data_4FHF # _model_server_result.job_id V7cqQnGBvQV4gILszOjuaw _model_server_result.datetime_utc '2024-11-20 11:38:49' _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 4fhf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4FHF # _exptl.entry_id 4FHF _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 4FHF _cell.length_a 53.2 _cell.length_b 58.99 _cell.length_c 131.48 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FHF _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc2 A SG CYS 121 A CYS 94 1_555 B FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 A SG CYS 124 A CYS 97 1_555 B FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc4 B FE2 SF4 . A SF4 401 1_555 C N EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc5 B FE2 SF4 . A SF4 401 1_555 C O EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? # _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 148 n y C2 N3 EEM sing 149 n y C2 H2 EEM sing 150 n n C4 N3 EEM doub 151 n y C5 C4 EEM sing 152 n y N9 C4 EEM sing 153 n y N9 C1' EEM sing 154 n n C1' O4' EEM sing 155 n n C1' C2' EEM sing 156 n n C1' H1' EEM sing 157 n n O2' C2' EEM sing 158 n n C2' C3' EEM sing 159 n n C2' H2' EEM sing 160 n n C4' C3' EEM sing 161 n n O3' C3' EEM sing 162 n n C3' H3' EEM sing 163 n n O4' C4' EEM sing 164 n n C4' C5' EEM sing 165 n n C4' H4' EEM sing 166 n n C5' H5' EEM sing 167 n n C5' "H5'A" EEM sing 168 n n C5' SE EEM sing 169 n n C O EEM doub 170 n n CA C EEM sing 171 n n C OXT EEM sing 172 n n OXT HOXT EEM sing 173 n n CB CA EEM sing 174 n n N CA EEM sing 175 n n CA HA EEM sing 176 n n N HN EEM sing 177 n n N HNA EEM sing 178 n n CB CG EEM sing 179 n n CB HB EEM sing 180 n n CB HBA EEM sing 181 n n SE CG EEM sing 182 n n CG HG EEM sing 183 n n CG HGA EEM sing 184 n n SE CE EEM sing 185 n n CE HE EEM sing 186 n n CE HEA EEM sing 187 n n CE HEB EEM sing 188 n n O3' HO3' EEM sing 189 n n O2' HO2' EEM sing 190 n n C8 N9 EEM sing 191 n y N7 C8 EEM doub 192 n y C8 H8 EEM sing 193 n n N7 C5 EEM sing 194 n y C6 C5 EEM doub 195 n y C6 N1 EEM sing 196 n y N6 C6 EEM sing 197 n n N6 HN6 EEM sing 198 n n N6 HN6A EEM sing 199 n n # _atom_sites.entry_id 4FHF _atom_sites.fract_transf_matrix[1][1] 0.018797 _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] 0.016952 _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] 0.007606 _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 6 SO4 SO4 . I 5 POP A 1 408 7 POP POP . J 6 0TT A 1 409 1 0TT SP . K 7 HOH A 1 501 1 HOH HOH . K 7 HOH A 2 502 2 HOH HOH . K 7 HOH A 3 503 3 HOH HOH . K 7 HOH A 4 504 4 HOH HOH . K 7 HOH A 5 505 5 HOH HOH . K 7 HOH A 6 506 6 HOH HOH . K 7 HOH A 7 507 7 HOH HOH . K 7 HOH A 8 508 8 HOH HOH . K 7 HOH A 9 509 9 HOH HOH . K 7 HOH A 10 510 10 HOH HOH . K 7 HOH A 11 511 11 HOH HOH . K 7 HOH A 12 512 12 HOH HOH . K 7 HOH A 13 513 13 HOH HOH . K 7 HOH A 14 514 14 HOH HOH . K 7 HOH A 15 515 15 HOH HOH . K 7 HOH A 16 516 16 HOH HOH . K 7 HOH A 17 517 17 HOH HOH . K 7 HOH A 18 518 18 HOH HOH . K 7 HOH A 19 519 21 HOH HOH . K 7 HOH A 20 520 22 HOH HOH . K 7 HOH A 21 521 23 HOH HOH . K 7 HOH A 22 522 26 HOH HOH . K 7 HOH A 23 523 28 HOH HOH . K 7 HOH A 24 524 29 HOH HOH . K 7 HOH A 25 525 30 HOH HOH . K 7 HOH A 26 526 31 HOH HOH . K 7 HOH A 27 527 33 HOH HOH . K 7 HOH A 28 528 34 HOH HOH . K 7 HOH A 29 529 36 HOH HOH . K 7 HOH A 30 530 37 HOH HOH . K 7 HOH A 31 531 38 HOH HOH . K 7 HOH A 32 532 39 HOH HOH . K 7 HOH A 33 533 41 HOH HOH . K 7 HOH A 34 534 43 HOH HOH . K 7 HOH A 35 535 44 HOH HOH . K 7 HOH A 36 536 45 HOH HOH . K 7 HOH A 37 537 46 HOH HOH . K 7 HOH A 38 538 47 HOH HOH . K 7 HOH A 39 539 49 HOH HOH . K 7 HOH A 40 540 51 HOH HOH . K 7 HOH A 41 541 52 HOH HOH . K 7 HOH A 42 542 54 HOH HOH . K 7 HOH A 43 543 57 HOH HOH . K 7 HOH A 44 544 59 HOH HOH . K 7 HOH A 45 545 60 HOH HOH . K 7 HOH A 46 546 61 HOH HOH . K 7 HOH A 47 547 62 HOH HOH . K 7 HOH A 48 548 63 HOH HOH . K 7 HOH A 49 549 65 HOH HOH . K 7 HOH A 50 550 66 HOH HOH . K 7 HOH A 51 551 69 HOH HOH . K 7 HOH A 52 552 73 HOH HOH . K 7 HOH A 53 553 74 HOH HOH . K 7 HOH A 54 554 75 HOH HOH . K 7 HOH A 55 555 77 HOH HOH . K 7 HOH A 56 556 79 HOH HOH . K 7 HOH A 57 557 81 HOH HOH . K 7 HOH A 58 558 82 HOH HOH . K 7 HOH A 59 559 83 HOH HOH . K 7 HOH A 60 560 84 HOH HOH . K 7 HOH A 61 561 85 HOH HOH . K 7 HOH A 62 562 86 HOH HOH . K 7 HOH A 63 563 87 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 -26.974 6.769 -24.761 1 37.84 ? C2 EEM 402 A 1 HETATM 2 N N3 EEM . . . C 3 -26.675 6.427 -23.461 1 38.07 ? N3 EEM 402 A 1 HETATM 3 C C4 EEM . . . C 3 -27.382 5.451 -22.84 1 38.7 ? C4 EEM 402 A 1 HETATM 4 C C1' EEM . . . C 3 -26.295 5.406 -20.611 1 40.21 ? C1' EEM 402 A 1 HETATM 5 C C2' EEM . . . C 3 -26.8 5.428 -19.181 1 40.81 ? C2' EEM 402 A 1 HETATM 6 C C3' EEM . . . C 3 -25.502 5.249 -18.427 1 41.36 ? C3' EEM 402 A 1 HETATM 7 C C4' EEM . . . C 3 -24.617 4.417 -19.349 1 42.24 ? C4' EEM 402 A 1 HETATM 8 C C5' EEM . . . C 3 -24.513 2.93 -18.998 1 43.75 ? C5' EEM 402 A 1 HETATM 9 O O EEM . . . C 3 -27.493 3.855 -15.724 1 44.6 ? O EEM 402 A 1 HETATM 10 C C EEM . . . C 3 -26.422 3.499 -15.225 1 44.63 ? C EEM 402 A 1 HETATM 11 O OXT EEM . . . C 3 -25.569 4.354 -14.99 1 44.44 ? OXT EEM 402 A 1 HETATM 12 C CA EEM . . . C 3 -26.165 2.032 -14.897 1 44.7 ? CA EEM 402 A 1 HETATM 13 N N EEM . . . C 3 -27.45 1.273 -14.946 1 44.63 ? N EEM 402 A 1 HETATM 14 C CB EEM . . . C 3 -25.102 1.442 -15.824 1 44.74 ? CB EEM 402 A 1 HETATM 15 C CG EEM . . . C 3 -25.582 0.797 -17.123 1 45.05 ? CG EEM 402 A 1 HETATM 16 SE SE EEM . . . C 3 -26.19 2.1 -18.441 1 46.29 ? SE EEM 402 A 1 HETATM 17 C CE EEM . . . C 3 -26.759 0.949 -19.898 1 47.08 ? CE EEM 402 A 1 HETATM 18 O O4' EEM . . . C 3 -25.166 4.556 -20.643 1 41.03 ? O4' EEM 402 A 1 HETATM 19 O O3' EEM . . . C 3 -24.915 6.509 -18.206 1 41.12 ? O3' EEM 402 A 1 HETATM 20 O O2' EEM . . . C 3 -27.459 6.637 -18.873 1 40.08 ? O2' EEM 402 A 1 HETATM 21 N N9 EEM . . . C 3 -27.289 4.936 -21.584 1 39.22 ? N9 EEM 402 A 1 HETATM 22 C C8 EEM . . . C 3 -28.238 3.956 -21.451 1 38.58 ? C8 EEM 402 A 1 HETATM 23 N N7 EEM . . . C 3 -28.915 3.873 -22.616 1 38.07 ? N7 EEM 402 A 1 HETATM 24 C C5 EEM . . . C 3 -28.41 4.78 -23.481 1 38.42 ? C5 EEM 402 A 1 HETATM 25 N N1 EEM . . . C 3 -27.998 6.114 -25.416 1 37.59 ? N1 EEM 402 A 1 HETATM 26 C C6 EEM . . . C 3 -28.721 5.119 -24.791 1 37.95 ? C6 EEM 402 A 1 HETATM 27 N N6 EEM . . . C 3 -29.702 4.492 -25.435 1 38.21 ? N6 EEM 402 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #