data_4FHC # _model_server_result.job_id 9k-n49p393luczLDDspZ_A _model_server_result.datetime_utc '2024-11-20 13:44:35' _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 4fhc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4FHC # _exptl.entry_id 4FHC _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 4FHC _cell.length_a 54.22 _cell.length_b 63.12 _cell.length_c 143.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FHC _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,J,K,L _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 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc3 A SG CYS 124 A CYS 97 1_555 B FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc4 B FE3 SF4 . A SF4 401 1_555 C N EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc5 B FE3 SF4 . A SF4 401 1_555 C O EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? # _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 4FHC _atom_sites.fract_transf_matrix[1][1] 0.018443 _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] 0.015843 _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] 0.006946 _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 4 SO4 A 1 407 5 SO4 SO4 . I 4 SO4 A 1 408 6 SO4 SO4 . J 4 SO4 A 1 409 7 SO4 SO4 . K 5 EDO A 1 410 8 EDO EDO . L 6 HOH A 1 501 2 HOH HOH . L 6 HOH A 2 502 3 HOH HOH . L 6 HOH A 3 503 4 HOH HOH . L 6 HOH A 4 504 5 HOH HOH . L 6 HOH A 5 505 7 HOH HOH . L 6 HOH A 6 506 8 HOH HOH . L 6 HOH A 7 507 10 HOH HOH . L 6 HOH A 8 508 11 HOH HOH . L 6 HOH A 9 509 12 HOH HOH . L 6 HOH A 10 510 13 HOH HOH . L 6 HOH A 11 511 14 HOH HOH . L 6 HOH A 12 512 15 HOH HOH . L 6 HOH A 13 513 17 HOH HOH . L 6 HOH A 14 514 19 HOH HOH . L 6 HOH A 15 515 20 HOH HOH . L 6 HOH A 16 516 22 HOH HOH . L 6 HOH A 17 517 23 HOH HOH . L 6 HOH A 18 518 24 HOH HOH . L 6 HOH A 19 519 25 HOH HOH . L 6 HOH A 20 520 26 HOH HOH . L 6 HOH A 21 521 28 HOH HOH . L 6 HOH A 22 522 29 HOH HOH . L 6 HOH A 23 523 30 HOH HOH . L 6 HOH A 24 524 32 HOH HOH . L 6 HOH A 25 525 34 HOH HOH . L 6 HOH A 26 526 35 HOH HOH . L 6 HOH A 27 527 37 HOH HOH . L 6 HOH A 28 528 38 HOH HOH . L 6 HOH A 29 529 39 HOH HOH . L 6 HOH A 30 530 40 HOH HOH . L 6 HOH A 31 531 41 HOH HOH . L 6 HOH A 32 532 42 HOH HOH . L 6 HOH A 33 533 43 HOH HOH . L 6 HOH A 34 534 44 HOH HOH . L 6 HOH A 35 535 45 HOH HOH . L 6 HOH A 36 536 48 HOH HOH . L 6 HOH A 37 537 50 HOH HOH . L 6 HOH A 38 538 52 HOH HOH . L 6 HOH A 39 539 53 HOH HOH . L 6 HOH A 40 540 55 HOH HOH . L 6 HOH A 41 541 56 HOH HOH . L 6 HOH A 42 542 57 HOH HOH . L 6 HOH A 43 543 58 HOH HOH . L 6 HOH A 44 544 60 HOH HOH . L 6 HOH A 45 545 61 HOH HOH . L 6 HOH A 46 546 65 HOH HOH . L 6 HOH A 47 547 66 HOH HOH . L 6 HOH A 48 548 69 HOH HOH . L 6 HOH A 49 549 70 HOH HOH . L 6 HOH A 50 550 71 HOH HOH . L 6 HOH A 51 551 72 HOH HOH . L 6 HOH A 52 552 73 HOH HOH . L 6 HOH A 53 553 74 HOH HOH . L 6 HOH A 54 554 75 HOH HOH . L 6 HOH A 55 555 78 HOH HOH . L 6 HOH A 56 556 79 HOH HOH . L 6 HOH A 57 557 80 HOH HOH . L 6 HOH A 58 558 81 HOH HOH . L 6 HOH A 59 559 83 HOH HOH . L 6 HOH A 60 560 84 HOH HOH . L 6 HOH A 61 561 88 HOH HOH . L 6 HOH A 62 562 89 HOH HOH . L 6 HOH A 63 563 92 HOH HOH . L 6 HOH A 64 564 96 HOH HOH . L 6 HOH A 65 565 98 HOH HOH . L 6 HOH A 66 566 100 HOH HOH . L 6 HOH A 67 567 101 HOH HOH . L 6 HOH A 68 568 102 HOH HOH . L 6 HOH A 69 569 103 HOH HOH . L 6 HOH A 70 570 104 HOH HOH . L 6 HOH A 71 571 106 HOH HOH . L 6 HOH A 72 572 107 HOH HOH . L 6 HOH A 73 573 108 HOH HOH . L 6 HOH A 74 574 109 HOH HOH . L 6 HOH A 75 575 110 HOH HOH . L 6 HOH A 76 576 113 HOH HOH . L 6 HOH A 77 577 114 HOH HOH . L 6 HOH A 78 578 115 HOH HOH . L 6 HOH A 79 579 116 HOH HOH . L 6 HOH A 80 580 117 HOH HOH . L 6 HOH A 81 581 120 HOH HOH . L 6 HOH A 82 582 121 HOH HOH . L 6 HOH A 83 583 123 HOH HOH . L 6 HOH A 84 584 124 HOH HOH . L 6 HOH A 85 585 128 HOH HOH . L 6 HOH A 86 586 129 HOH HOH . L 6 HOH A 87 587 130 HOH HOH . L 6 HOH A 88 588 131 HOH HOH . L 6 HOH A 89 589 142 HOH HOH . L 6 HOH A 90 590 147 HOH HOH . L 6 HOH A 91 591 151 HOH HOH . L 6 HOH A 92 592 153 HOH HOH . L 6 HOH A 93 593 154 HOH HOH . L 6 HOH A 94 594 158 HOH HOH . L 6 HOH A 95 595 164 HOH HOH . L 6 HOH A 96 596 165 HOH HOH . L 6 HOH A 97 597 166 HOH HOH . L 6 HOH A 98 598 167 HOH HOH . L 6 HOH A 99 599 168 HOH HOH . L 6 HOH A 100 600 169 HOH HOH . L 6 HOH A 101 601 170 HOH HOH . L 6 HOH A 102 602 171 HOH HOH . L 6 HOH A 103 603 172 HOH HOH . L 6 HOH A 104 604 173 HOH HOH . L 6 HOH A 105 605 174 HOH HOH . L 6 HOH A 106 606 175 HOH HOH . L 6 HOH A 107 607 177 HOH HOH . L 6 HOH A 108 608 178 HOH HOH . L 6 HOH A 109 609 179 HOH HOH . L 6 HOH A 110 610 180 HOH HOH . L 6 HOH A 111 611 182 HOH HOH . L 6 HOH A 112 612 183 HOH HOH . L 6 HOH A 113 613 184 HOH HOH . L 6 HOH A 114 614 185 HOH HOH . L 6 HOH A 115 615 186 HOH HOH . L 6 HOH A 116 616 187 HOH HOH . L 6 HOH A 117 617 189 HOH HOH . L 6 HOH A 118 618 190 HOH HOH . L 6 HOH A 119 619 191 HOH HOH . L 6 HOH A 120 620 192 HOH HOH . L 6 HOH A 121 621 194 HOH HOH . L 6 HOH A 122 622 195 HOH HOH . L 6 HOH A 123 623 196 HOH HOH . L 6 HOH A 124 624 197 HOH HOH . L 6 HOH A 125 625 200 HOH HOH . L 6 HOH A 126 626 201 HOH HOH . L 6 HOH A 127 627 202 HOH HOH . L 6 HOH A 128 628 204 HOH HOH . L 6 HOH A 129 629 205 HOH HOH . L 6 HOH A 130 630 206 HOH HOH . L 6 HOH A 131 631 207 HOH HOH . L 6 HOH A 132 632 209 HOH HOH . L 6 HOH A 133 633 210 HOH HOH . L 6 HOH A 134 634 211 HOH HOH . L 6 HOH A 135 635 212 HOH HOH . L 6 HOH A 136 636 215 HOH HOH . L 6 HOH A 137 637 218 HOH HOH . L 6 HOH A 138 638 219 HOH HOH . L 6 HOH A 139 639 220 HOH HOH . L 6 HOH A 140 640 221 HOH HOH . L 6 HOH A 141 641 222 HOH HOH . L 6 HOH A 142 642 224 HOH HOH . L 6 HOH A 143 643 225 HOH HOH . L 6 HOH A 144 644 226 HOH HOH . L 6 HOH A 145 645 227 HOH HOH . L 6 HOH A 146 646 228 HOH HOH . L 6 HOH A 147 647 229 HOH HOH . L 6 HOH A 148 648 230 HOH HOH . L 6 HOH A 149 649 232 HOH HOH . L 6 HOH A 150 650 233 HOH HOH . L 6 HOH A 151 651 237 HOH HOH . L 6 HOH A 152 652 238 HOH HOH . L 6 HOH A 153 653 239 HOH HOH . L 6 HOH A 154 654 240 HOH HOH . L 6 HOH A 155 655 241 HOH HOH . L 6 HOH A 156 656 242 HOH HOH . L 6 HOH A 157 657 243 HOH HOH . L 6 HOH A 158 658 244 HOH HOH . L 6 HOH A 159 659 245 HOH HOH . L 6 HOH A 160 660 246 HOH HOH . L 6 HOH A 161 661 247 HOH HOH . L 6 HOH A 162 662 248 HOH HOH . L 6 HOH A 163 663 249 HOH HOH . L 6 HOH A 164 664 250 HOH HOH . L 6 HOH A 165 665 251 HOH HOH . L 6 HOH A 166 666 252 HOH HOH . L 6 HOH A 167 667 253 HOH HOH . L 6 HOH A 168 668 254 HOH HOH . L 6 HOH A 169 669 255 HOH HOH . L 6 HOH A 170 670 256 HOH HOH . L 6 HOH A 171 671 257 HOH HOH . L 6 HOH A 172 672 258 HOH HOH . L 6 HOH A 173 673 259 HOH HOH . L 6 HOH A 174 674 260 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 -0.234 33.962 -44.464 1 15.52 ? C2 EEM 402 A 1 HETATM 2 N N3 EEM . . . C 3 -0.552 33.792 -45.794 1 15.57 ? N3 EEM 402 A 1 HETATM 3 C C4 EEM . . . C 3 0.155 32.924 -46.554 1 16.11 ? C4 EEM 402 A 1 HETATM 4 C C1' EEM . . . C 3 -0.963 33.152 -48.775 1 18.22 ? C1' EEM 402 A 1 HETATM 5 C C2' EEM . . . C 3 -0.451 33.349 -50.193 1 18.77 ? C2' EEM 402 A 1 HETATM 6 C C3' EEM . . . C 3 -1.725 33.227 -51.004 1 19.37 ? C3' EEM 402 A 1 HETATM 7 C C4' EEM . . . C 3 -2.642 32.34 -50.162 1 20.29 ? C4' EEM 402 A 1 HETATM 8 C C5' EEM . . . C 3 -2.8 30.907 -50.679 1 21.7 ? C5' EEM 402 A 1 HETATM 9 O O EEM . . . C 3 0.27 32.164 -53.861 1 21.13 ? O EEM 402 A 1 HETATM 10 C C EEM . . . C 3 -0.81 31.966 -54.426 1 21.28 ? C EEM 402 A 1 HETATM 11 O OXT EEM . . . C 3 -1.584 32.914 -54.556 1 21.02 ? OXT EEM 402 A 1 HETATM 12 C CA EEM . . . C 3 -1.179 30.582 -54.951 1 21.39 ? CA EEM 402 A 1 HETATM 13 N N EEM . . . C 3 0.035 29.719 -55.025 1 21.28 ? N EEM 402 A 1 HETATM 14 C CB EEM . . . C 3 -2.275 29.956 -54.083 1 21.52 ? CB EEM 402 A 1 HETATM 15 C CG EEM . . . C 3 -1.81 29.098 -52.909 1 22.2 ? CG EEM 402 A 1 HETATM 16 SE SE EEM . . . C 3 -1.155 30.138 -51.396 0.98 24.77 ? SE EEM 402 A 1 HETATM 17 C CE EEM . . . C 3 -0.684 28.716 -50.157 1 24.04 ? CE EEM 402 A 1 HETATM 18 O O4' EEM . . . C 3 -2.086 32.297 -48.863 1 18.79 ? O4' EEM 402 A 1 HETATM 19 O O3' EEM . . . C 3 -2.298 34.498 -51.207 1 19.2 ? O3' EEM 402 A 1 HETATM 20 O O2' EEM . . . C 3 0.206 34.586 -50.349 1 18.52 ? O2' EEM 402 A 1 HETATM 21 N N9 EEM . . . C 3 0.047 32.58 -47.868 1 16.91 ? N9 EEM 402 A 1 HETATM 22 C C8 EEM . . . C 3 1.012 31.644 -48.14 1 16.4 ? C8 EEM 402 A 1 HETATM 23 N N7 EEM . . . C 3 1.709 31.423 -47.003 1 15.77 ? N7 EEM 402 A 1 HETATM 24 C C5 EEM . . . C 3 1.204 32.192 -46.018 1 15.82 ? C5 EEM 402 A 1 HETATM 25 N N1 EEM . . . C 3 0.809 33.242 -43.912 1 15.46 ? N1 EEM 402 A 1 HETATM 26 C C6 EEM . . . C 3 1.537 32.355 -44.678 1 15.5 ? C6 EEM 402 A 1 HETATM 27 N N6 EEM . . . C 3 2.537 31.668 -44.134 1 15.07 ? N6 EEM 402 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #