data_9CKF # _model_server_result.job_id 9u709egIw0zytHjKFxGaaA _model_server_result.datetime_utc '2025-01-15 16:22:38' _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 9ckf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":503}' # _entry.id 9CKF # _exptl.entry_id 9CKF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 134.746 _cell.angle_gamma 90 _cell.entry_id 9CKF _cell.length_a 215.188 _cell.length_b 52.909 _cell.length_c 151.903 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 J N 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 52 A CYS 52 1_555 G ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc2 A SG CYS 55 A CYS 55 1_555 G ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 A SG CYS 65 A CYS 65 1_555 E ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc4 A SG CYS 68 A CYS 68 1_555 E ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc5 A SG CYS 74 A CYS 74 1_555 G ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc6 A SG CYS 78 A CYS 78 1_555 G ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc7 A NE2 HIS 86 A HIS 86 1_555 E ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc8 A SG CYS 90 A CYS 90 1_555 E ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc9 A SG CYS 209 A CYS 209 1_555 F ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc10 A SG CYS 262 A CYS 262 1_555 F ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc11 A SG CYS 264 A CYS 264 1_555 F ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc12 A SG CYS 267 A CYS 267 1_555 F ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc13 B SG CYS 52 B CYS 52 1_555 M ZN ZN . B ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc14 B SG CYS 55 B CYS 55 1_555 M ZN ZN . B ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc15 B SG CYS 65 B CYS 65 1_555 K ZN ZN . B ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc16 B SG CYS 68 B CYS 68 1_555 K ZN ZN . B ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc17 B SG CYS 74 B CYS 74 1_555 M ZN ZN . B ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc18 B SG CYS 78 B CYS 78 1_555 M ZN ZN . B ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc19 B NE2 HIS 86 B HIS 86 1_555 K ZN ZN . B ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc20 B SG CYS 90 B CYS 90 1_555 K ZN ZN . B ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc21 B SG CYS 209 B CYS 209 1_555 L ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc22 B SG CYS 262 B CYS 262 1_555 L ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc23 B SG CYS 264 B CYS 264 1_555 L ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc24 B SG CYS 267 B CYS 267 1_555 L ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N CA SAH sing 290 n n N HN1 SAH sing 291 n n N HN2 SAH sing 292 n n CA CB SAH sing 293 n n CA C SAH sing 294 n n CA HA SAH sing 295 n n CB CG SAH sing 296 n n CB HB1 SAH sing 297 n n CB HB2 SAH sing 298 n n CG SD SAH sing 299 n n CG HG1 SAH sing 300 n n CG HG2 SAH sing 301 n n SD C5' SAH sing 302 n n C O SAH doub 303 n n C OXT SAH sing 304 n n OXT HXT SAH sing 305 n n C5' C4' SAH sing 306 n n C5' "H5'1" SAH sing 307 n n C5' "H5'2" SAH sing 308 n n C4' O4' SAH sing 309 n n C4' C3' SAH sing 310 n n C4' H4' SAH sing 311 n n O4' C1' SAH sing 312 n n C3' O3' SAH sing 313 n n C3' C2' SAH sing 314 n n C3' H3' SAH sing 315 n n O3' HO3' SAH sing 316 n n C2' O2' SAH sing 317 n n C2' C1' SAH sing 318 n n C2' H2' SAH sing 319 n n O2' HO2' SAH sing 320 n n C1' N9 SAH sing 321 n n C1' H1' SAH sing 322 n n N9 C8 SAH sing 323 n y N9 C4 SAH sing 324 n y C8 N7 SAH doub 325 n y C8 H8 SAH sing 326 n n N7 C5 SAH sing 327 n y C5 C6 SAH sing 328 n y C5 C4 SAH doub 329 n y C6 N6 SAH sing 330 n n C6 N1 SAH doub 331 n y N6 HN61 SAH sing 332 n n N6 HN62 SAH sing 333 n n N1 C2 SAH sing 334 n y C2 N3 SAH doub 335 n y C2 H2 SAH sing 336 n n N3 C4 SAH sing 337 n y # _atom_sites.entry_id 9CKF _atom_sites.fract_transf_matrix[1][1] 0.004647 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004606 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0189 _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] 0.009269 _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 C 2 GOL A 1 501 1 GOL GOL . D 3 SAH A 1 502 1 SAH SAH . E 4 ZN A 1 503 501 ZN ZN . F 4 ZN A 1 504 502 ZN ZN . G 4 ZN A 1 505 503 ZN ZN . H 2 GOL B 1 501 2 GOL GOL . I 2 GOL B 1 502 3 GOL GOL . J 3 SAH B 1 503 2 SAH SAH . K 4 ZN B 1 504 506 ZN ZN . L 4 ZN B 1 505 507 ZN ZN . M 4 ZN B 1 506 508 ZN ZN . N 5 HOH A 1 601 16 HOH HOH . N 5 HOH A 2 602 40 HOH HOH . N 5 HOH A 3 603 71 HOH HOH . N 5 HOH A 4 604 46 HOH HOH . N 5 HOH A 5 605 17 HOH HOH . N 5 HOH A 6 606 59 HOH HOH . N 5 HOH A 7 607 53 HOH HOH . N 5 HOH A 8 608 121 HOH HOH . N 5 HOH A 9 609 81 HOH HOH . N 5 HOH A 10 610 80 HOH HOH . N 5 HOH A 11 611 39 HOH HOH . N 5 HOH A 12 612 104 HOH HOH . N 5 HOH A 13 613 14 HOH HOH . N 5 HOH A 14 614 22 HOH HOH . N 5 HOH A 15 615 8 HOH HOH . N 5 HOH A 16 616 44 HOH HOH . N 5 HOH A 17 617 68 HOH HOH . N 5 HOH A 18 618 98 HOH HOH . N 5 HOH A 19 619 66 HOH HOH . N 5 HOH A 20 620 125 HOH HOH . N 5 HOH A 21 621 37 HOH HOH . N 5 HOH A 22 622 107 HOH HOH . N 5 HOH A 23 623 42 HOH HOH . N 5 HOH A 24 624 109 HOH HOH . N 5 HOH A 25 625 15 HOH HOH . N 5 HOH A 26 626 12 HOH HOH . N 5 HOH A 27 627 95 HOH HOH . N 5 HOH A 28 628 101 HOH HOH . N 5 HOH A 29 629 6 HOH HOH . N 5 HOH A 30 630 36 HOH HOH . N 5 HOH A 31 631 63 HOH HOH . N 5 HOH A 32 632 35 HOH HOH . N 5 HOH A 33 633 31 HOH HOH . N 5 HOH A 34 634 19 HOH HOH . N 5 HOH A 35 635 89 HOH HOH . N 5 HOH A 36 636 20 HOH HOH . N 5 HOH A 37 637 28 HOH HOH . N 5 HOH A 38 638 34 HOH HOH . N 5 HOH A 39 639 23 HOH HOH . N 5 HOH A 40 640 87 HOH HOH . N 5 HOH A 41 641 91 HOH HOH . N 5 HOH A 42 642 78 HOH HOH . N 5 HOH A 43 643 11 HOH HOH . N 5 HOH A 44 644 69 HOH HOH . N 5 HOH A 45 645 79 HOH HOH . N 5 HOH A 46 646 103 HOH HOH . N 5 HOH A 47 647 45 HOH HOH . N 5 HOH A 48 648 32 HOH HOH . N 5 HOH A 49 649 97 HOH HOH . N 5 HOH A 50 650 55 HOH HOH . N 5 HOH A 51 651 54 HOH HOH . N 5 HOH A 52 652 122 HOH HOH . N 5 HOH A 53 653 77 HOH HOH . N 5 HOH A 54 654 75 HOH HOH . N 5 HOH A 55 655 82 HOH HOH . N 5 HOH A 56 656 94 HOH HOH . N 5 HOH A 57 657 58 HOH HOH . N 5 HOH A 58 658 41 HOH HOH . N 5 HOH A 59 659 115 HOH HOH . N 5 HOH A 60 660 43 HOH HOH . N 5 HOH A 61 661 105 HOH HOH . N 5 HOH A 62 662 93 HOH HOH . N 5 HOH A 63 663 38 HOH HOH . N 5 HOH A 64 664 56 HOH HOH . N 5 HOH A 65 665 61 HOH HOH . N 5 HOH A 66 666 74 HOH HOH . N 5 HOH A 67 667 73 HOH HOH . N 5 HOH A 68 668 57 HOH HOH . O 5 HOH B 1 601 47 HOH HOH . O 5 HOH B 2 602 1 HOH HOH . O 5 HOH B 3 603 123 HOH HOH . O 5 HOH B 4 604 24 HOH HOH . O 5 HOH B 5 605 29 HOH HOH . O 5 HOH B 6 606 13 HOH HOH . O 5 HOH B 7 607 5 HOH HOH . O 5 HOH B 8 608 67 HOH HOH . O 5 HOH B 9 609 4 HOH HOH . O 5 HOH B 10 610 117 HOH HOH . O 5 HOH B 11 611 60 HOH HOH . O 5 HOH B 12 612 106 HOH HOH . O 5 HOH B 13 613 48 HOH HOH . O 5 HOH B 14 614 9 HOH HOH . O 5 HOH B 15 615 26 HOH HOH . O 5 HOH B 16 616 119 HOH HOH . O 5 HOH B 17 617 2 HOH HOH . O 5 HOH B 18 618 112 HOH HOH . O 5 HOH B 19 619 25 HOH HOH . O 5 HOH B 20 620 114 HOH HOH . O 5 HOH B 21 621 18 HOH HOH . O 5 HOH B 22 622 21 HOH HOH . O 5 HOH B 23 623 10 HOH HOH . O 5 HOH B 24 624 7 HOH HOH . O 5 HOH B 25 625 27 HOH HOH . O 5 HOH B 26 626 33 HOH HOH . O 5 HOH B 27 627 30 HOH HOH . O 5 HOH B 28 628 64 HOH HOH . O 5 HOH B 29 629 96 HOH HOH . O 5 HOH B 30 630 62 HOH HOH . O 5 HOH B 31 631 52 HOH HOH . O 5 HOH B 32 632 50 HOH HOH . O 5 HOH B 33 633 116 HOH HOH . O 5 HOH B 34 634 72 HOH HOH . O 5 HOH B 35 635 120 HOH HOH . O 5 HOH B 36 636 88 HOH HOH . O 5 HOH B 37 637 86 HOH HOH . O 5 HOH B 38 638 70 HOH HOH . O 5 HOH B 39 639 51 HOH HOH . O 5 HOH B 40 640 108 HOH HOH . O 5 HOH B 41 641 110 HOH HOH . O 5 HOH B 42 642 65 HOH HOH . O 5 HOH B 43 643 90 HOH HOH . O 5 HOH B 44 644 102 HOH HOH . O 5 HOH B 45 645 100 HOH HOH . O 5 HOH B 46 646 84 HOH HOH . O 5 HOH B 47 647 85 HOH HOH . O 5 HOH B 48 648 118 HOH HOH . O 5 HOH B 49 649 113 HOH HOH . O 5 HOH B 50 650 111 HOH HOH . O 5 HOH B 51 651 49 HOH HOH . O 5 HOH B 52 652 92 HOH HOH . O 5 HOH B 53 653 76 HOH HOH . O 5 HOH B 54 654 124 HOH HOH . O 5 HOH B 55 655 99 HOH HOH . O 5 HOH B 56 656 3 HOH HOH . O 5 HOH B 57 657 83 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 N N SAH . . . J 3 -1.713 -46.79 -24.514 1 45.03 ? N SAH 503 B 1 HETATM 2 C CA SAH . . . J 3 -2.376 -45.705 -23.851 1 43.89 ? CA SAH 503 B 1 HETATM 3 C CB SAH . . . J 3 -3.267 -44.946 -24.798 1 44.39 ? CB SAH 503 B 1 HETATM 4 C CG SAH . . . J 3 -3.279 -43.614 -25.566 1 40.87 ? CG SAH 503 B 1 HETATM 5 S SD SAH . . . J 3 -2.639 -42.186 -24.678 1 52.01 ? SD SAH 503 B 1 HETATM 6 C C SAH . . . J 3 -3.335 -46.27 -22.767 1 45.64 ? C SAH 503 B 1 HETATM 7 O O SAH . . . J 3 -2.989 -47.144 -21.992 1 48.04 ? O SAH 503 B 1 HETATM 8 O OXT SAH . . . J 3 -4.432 -46.023 -22.51 1 44.68 ? OXT SAH 503 B 1 HETATM 9 C C5' SAH . . . J 3 -0.889 -42.341 -25.12 1 42.52 ? C5' SAH 503 B 1 HETATM 10 C C4' SAH . . . J 3 0.117 -43.011 -24.26 1 47.38 ? C4' SAH 503 B 1 HETATM 11 O O4' SAH . . . J 3 0.519 -44.285 -24.772 1 42.69 ? O4' SAH 503 B 1 HETATM 12 C C3' SAH . . . J 3 1.344 -42.206 -24.357 1 50.09 ? C3' SAH 503 B 1 HETATM 13 O O3' SAH . . . J 3 1.19 -41.102 -23.516 1 54.74 ? O3' SAH 503 B 1 HETATM 14 C C2' SAH . . . J 3 2.439 -43.221 -24.084 1 50.17 ? C2' SAH 503 B 1 HETATM 15 O O2' SAH . . . J 3 2.467 -43.576 -22.771 1 52.63 ? O2' SAH 503 B 1 HETATM 16 C C1' SAH . . . J 3 1.9 -44.354 -24.914 1 43.3 ? C1' SAH 503 B 1 HETATM 17 N N9 SAH . . . J 3 2.221 -44.36 -26.329 1 45.03 ? N9 SAH 503 B 1 HETATM 18 C C8 SAH . . . J 3 1.459 -43.875 -27.345 1 42.37 ? C8 SAH 503 B 1 HETATM 19 N N7 SAH . . . J 3 1.97 -44.084 -28.511 1 40.17 ? N7 SAH 503 B 1 HETATM 20 C C5 SAH . . . J 3 3.135 -44.758 -28.262 1 43.61 ? C5 SAH 503 B 1 HETATM 21 C C6 SAH . . . J 3 4.146 -45.265 -29.088 1 44.62 ? C6 SAH 503 B 1 HETATM 22 N N6 SAH . . . J 3 4.149 -45.178 -30.399 1 43.8 ? N6 SAH 503 B 1 HETATM 23 N N1 SAH . . . J 3 5.189 -45.878 -28.511 1 44.49 ? N1 SAH 503 B 1 HETATM 24 C C2 SAH . . . J 3 5.204 -45.961 -27.19 1 49.18 ? C2 SAH 503 B 1 HETATM 25 N N3 SAH . . . J 3 4.309 -45.545 -26.317 1 46.63 ? N3 SAH 503 B 1 HETATM 26 C C4 SAH . . . J 3 3.299 -44.934 -26.92 1 44.91 ? C4 SAH 503 B 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 56 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 26 #