data_7JIB # _model_server_result.job_id PpjRh6uvJzo_jQiv8z2jxg _model_server_result.datetime_utc '2024-11-01 05:34:29' _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 7jib # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":7104}' # _entry.id 7JIB # _exptl.entry_id 7JIB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 120 _cell.entry_id 7JIB _cell.length_a 170.83 _cell.length_b 170.83 _cell.length_c 52.738 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JIB _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,M _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 5 _struct_asym.id F _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 B SG CYS 77 B CYS 74 1_555 J ZN ZN . B ZN 4401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc2 B SG CYS 80 B CYS 77 1_555 J ZN ZN . B ZN 4401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc3 B NE2 HIS 86 B HIS 83 1_555 J ZN ZN . B ZN 4401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc4 B SG CYS 93 B CYS 90 1_555 J ZN ZN . B ZN 4401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc5 B SG CYS 120 B CYS 117 1_555 K ZN ZN . B ZN 4402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc6 B SG CYS 123 B CYS 120 1_555 K ZN ZN . B ZN 4402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc7 B SG CYS 131 B CYS 128 1_555 K ZN ZN . B ZN 4402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc8 B SG CYS 133 B CYS 130 1_555 K ZN ZN . B ZN 4402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 417 n n N HN1 SAH sing 418 n n N HN2 SAH sing 419 n n CA CB SAH sing 420 n n CA C SAH sing 421 n n CA HA SAH sing 422 n n CB CG SAH sing 423 n n CB HB1 SAH sing 424 n n CB HB2 SAH sing 425 n n CG SD SAH sing 426 n n CG HG1 SAH sing 427 n n CG HG2 SAH sing 428 n n SD C5' SAH sing 429 n n C O SAH doub 430 n n C OXT SAH sing 431 n n OXT HXT SAH sing 432 n n C5' C4' SAH sing 433 n n C5' "H5'1" SAH sing 434 n n C5' "H5'2" SAH sing 435 n n C4' O4' SAH sing 436 n n C4' C3' SAH sing 437 n n C4' H4' SAH sing 438 n n O4' C1' SAH sing 439 n n C3' O3' SAH sing 440 n n C3' C2' SAH sing 441 n n C3' H3' SAH sing 442 n n O3' HO3' SAH sing 443 n n C2' O2' SAH sing 444 n n C2' C1' SAH sing 445 n n C2' H2' SAH sing 446 n n O2' HO2' SAH sing 447 n n C1' N9 SAH sing 448 n n C1' H1' SAH sing 449 n n N9 C8 SAH sing 450 n y N9 C4 SAH sing 451 n y C8 N7 SAH doub 452 n y C8 H8 SAH sing 453 n n N7 C5 SAH sing 454 n y C5 C6 SAH sing 455 n y C5 C4 SAH doub 456 n y C6 N6 SAH sing 457 n n C6 N1 SAH doub 458 n y N6 HN61 SAH sing 459 n n N6 HN62 SAH sing 460 n n N1 C2 SAH sing 461 n y C2 N3 SAH doub 462 n y C2 H2 SAH sing 463 n n N3 C4 SAH sing 464 n y # _atom_sites.entry_id 7JIB _atom_sites.fract_transf_matrix[1][1] 0.005854 _atom_sites.fract_transf_matrix[1][2] 0.00338 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006759 _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] 0.018962 _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 3 CL A 1 7101 3 CL CL . D 3 CL A 1 7102 4 CL CL . E 4 SAM A 1 7103 5 SAM SAM . F 5 SAH A 1 7104 6 SAH SAH . G 6 GTA A 1 7105 7 GTA GTA . H 7 V9G A 1 7106 8 V9G V9G . I 8 MGP A 1 7107 9 MGP MGP . J 9 ZN B 1 4401 1 ZN ZN . K 9 ZN B 1 4402 2 ZN ZN . L 10 HOH A 1 7201 87 HOH HOH . L 10 HOH A 2 7202 71 HOH HOH . L 10 HOH A 3 7203 90 HOH HOH . L 10 HOH A 4 7204 104 HOH HOH . L 10 HOH A 5 7205 114 HOH HOH . L 10 HOH A 6 7206 66 HOH HOH . L 10 HOH A 7 7207 92 HOH HOH . L 10 HOH A 8 7208 48 HOH HOH . L 10 HOH A 9 7209 63 HOH HOH . L 10 HOH A 10 7210 100 HOH HOH . L 10 HOH A 11 7211 61 HOH HOH . L 10 HOH A 12 7212 112 HOH HOH . L 10 HOH A 13 7213 60 HOH HOH . L 10 HOH A 14 7214 46 HOH HOH . L 10 HOH A 15 7215 146 HOH HOH . L 10 HOH A 16 7216 29 HOH HOH . L 10 HOH A 17 7217 78 HOH HOH . L 10 HOH A 18 7218 32 HOH HOH . L 10 HOH A 19 7219 110 HOH HOH . L 10 HOH A 20 7220 83 HOH HOH . L 10 HOH A 21 7221 89 HOH HOH . L 10 HOH A 22 7222 69 HOH HOH . L 10 HOH A 23 7223 93 HOH HOH . L 10 HOH A 24 7224 82 HOH HOH . L 10 HOH A 25 7225 22 HOH HOH . L 10 HOH A 26 7226 127 HOH HOH . L 10 HOH A 27 7227 38 HOH HOH . L 10 HOH A 28 7228 11 HOH HOH . L 10 HOH A 29 7229 126 HOH HOH . L 10 HOH A 30 7230 27 HOH HOH . L 10 HOH A 31 7231 43 HOH HOH . L 10 HOH A 32 7232 141 HOH HOH . L 10 HOH A 33 7233 58 HOH HOH . L 10 HOH A 34 7234 24 HOH HOH . L 10 HOH A 35 7235 39 HOH HOH . L 10 HOH A 36 7236 85 HOH HOH . L 10 HOH A 37 7237 10 HOH HOH . L 10 HOH A 38 7238 23 HOH HOH . L 10 HOH A 39 7239 103 HOH HOH . L 10 HOH A 40 7240 145 HOH HOH . L 10 HOH A 41 7241 18 HOH HOH . L 10 HOH A 42 7242 62 HOH HOH . L 10 HOH A 43 7243 99 HOH HOH . L 10 HOH A 44 7244 119 HOH HOH . L 10 HOH A 45 7245 19 HOH HOH . L 10 HOH A 46 7246 31 HOH HOH . L 10 HOH A 47 7247 36 HOH HOH . L 10 HOH A 48 7248 55 HOH HOH . L 10 HOH A 49 7249 151 HOH HOH . L 10 HOH A 50 7250 13 HOH HOH . L 10 HOH A 51 7251 121 HOH HOH . L 10 HOH A 52 7252 117 HOH HOH . L 10 HOH A 53 7253 130 HOH HOH . L 10 HOH A 54 7254 139 HOH HOH . L 10 HOH A 55 7255 35 HOH HOH . L 10 HOH A 56 7256 21 HOH HOH . L 10 HOH A 57 7257 96 HOH HOH . L 10 HOH A 58 7258 25 HOH HOH . L 10 HOH A 59 7259 107 HOH HOH . L 10 HOH A 60 7260 45 HOH HOH . L 10 HOH A 61 7261 14 HOH HOH . L 10 HOH A 62 7262 95 HOH HOH . L 10 HOH A 63 7263 150 HOH HOH . L 10 HOH A 64 7264 101 HOH HOH . L 10 HOH A 65 7265 50 HOH HOH . L 10 HOH A 66 7266 79 HOH HOH . L 10 HOH A 67 7267 77 HOH HOH . L 10 HOH A 68 7268 49 HOH HOH . L 10 HOH A 69 7269 42 HOH HOH . L 10 HOH A 70 7270 132 HOH HOH . L 10 HOH A 71 7271 111 HOH HOH . L 10 HOH A 72 7272 15 HOH HOH . L 10 HOH A 73 7273 74 HOH HOH . L 10 HOH A 74 7274 72 HOH HOH . L 10 HOH A 75 7275 17 HOH HOH . L 10 HOH A 76 7276 138 HOH HOH . L 10 HOH A 77 7277 41 HOH HOH . L 10 HOH A 78 7278 149 HOH HOH . L 10 HOH A 79 7279 97 HOH HOH . L 10 HOH A 80 7280 54 HOH HOH . L 10 HOH A 81 7281 109 HOH HOH . L 10 HOH A 82 7282 12 HOH HOH . L 10 HOH A 83 7283 140 HOH HOH . L 10 HOH A 84 7284 84 HOH HOH . L 10 HOH A 85 7285 34 HOH HOH . L 10 HOH A 86 7286 133 HOH HOH . L 10 HOH A 87 7287 52 HOH HOH . L 10 HOH A 88 7288 88 HOH HOH . L 10 HOH A 89 7289 116 HOH HOH . L 10 HOH A 90 7290 86 HOH HOH . L 10 HOH A 91 7291 75 HOH HOH . L 10 HOH A 92 7292 57 HOH HOH . L 10 HOH A 93 7293 125 HOH HOH . L 10 HOH A 94 7294 128 HOH HOH . L 10 HOH A 95 7295 68 HOH HOH . L 10 HOH A 96 7296 53 HOH HOH . L 10 HOH A 97 7297 28 HOH HOH . L 10 HOH A 98 7298 102 HOH HOH . L 10 HOH A 99 7299 120 HOH HOH . L 10 HOH A 100 7300 137 HOH HOH . L 10 HOH A 101 7301 143 HOH HOH . L 10 HOH A 102 7302 98 HOH HOH . L 10 HOH A 103 7303 16 HOH HOH . L 10 HOH A 104 7304 142 HOH HOH . L 10 HOH A 105 7305 64 HOH HOH . L 10 HOH A 106 7306 70 HOH HOH . L 10 HOH A 107 7307 80 HOH HOH . L 10 HOH A 108 7308 20 HOH HOH . L 10 HOH A 109 7309 108 HOH HOH . L 10 HOH A 110 7310 105 HOH HOH . L 10 HOH A 111 7311 94 HOH HOH . L 10 HOH A 112 7312 122 HOH HOH . L 10 HOH A 113 7313 136 HOH HOH . L 10 HOH A 114 7314 106 HOH HOH . L 10 HOH A 115 7315 135 HOH HOH . L 10 HOH A 116 7316 118 HOH HOH . L 10 HOH A 117 7317 123 HOH HOH . L 10 HOH A 118 7318 56 HOH HOH . L 10 HOH A 119 7319 129 HOH HOH . L 10 HOH A 120 7320 51 HOH HOH . L 10 HOH A 121 7321 134 HOH HOH . L 10 HOH A 122 7322 131 HOH HOH . L 10 HOH A 123 7323 81 HOH HOH . L 10 HOH A 124 7324 124 HOH HOH . M 10 HOH B 1 4501 33 HOH HOH . M 10 HOH B 2 4502 91 HOH HOH . M 10 HOH B 3 4503 47 HOH HOH . M 10 HOH B 4 4504 30 HOH HOH . M 10 HOH B 5 4505 73 HOH HOH . M 10 HOH B 6 4506 40 HOH HOH . M 10 HOH B 7 4507 147 HOH HOH . M 10 HOH B 8 4508 37 HOH HOH . M 10 HOH B 9 4509 59 HOH HOH . M 10 HOH B 10 4510 67 HOH HOH . M 10 HOH B 11 4511 65 HOH HOH . M 10 HOH B 12 4512 148 HOH HOH . M 10 HOH B 13 4513 115 HOH HOH . M 10 HOH B 14 4514 44 HOH HOH . M 10 HOH B 15 4515 26 HOH HOH . M 10 HOH B 16 4516 144 HOH HOH . M 10 HOH B 17 4517 76 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 . B . F 5 -87.572 19.924 -2.312 0.3 38.58 ? N SAH 7104 A 1 HETATM 2 C CA SAH . B . F 5 -88.844 19.329 -1.813 0.3 38.68 ? CA SAH 7104 A 1 HETATM 3 C CB SAH . B . F 5 -88.934 19.421 -0.286 0.3 38.41 ? CB SAH 7104 A 1 HETATM 4 C CG SAH . B . F 5 -87.851 18.633 0.431 0.3 38.76 ? CG SAH 7104 A 1 HETATM 5 S SD SAH . B . F 5 -88.101 18.508 2.218 0.3 39.02 ? SD SAH 7104 A 1 HETATM 6 C C SAH . B . F 5 -90.028 20.071 -2.442 0.3 38.47 ? C SAH 7104 A 1 HETATM 7 O O SAH . B . F 5 -91.126 20.1 -1.884 0.3 39.52 ? O SAH 7104 A 1 HETATM 8 O OXT SAH . B . F 5 -89.905 20.654 -3.52 0.3 37.84 ? OXT SAH 7104 A 1 HETATM 9 C C5' SAH . B . F 5 -86.609 17.623 2.737 0.3 38.59 ? C5' SAH 7104 A 1 HETATM 10 C C4' SAH . B . F 5 -86.487 16.27 2.082 0.3 38.52 ? C4' SAH 7104 A 1 HETATM 11 O O4' SAH . B . F 5 -85.177 15.716 2.332 0.3 38.87 ? O4' SAH 7104 A 1 HETATM 12 C C3' SAH . B . F 5 -87.487 15.227 2.594 0.3 38.44 ? C3' SAH 7104 A 1 HETATM 13 O O3' SAH . B . F 5 -88.403 14.871 1.567 0.3 37.81 ? O3' SAH 7104 A 1 HETATM 14 C C2' SAH . B . F 5 -86.617 14.03 3.005 0.3 38.42 ? C2' SAH 7104 A 1 HETATM 15 O O2' SAH . B . F 5 -87.162 12.798 2.587 0.3 38.65 ? O2' SAH 7104 A 1 HETATM 16 C C1' SAH . B . F 5 -85.308 14.318 2.281 0.3 38.91 ? C1' SAH 7104 A 1 HETATM 17 N N9 SAH . B . F 5 -84.141 13.693 2.892 0.3 39.82 ? N9 SAH 7104 A 1 HETATM 18 C C8 SAH . B . F 5 -83.631 13.935 4.143 0.3 40.37 ? C8 SAH 7104 A 1 HETATM 19 N N7 SAH . B . F 5 -82.574 13.214 4.422 0.3 39.99 ? N7 SAH 7104 A 1 HETATM 20 C C5 SAH . B . F 5 -82.374 12.442 3.287 0.3 39.92 ? C5 SAH 7104 A 1 HETATM 21 C C6 SAH . B . F 5 -81.409 11.47 2.96 0.3 40.01 ? C6 SAH 7104 A 1 HETATM 22 N N6 SAH . B . F 5 -80.429 11.095 3.778 0.3 39.48 ? N6 SAH 7104 A 1 HETATM 23 N N1 SAH . B . F 5 -81.497 10.889 1.74 0.3 39.86 ? N1 SAH 7104 A 1 HETATM 24 C C2 SAH . B . F 5 -82.485 11.27 0.922 0.3 39.8 ? C2 SAH 7104 A 1 HETATM 25 N N3 SAH . B . F 5 -83.445 12.168 1.12 0.3 39.77 ? N3 SAH 7104 A 1 HETATM 26 C C4 SAH . B . F 5 -83.335 12.727 2.336 0.3 39.82 ? C4 SAH 7104 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 26 #