data_4K9R # _model_server_result.job_id KcH1NQCDCVMC8FJXPjjd0A _model_server_result.datetime_utc '2024-11-12 20:39:06' _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 4k9r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4K9R # _exptl.entry_id 4K9R _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 4K9R _cell.length_a 54.02 _cell.length_b 62.72 _cell.length_c 142.62 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K9R _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 _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 FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc2 A SG CYS 121 A CYS 94 1_555 B FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc3 A SG CYS 124 A CYS 97 1_555 B FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc4 B FE1 SF4 . A SF4 401 1_555 C O EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc5 B FE1 SF4 . A SF4 401 1_555 C N EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? # _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 83 n y C2 N3 EEM sing 84 n y C2 H2 EEM sing 85 n n C4 N3 EEM doub 86 n y C5 C4 EEM sing 87 n y N9 C4 EEM sing 88 n y N9 C1' EEM sing 89 n n C1' O4' EEM sing 90 n n C1' C2' EEM sing 91 n n C1' H1' EEM sing 92 n n O2' C2' EEM sing 93 n n C2' C3' EEM sing 94 n n C2' H2' EEM sing 95 n n C4' C3' EEM sing 96 n n O3' C3' EEM sing 97 n n C3' H3' EEM sing 98 n n O4' C4' EEM sing 99 n n C4' C5' EEM sing 100 n n C4' H4' EEM sing 101 n n C5' H5' EEM sing 102 n n C5' "H5'A" EEM sing 103 n n C5' SE EEM sing 104 n n C O EEM doub 105 n n CA C EEM sing 106 n n C OXT EEM sing 107 n n OXT HOXT EEM sing 108 n n CB CA EEM sing 109 n n N CA EEM sing 110 n n CA HA EEM sing 111 n n N HN EEM sing 112 n n N HNA EEM sing 113 n n CB CG EEM sing 114 n n CB HB EEM sing 115 n n CB HBA EEM sing 116 n n SE CG EEM sing 117 n n CG HG EEM sing 118 n n CG HGA EEM sing 119 n n SE CE EEM sing 120 n n CE HE EEM sing 121 n n CE HEA EEM sing 122 n n CE HEB EEM sing 123 n n O3' HO3' EEM sing 124 n n O2' HO2' EEM sing 125 n n C8 N9 EEM sing 126 n y N7 C8 EEM doub 127 n y C8 H8 EEM sing 128 n n N7 C5 EEM sing 129 n y C6 C5 EEM doub 130 n y C6 N1 EEM sing 131 n y N6 C6 EEM sing 132 n n N6 HN6 EEM sing 133 n n N6 HN6A EEM sing 134 n n # _atom_sites.entry_id 4K9R _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] 0.015944 _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] 0.007012 _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 HOH A 1 501 2 HOH HOH . H 5 HOH A 2 502 6 HOH HOH . H 5 HOH A 3 503 8 HOH HOH . H 5 HOH A 4 504 9 HOH HOH . H 5 HOH A 5 505 10 HOH HOH . H 5 HOH A 6 506 11 HOH HOH . H 5 HOH A 7 507 14 HOH HOH . H 5 HOH A 8 508 15 HOH HOH . H 5 HOH A 9 509 16 HOH HOH . H 5 HOH A 10 510 17 HOH HOH . H 5 HOH A 11 511 18 HOH HOH . H 5 HOH A 12 512 19 HOH HOH . H 5 HOH A 13 513 20 HOH HOH . H 5 HOH A 14 514 21 HOH HOH . H 5 HOH A 15 515 22 HOH HOH . H 5 HOH A 16 516 23 HOH HOH . H 5 HOH A 17 517 24 HOH HOH . H 5 HOH A 18 518 25 HOH HOH . H 5 HOH A 19 519 26 HOH HOH . H 5 HOH A 20 520 27 HOH HOH . H 5 HOH A 21 521 29 HOH HOH . H 5 HOH A 22 522 31 HOH HOH . H 5 HOH A 23 523 32 HOH HOH . H 5 HOH A 24 524 34 HOH HOH . H 5 HOH A 25 525 35 HOH HOH . H 5 HOH A 26 526 42 HOH HOH . H 5 HOH A 27 527 44 HOH HOH . H 5 HOH A 28 528 45 HOH HOH . H 5 HOH A 29 529 46 HOH HOH . H 5 HOH A 30 530 49 HOH HOH . H 5 HOH A 31 531 51 HOH HOH . H 5 HOH A 32 532 52 HOH HOH . H 5 HOH A 33 533 53 HOH HOH . H 5 HOH A 34 534 55 HOH HOH . H 5 HOH A 35 535 56 HOH HOH . H 5 HOH A 36 536 58 HOH HOH . H 5 HOH A 37 537 63 HOH HOH . H 5 HOH A 38 538 64 HOH HOH . H 5 HOH A 39 539 65 HOH HOH . H 5 HOH A 40 540 68 HOH HOH . H 5 HOH A 41 541 69 HOH HOH . H 5 HOH A 42 542 81 HOH HOH . H 5 HOH A 43 543 83 HOH HOH . H 5 HOH A 44 544 86 HOH HOH . H 5 HOH A 45 545 87 HOH HOH . H 5 HOH A 46 546 91 HOH HOH . H 5 HOH A 47 547 96 HOH HOH . H 5 HOH A 48 548 99 HOH HOH . H 5 HOH A 49 549 101 HOH HOH . H 5 HOH A 50 550 105 HOH HOH . H 5 HOH A 51 551 106 HOH HOH . H 5 HOH A 52 552 109 HOH HOH . H 5 HOH A 53 553 110 HOH HOH . H 5 HOH A 54 554 122 HOH HOH . H 5 HOH A 55 555 126 HOH HOH . H 5 HOH A 56 556 127 HOH HOH . H 5 HOH A 57 557 128 HOH HOH . H 5 HOH A 58 558 129 HOH HOH . H 5 HOH A 59 559 130 HOH HOH . H 5 HOH A 60 560 131 HOH HOH . H 5 HOH A 61 561 132 HOH HOH . H 5 HOH A 62 562 133 HOH HOH . H 5 HOH A 63 563 135 HOH HOH . H 5 HOH A 64 564 137 HOH HOH . H 5 HOH A 65 565 138 HOH HOH . H 5 HOH A 66 566 140 HOH HOH . H 5 HOH A 67 567 142 HOH HOH . H 5 HOH A 68 568 143 HOH HOH . H 5 HOH A 69 569 144 HOH HOH . H 5 HOH A 70 570 145 HOH HOH . H 5 HOH A 71 571 146 HOH HOH . H 5 HOH A 72 572 147 HOH HOH . H 5 HOH A 73 573 148 HOH HOH . H 5 HOH A 74 574 149 HOH HOH . H 5 HOH A 75 575 150 HOH HOH . H 5 HOH A 76 576 151 HOH HOH . H 5 HOH A 77 577 152 HOH HOH . H 5 HOH A 78 578 153 HOH HOH . H 5 HOH A 79 579 154 HOH HOH . H 5 HOH A 80 580 155 HOH HOH . H 5 HOH A 81 581 156 HOH HOH . H 5 HOH A 82 582 158 HOH HOH . H 5 HOH A 83 583 159 HOH HOH . H 5 HOH A 84 584 160 HOH HOH . H 5 HOH A 85 585 161 HOH HOH . H 5 HOH A 86 586 162 HOH HOH . H 5 HOH A 87 587 163 HOH HOH . H 5 HOH A 88 588 164 HOH HOH . H 5 HOH A 89 589 165 HOH HOH . H 5 HOH A 90 590 167 HOH HOH . H 5 HOH A 91 591 168 HOH HOH . H 5 HOH A 92 592 169 HOH HOH . H 5 HOH A 93 593 170 HOH HOH . H 5 HOH A 94 594 171 HOH HOH . H 5 HOH A 95 595 172 HOH HOH . H 5 HOH A 96 596 174 HOH HOH . H 5 HOH A 97 597 176 HOH HOH . H 5 HOH A 98 598 177 HOH HOH . H 5 HOH A 99 599 178 HOH HOH . H 5 HOH A 100 600 179 HOH HOH . H 5 HOH A 101 601 180 HOH HOH . H 5 HOH A 102 602 181 HOH HOH . H 5 HOH A 103 603 182 HOH HOH . H 5 HOH A 104 604 183 HOH HOH . H 5 HOH A 105 605 184 HOH HOH . H 5 HOH A 106 606 186 HOH HOH . H 5 HOH A 107 607 189 HOH HOH . H 5 HOH A 108 608 190 HOH HOH . H 5 HOH A 109 609 193 HOH HOH . H 5 HOH A 110 610 194 HOH HOH . H 5 HOH A 111 611 195 HOH HOH . H 5 HOH A 112 612 196 HOH HOH . H 5 HOH A 113 613 199 HOH HOH . H 5 HOH A 114 614 200 HOH HOH . H 5 HOH A 115 615 201 HOH HOH . H 5 HOH A 116 616 202 HOH HOH . H 5 HOH A 117 617 203 HOH HOH . H 5 HOH A 118 618 204 HOH HOH . H 5 HOH A 119 619 205 HOH HOH . H 5 HOH A 120 620 206 HOH HOH . H 5 HOH A 121 621 207 HOH HOH . H 5 HOH A 122 622 208 HOH HOH . H 5 HOH A 123 623 209 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 -0.157 34.258 -44.135 1 22.86 ? C2 EEM 402 A 1 HETATM 2 N N3 EEM . . . C 3 -0.488 34.035 -45.452 1 21.85 ? N3 EEM 402 A 1 HETATM 3 C C4 EEM . . . C 3 0.221 33.131 -46.168 1 24.05 ? C4 EEM 402 A 1 HETATM 4 C C1' EEM . . . C 3 -0.883 33.27 -48.374 1 26.39 ? C1' EEM 402 A 1 HETATM 5 C C2' EEM . . . C 3 -0.348 33.519 -49.77 1 27.17 ? C2' EEM 402 A 1 HETATM 6 C C3' EEM . . . C 3 -1.64 33.459 -50.552 1 27.21 ? C3' EEM 402 A 1 HETATM 7 C C4' EEM . . . C 3 -2.548 32.534 -49.751 1 28.47 ? C4' EEM 402 A 1 HETATM 8 C C5' EEM . . . C 3 -2.768 31.148 -50.352 1 30.53 ? C5' EEM 402 A 1 HETATM 9 O O EEM . . . C 3 0.26 32.135 -53.329 1 28.92 ? O EEM 402 A 1 HETATM 10 C C EEM . . . C 3 -0.814 31.973 -53.921 1 29.08 ? C EEM 402 A 1 HETATM 11 O OXT EEM . . . C 3 -1.599 32.918 -54.042 1 28.44 ? OXT EEM 402 A 1 HETATM 12 C CA EEM . . . C 3 -1.146 30.603 -54.484 1 29.23 ? CA EEM 402 A 1 HETATM 13 N N EEM . . . C 3 0.107 29.793 -54.558 1 29.16 ? N EEM 402 A 1 HETATM 14 C CB EEM . . . C 3 -2.228 29.937 -53.626 1 29.39 ? CB EEM 402 A 1 HETATM 15 C CG EEM . . . C 3 -1.748 29.156 -52.404 1 30.43 ? CG EEM 402 A 1 HETATM 16 SE SE EEM . . . C 3 -1.122 30.292 -50.942 1 34.22 ? SE EEM 402 A 1 HETATM 17 C CE EEM . . . C 3 -0.692 28.963 -49.593 1 34.92 ? CE EEM 402 A 1 HETATM 18 O O4' EEM . . . C 3 -1.95 32.367 -48.487 1 25.95 ? O4' EEM 402 A 1 HETATM 19 O O3' EEM . . . C 3 -2.181 34.753 -50.62 1 27.31 ? O3' EEM 402 A 1 HETATM 20 O O2' EEM . . . C 3 0.331 34.752 -49.89 1 26.64 ? O2' EEM 402 A 1 HETATM 21 N N9 EEM . . . C 3 0.119 32.728 -47.461 1 24.95 ? N9 EEM 402 A 1 HETATM 22 C C8 EEM . . . C 3 1.063 31.772 -47.695 1 25.24 ? C8 EEM 402 A 1 HETATM 23 N N7 EEM . . . C 3 1.763 31.593 -46.56 1 23.58 ? N7 EEM 402 A 1 HETATM 24 C C5 EEM . . . C 3 1.26 32.41 -45.613 1 23.74 ? C5 EEM 402 A 1 HETATM 25 N N1 EEM . . . C 3 0.889 33.548 -43.56 1 23.03 ? N1 EEM 402 A 1 HETATM 26 C C6 EEM . . . C 3 1.603 32.623 -44.293 1 23.15 ? C6 EEM 402 A 1 HETATM 27 N N6 EEM . . . C 3 2.603 31.928 -43.758 1 23.06 ? N6 EEM 402 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #