovIx6XXCSwq8s2Eg _model_server_result.datetime_utc '2024-11-20 11:32:32' _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 4fhg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4FHG # _exptl.entry_id 4FHG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 446.34 _entity.id 3 _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 4FHG _cell.length_a 54.21 _cell.length_b 63.09 _cell.length_c 143.29 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FHG _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 3 _struct_asym.id C _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 FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc2 A SG CYS 121 A CYS 94 1_555 B FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 A SG CYS 124 A CYS 97 1_555 B FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc4 B FE3 SF4 . A SF4 401 1_555 C N EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc5 B FE3 SF4 . A SF4 401 1_555 C O EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? # _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 4FHG _atom_sites.fract_transf_matrix[1][1] 0.018447 _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] 0.01585 _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] 0.006979 _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 EEM A 1 402 1 EEM SA2 . D 4 SO4 A 1 403 1 SO4 SO4 . E 4 SO4 A 1 404 2 SO4 SO4 . F 4 SO4 A 1 405 3 SO4 SO4 . G 4 SO4 A 1 406 4 SO4 SO4 . H 5 EDO A 1 407 5 EDO EDO . I 6 HOH A 1 501 2 HOH HOH . I 6 HOH A 2 502 6 HOH HOH . I 6 HOH A 3 503 7 HOH HOH . I 6 HOH A 4 504 9 HOH HOH . I 6 HOH A 5 505 11 HOH HOH . I 6 HOH A 6 506 12 HOH HOH . I 6 HOH A 7 507 13 HOH HOH . I 6 HOH A 8 508 17 HOH HOH . I 6 HOH A 9 509 18 HOH HOH . I 6 HOH A 10 510 22 HOH HOH . I 6 HOH A 11 511 24 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 29 HOH HOH . I 6 HOH A 16 516 30 HOH HOH . I 6 HOH A 17 517 32 HOH HOH . I 6 HOH A 18 518 33 HOH HOH . I 6 HOH A 19 519 35 HOH HOH . I 6 HOH A 20 520 36 HOH HOH . I 6 HOH A 21 521 40 HOH HOH . I 6 HOH A 22 522 41 HOH HOH . I 6 HOH A 23 523 42 HOH HOH . I 6 HOH A 24 524 43 HOH HOH . I 6 HOH A 25 525 45 HOH HOH . I 6 HOH A 26 526 48 HOH HOH . I 6 HOH A 27 527 49 HOH HOH . I 6 HOH A 28 528 50 HOH HOH . I 6 HOH A 29 529 51 HOH HOH . I 6 HOH A 30 530 52 HOH HOH . I 6 HOH A 31 531 54 HOH HOH . I 6 HOH A 32 532 55 HOH HOH . I 6 HOH A 33 533 58 HOH HOH . I 6 HOH A 34 534 60 HOH HOH . I 6 HOH A 35 535 62 HOH HOH . I 6 HOH A 36 536 63 HOH HOH . I 6 HOH A 37 537 64 HOH HOH . I 6 HOH A 38 538 65 HOH HOH . I 6 HOH A 39 539 67 HOH HOH . I 6 HOH A 40 540 70 HOH HOH . I 6 HOH A 41 541 74 HOH HOH . I 6 HOH A 42 542 75 HOH HOH . I 6 HOH A 43 543 77 HOH HOH . I 6 HOH A 44 544 78 HOH HOH . I 6 HOH A 45 545 82 HOH HOH . I 6 HOH A 46 546 84 HOH HOH . I 6 HOH A 47 547 89 HOH HOH . I 6 HOH A 48 548 90 HOH HOH . I 6 HOH A 49 549 91 HOH HOH . I 6 HOH A 50 550 93 HOH HOH . I 6 HOH A 51 551 95 HOH HOH . I 6 HOH A 52 552 98 HOH HOH . I 6 HOH A 53 553 99 HOH HOH . I 6 HOH A 54 554 103 HOH HOH . I 6 HOH A 55 555 105 HOH HOH . I 6 HOH A 56 556 108 HOH HOH . I 6 HOH A 57 557 109 HOH HOH . I 6 HOH A 58 558 110 HOH HOH . I 6 HOH A 59 559 111 HOH HOH . I 6 HOH A 60 560 113 HOH HOH . I 6 HOH A 61 561 116 HOH HOH . I 6 HOH A 62 562 117 HOH HOH . I 6 HOH A 63 563 118 HOH HOH . I 6 HOH A 64 564 125 HOH HOH . I 6 HOH A 65 565 126 HOH HOH . I 6 HOH A 66 566 128 HOH HOH . I 6 HOH A 67 567 132 HOH HOH . I 6 HOH A 68 568 133 HOH HOH . I 6 HOH A 69 569 136 HOH HOH . I 6 HOH A 70 570 137 HOH HOH . I 6 HOH A 71 571 144 HOH HOH . I 6 HOH A 72 572 146 HOH HOH . I 6 HOH A 73 573 147 HOH HOH . I 6 HOH A 74 574 148 HOH HOH . I 6 HOH A 75 575 150 HOH HOH . I 6 HOH A 76 576 151 HOH HOH . I 6 HOH A 77 577 152 HOH HOH . I 6 HOH A 78 578 153 HOH HOH . I 6 HOH A 79 579 154 HOH HOH . I 6 HOH A 80 580 155 HOH HOH . I 6 HOH A 81 581 156 HOH HOH . I 6 HOH A 82 582 157 HOH HOH . I 6 HOH A 83 583 158 HOH HOH . I 6 HOH A 84 584 161 HOH HOH . I 6 HOH A 85 585 165 HOH HOH . I 6 HOH A 86 586 166 HOH HOH . I 6 HOH A 87 587 168 HOH HOH . I 6 HOH A 88 588 169 HOH HOH . I 6 HOH A 89 589 170 HOH HOH . I 6 HOH A 90 590 171 HOH HOH . I 6 HOH A 91 591 172 HOH HOH . I 6 HOH A 92 592 173 HOH HOH . I 6 HOH A 93 593 175 HOH HOH . I 6 HOH A 94 594 176 HOH HOH . I 6 HOH A 95 595 177 HOH HOH . I 6 HOH A 96 596 179 HOH HOH . I 6 HOH A 97 597 180 HOH HOH . I 6 HOH A 98 598 181 HOH HOH . I 6 HOH A 99 599 182 HOH HOH . I 6 HOH A 100 600 183 HOH HOH . I 6 HOH A 101 601 184 HOH HOH . I 6 HOH A 102 602 187 HOH HOH . I 6 HOH A 103 603 189 HOH HOH . I 6 HOH A 104 604 192 HOH HOH . I 6 HOH A 105 605 193 HOH HOH . I 6 HOH A 106 606 194 HOH HOH . I 6 HOH A 107 607 195 HOH HOH . I 6 HOH A 108 608 196 HOH HOH . I 6 HOH A 109 609 197 HOH HOH . I 6 HOH A 110 610 199 HOH HOH . I 6 HOH A 111 611 200 HOH HOH . I 6 HOH A 112 612 202 HOH HOH . I 6 HOH A 113 613 203 HOH HOH . I 6 HOH A 114 614 204 HOH HOH . I 6 HOH A 115 615 205 HOH HOH . I 6 HOH A 116 616 208 HOH HOH . I 6 HOH A 117 617 209 HOH HOH . I 6 HOH A 118 618 210 HOH HOH . I 6 HOH A 119 619 212 HOH HOH . I 6 HOH A 120 620 213 HOH HOH . I 6 HOH A 121 621 214 HOH HOH . I 6 HOH A 122 622 215 HOH HOH . I 6 HOH A 123 623 216 HOH HOH . I 6 HOH A 124 624 217 HOH HOH . I 6 HOH A 125 625 218 HOH HOH . I 6 HOH A 126 626 219 HOH HOH . I 6 HOH A 127 627 220 HOH HOH . I 6 HOH A 128 628 221 HOH HOH . I 6 HOH A 129 629 224 HOH HOH . I 6 HOH A 130 630 225 HOH HOH . I 6 HOH A 131 631 226 HOH HOH . I 6 HOH A 132 632 227 HOH HOH . I 6 HOH A 133 633 228 HOH HOH . I 6 HOH A 134 634 229 HOH HOH . I 6 HOH A 135 635 230 HOH HOH . I 6 HOH A 136 636 231 HOH HOH . I 6 HOH A 137 637 232 HOH HOH . I 6 HOH A 138 638 233 HOH HOH . I 6 HOH A 139 639 234 HOH HOH . I 6 HOH A 140 640 235 HOH HOH . I 6 HOH A 141 641 239 HOH HOH . I 6 HOH A 142 642 240 HOH HOH . I 6 HOH A 143 643 242 HOH HOH . I 6 HOH A 144 644 246 HOH HOH . I 6 HOH A 145 645 248 HOH HOH . I 6 HOH A 146 646 249 HOH HOH . I 6 HOH A 147 647 251 HOH HOH . I 6 HOH A 148 648 255 HOH HOH . I 6 HOH A 149 649 256 HOH HOH . I 6 HOH A 150 650 258 HOH HOH . I 6 HOH A 151 651 261 HOH HOH . I 6 HOH A 152 652 262 HOH HOH . I 6 HOH A 153 653 264 HOH HOH . I 6 HOH A 154 654 265 HOH HOH . I 6 HOH A 155 655 267 HOH HOH . I 6 HOH A 156 656 271 HOH HOH . I 6 HOH A 157 657 272 HOH HOH . I 6 HOH A 158 658 275 HOH HOH . I 6 HOH A 159 659 276 HOH HOH . I 6 HOH A 160 660 277 HOH HOH . I 6 HOH A 161 661 278 HOH HOH . I 6 HOH A 162 662 279 HOH HOH . I 6 HOH A 163 663 280 HOH HOH . I 6 HOH A 164 664 281 HOH HOH . I 6 HOH A 165 665 282 HOH HOH . I 6 HOH A 166 666 283 HOH HOH . I 6 HOH A 167 667 284 HOH HOH . I 6 HOH A 168 668 285 HOH HOH . I 6 HOH A 169 669 286 HOH HOH . I 6 HOH A 170 670 287 HOH HOH . I 6 HOH A 171 671 288 HOH HOH . I 6 HOH A 172 672 289 HOH HOH . I 6 HOH A 173 673 290 HOH HOH . I 6 HOH A 174 674 291 HOH HOH . I 6 HOH A 175 675 292 HOH HOH . I 6 HOH A 176 676 293 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 . . . C 3 -0.305 34.239 -44.313 1 20.53 ? C2 EEM 402 A 1 HETATM 2 N N3 EEM . . . C 3 -0.599 34.055 -45.646 1 20.38 ? N3 EEM 402 A 1 HETATM 3 C C4 EEM . . . C 3 0.132 33.193 -46.389 1 19.93 ? C4 EEM 402 A 1 HETATM 4 C C1' EEM . . . C 3 -0.951 33.371 -48.636 1 20.87 ? C1' EEM 402 A 1 HETATM 5 C C2' EEM . . . C 3 -0.424 33.647 -50.035 1 21.07 ? C2' EEM 402 A 1 HETATM 6 C C3' EEM . . . C 3 -1.709 33.615 -50.833 1 21.56 ? C3' EEM 402 A 1 HETATM 7 C C4' EEM . . . C 3 -2.616 32.665 -50.06 1 22.28 ? C4' EEM 402 A 1 HETATM 8 C C5' EEM . . . C 3 -2.834 31.332 -50.766 1 23.89 ? C5' EEM 402 A 1 HETATM 9 O O EEM . . . C 3 0.227 32.432 -53.629 1 23.48 ? O EEM 402 A 1 HETATM 10 C C EEM . . . C 3 -0.851 32.144 -54.173 1 23.66 ? C EEM 402 A 1 HETATM 11 O OXT EEM . . . C 3 -1.707 33.027 -54.28 1 23 ? OXT EEM 402 A 1 HETATM 12 C CA EEM . . . C 3 -1.121 30.737 -54.707 1 23.75 ? CA EEM 402 A 1 HETATM 13 N N EEM . . . C 3 0.135 29.93 -54.759 1 24.04 ? N EEM 402 A 1 HETATM 14 C CB EEM . . . C 3 -2.188 30.028 -53.873 1 24.12 ? CB EEM 402 A 1 HETATM 15 C CG EEM . . . C 3 -1.713 29.249 -52.646 1 24.6 ? CG EEM 402 A 1 HETATM 16 SE SE EEM . . . C 3 -1.187 30.333 -51.109 1 27.03 ? SE EEM 402 A 1 HETATM 17 C CE EEM . . . C 3 -1.282 28.958 -49.747 1 27.78 ? CE EEM 402 A 1 HETATM 18 O O4' EEM . . . C 3 -2.01 32.441 -48.804 1 21.22 ? O4' EEM 402 A 1 HETATM 19 O O3' EEM . . . C 3 -2.27 34.908 -50.908 1 22.69 ? O3' EEM 402 A 1 HETATM 20 O O2' EEM . . . C 3 0.263 34.877 -50.15 1 20.81 ? O2' EEM 402 A 1 HETATM 21 N N9 EEM . . . C 3 0.051 32.838 -47.703 1 20.39 ? N9 EEM 402 A 1 HETATM 22 C C8 EEM . . . C 3 1.038 31.915 -47.95 1 20.06 ? C8 EEM 402 A 1 HETATM 23 N N7 EEM . . . C 3 1.719 31.721 -46.798 1 19.83 ? N7 EEM 402 A 1 HETATM 24 C C5 EEM . . . C 3 1.184 32.486 -45.833 1 19.67 ? C5 EEM 402 A 1 HETATM 25 N N1 EEM . . . C 3 0.743 33.543 -43.742 1 20.36 ? N1 EEM 402 A 1 HETATM 26 C C6 EEM . . . C 3 1.496 32.664 -44.494 1 20.62 ? C6 EEM 402 A 1 HETATM 27 N N6 EEM . . . C 3 2.505 31.996 -43.942 1 20 ? N6 EEM 402 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 1067 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #