data_6XKM # _model_server_result.job_id Kz5faaA9isf665Q-9QxHfQ _model_server_result.datetime_utc '2025-03-04 16:14:18' _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 6xkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":7102}' # _entry.id 6XKM # _exptl.entry_id 6XKM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 6XKM _cell.length_a 170.41 _cell.length_b 170.41 _cell.length_c 52.631 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XKM _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 _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 4 _struct_asym.id D _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 E ZN ZN . B ZN 4401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 B SG CYS 80 B CYS 77 1_555 E ZN ZN . B ZN 4401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 B NE2 HIS 86 B HIS 83 1_555 E ZN ZN . B ZN 4401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc4 B SG CYS 93 B CYS 90 1_555 E ZN ZN . B ZN 4401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc5 B SG CYS 120 B CYS 117 1_555 F ZN ZN . B ZN 4402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc6 B SG CYS 123 B CYS 120 1_555 F ZN ZN . B ZN 4402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc7 B SG CYS 131 B CYS 128 1_555 F ZN ZN . B ZN 4402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc8 B SG CYS 133 B CYS 130 1_555 F ZN ZN . B ZN 4402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 SAM sing 277 n n N HN1 SAM sing 278 n n N HN2 SAM sing 279 n n CA C SAM sing 280 n n CA CB SAM sing 281 n n CA HA SAM sing 282 n n C O SAM doub 283 n n C OXT SAM sing 284 n n CB CG SAM sing 285 n n CB HB1 SAM sing 286 n n CB HB2 SAM sing 287 n n CG SD SAM sing 288 n n CG HG1 SAM sing 289 n n CG HG2 SAM sing 290 n n SD CE SAM sing 291 n n SD C5' SAM sing 292 n n CE HE1 SAM sing 293 n n CE HE2 SAM sing 294 n n CE HE3 SAM sing 295 n n C5' C4' SAM sing 296 n n C5' "H5'1" SAM sing 297 n n C5' "H5'2" SAM sing 298 n n C4' O4' SAM sing 299 n n C4' C3' SAM sing 300 n n C4' H4' SAM sing 301 n n O4' C1' SAM sing 302 n n C3' O3' SAM sing 303 n n C3' C2' SAM sing 304 n n C3' H3' SAM sing 305 n n O3' HO3' SAM sing 306 n n C2' O2' SAM sing 307 n n C2' C1' SAM sing 308 n n C2' H2' SAM sing 309 n n O2' HO2' SAM sing 310 n n C1' N9 SAM sing 311 n n C1' H1' SAM sing 312 n n N9 C8 SAM sing 313 n y N9 C4 SAM sing 314 n y C8 N7 SAM doub 315 n y C8 H8 SAM sing 316 n n N7 C5 SAM sing 317 n y C5 C6 SAM sing 318 n y C5 C4 SAM doub 319 n y C6 N6 SAM sing 320 n n C6 N1 SAM doub 321 n y N6 HN61 SAM sing 322 n n N6 HN62 SAM sing 323 n n N1 C2 SAM sing 324 n y C2 N3 SAM doub 325 n y C2 H2 SAM sing 326 n n N3 C4 SAM sing 327 n y # _atom_sites.entry_id 6XKM _atom_sites.fract_transf_matrix[1][1] 0.005868 _atom_sites.fract_transf_matrix[1][2] 0.003388 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006776 _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] 0.019 _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 4 SAM A 1 7102 4 SAM SAM . E 5 ZN B 1 4401 1 ZN ZN . F 5 ZN B 1 4402 2 ZN ZN . G 6 HOH A 1 7201 71 HOH HOH . G 6 HOH A 2 7202 19 HOH HOH . G 6 HOH A 3 7203 23 HOH HOH . G 6 HOH A 4 7204 34 HOH HOH . G 6 HOH A 5 7205 52 HOH HOH . G 6 HOH A 6 7206 16 HOH HOH . G 6 HOH A 7 7207 58 HOH HOH . G 6 HOH A 8 7208 27 HOH HOH . G 6 HOH A 9 7209 6 HOH HOH . G 6 HOH A 10 7210 63 HOH HOH . G 6 HOH A 11 7211 38 HOH HOH . G 6 HOH A 12 7212 82 HOH HOH . G 6 HOH A 13 7213 122 HOH HOH . G 6 HOH A 14 7214 57 HOH HOH . G 6 HOH A 15 7215 17 HOH HOH . G 6 HOH A 16 7216 69 HOH HOH . G 6 HOH A 17 7217 75 HOH HOH . G 6 HOH A 18 7218 49 HOH HOH . G 6 HOH A 19 7219 119 HOH HOH . G 6 HOH A 20 7220 129 HOH HOH . G 6 HOH A 21 7221 12 HOH HOH . G 6 HOH A 22 7222 21 HOH HOH . G 6 HOH A 23 7223 83 HOH HOH . G 6 HOH A 24 7224 84 HOH HOH . G 6 HOH A 25 7225 11 HOH HOH . G 6 HOH A 26 7226 90 HOH HOH . G 6 HOH A 27 7227 10 HOH HOH . G 6 HOH A 28 7228 20 HOH HOH . G 6 HOH A 29 7229 25 HOH HOH . G 6 HOH A 30 7230 85 HOH HOH . G 6 HOH A 31 7231 78 HOH HOH . G 6 HOH A 32 7232 117 HOH HOH . G 6 HOH A 33 7233 98 HOH HOH . G 6 HOH A 34 7234 53 HOH HOH . G 6 HOH A 35 7235 111 HOH HOH . G 6 HOH A 36 7236 8 HOH HOH . G 6 HOH A 37 7237 15 HOH HOH . G 6 HOH A 38 7238 55 HOH HOH . G 6 HOH A 39 7239 9 HOH HOH . G 6 HOH A 40 7240 107 HOH HOH . G 6 HOH A 41 7241 120 HOH HOH . G 6 HOH A 42 7242 62 HOH HOH . G 6 HOH A 43 7243 79 HOH HOH . G 6 HOH A 44 7244 7 HOH HOH . G 6 HOH A 45 7245 40 HOH HOH . G 6 HOH A 46 7246 5 HOH HOH . G 6 HOH A 47 7247 44 HOH HOH . G 6 HOH A 48 7248 92 HOH HOH . G 6 HOH A 49 7249 61 HOH HOH . G 6 HOH A 50 7250 64 HOH HOH . G 6 HOH A 51 7251 127 HOH HOH . G 6 HOH A 52 7252 45 HOH HOH . G 6 HOH A 53 7253 48 HOH HOH . G 6 HOH A 54 7254 29 HOH HOH . G 6 HOH A 55 7255 26 HOH HOH . G 6 HOH A 56 7256 35 HOH HOH . G 6 HOH A 57 7257 80 HOH HOH . G 6 HOH A 58 7258 94 HOH HOH . G 6 HOH A 59 7259 99 HOH HOH . G 6 HOH A 60 7260 60 HOH HOH . G 6 HOH A 61 7261 125 HOH HOH . G 6 HOH A 62 7262 102 HOH HOH . G 6 HOH A 63 7263 66 HOH HOH . G 6 HOH A 64 7264 124 HOH HOH . G 6 HOH A 65 7265 22 HOH HOH . G 6 HOH A 66 7266 28 HOH HOH . G 6 HOH A 67 7267 51 HOH HOH . G 6 HOH A 68 7268 115 HOH HOH . G 6 HOH A 69 7269 131 HOH HOH . G 6 HOH A 70 7270 97 HOH HOH . G 6 HOH A 71 7271 123 HOH HOH . G 6 HOH A 72 7272 56 HOH HOH . G 6 HOH A 73 7273 68 HOH HOH . G 6 HOH A 74 7274 31 HOH HOH . G 6 HOH A 75 7275 93 HOH HOH . G 6 HOH A 76 7276 126 HOH HOH . G 6 HOH A 77 7277 100 HOH HOH . G 6 HOH A 78 7278 118 HOH HOH . G 6 HOH A 79 7279 74 HOH HOH . G 6 HOH A 80 7280 112 HOH HOH . G 6 HOH A 81 7281 73 HOH HOH . G 6 HOH A 82 7282 30 HOH HOH . G 6 HOH A 83 7283 106 HOH HOH . G 6 HOH A 84 7284 54 HOH HOH . G 6 HOH A 85 7285 47 HOH HOH . G 6 HOH A 86 7286 46 HOH HOH . G 6 HOH A 87 7287 76 HOH HOH . G 6 HOH A 88 7288 14 HOH HOH . G 6 HOH A 89 7289 70 HOH HOH . G 6 HOH A 90 7290 114 HOH HOH . G 6 HOH A 91 7291 89 HOH HOH . G 6 HOH A 92 7292 116 HOH HOH . G 6 HOH A 93 7293 65 HOH HOH . G 6 HOH A 94 7294 103 HOH HOH . G 6 HOH A 95 7295 39 HOH HOH . G 6 HOH A 96 7296 50 HOH HOH . G 6 HOH A 97 7297 108 HOH HOH . G 6 HOH A 98 7298 91 HOH HOH . G 6 HOH A 99 7299 128 HOH HOH . G 6 HOH A 100 7300 113 HOH HOH . G 6 HOH A 101 7301 104 HOH HOH . G 6 HOH A 102 7302 105 HOH HOH . G 6 HOH A 103 7303 88 HOH HOH . G 6 HOH A 104 7304 109 HOH HOH . G 6 HOH A 105 7305 81 HOH HOH . G 6 HOH A 106 7306 87 HOH HOH . G 6 HOH A 107 7307 121 HOH HOH . G 6 HOH A 108 7308 95 HOH HOH . G 6 HOH A 109 7309 132 HOH HOH . H 6 HOH B 1 4501 37 HOH HOH . H 6 HOH B 2 4502 41 HOH HOH . H 6 HOH B 3 4503 42 HOH HOH . H 6 HOH B 4 4504 96 HOH HOH . H 6 HOH B 5 4505 32 HOH HOH . H 6 HOH B 6 4506 130 HOH HOH . H 6 HOH B 7 4507 24 HOH HOH . H 6 HOH B 8 4508 18 HOH HOH . H 6 HOH B 9 4509 59 HOH HOH . H 6 HOH B 10 4510 67 HOH HOH . H 6 HOH B 11 4511 33 HOH HOH . H 6 HOH B 12 4512 13 HOH HOH . H 6 HOH B 13 4513 36 HOH HOH . H 6 HOH B 14 4514 72 HOH HOH . H 6 HOH B 15 4515 43 HOH HOH . H 6 HOH B 16 4516 77 HOH HOH . H 6 HOH B 17 4517 101 HOH HOH . H 6 HOH B 18 4518 110 HOH HOH . H 6 HOH B 19 4519 86 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 SAM . . . D 4 -60.749 65.574 1.893 1 24.1 ? N SAM 7102 A 1 HETATM 2 C CA SAM . . . D 4 -60.802 67.001 1.463 1 24.01 ? CA SAM 7102 A 1 HETATM 3 C C SAM . . . D 4 -62.057 67.66 2.051 1 24.12 ? C SAM 7102 A 1 HETATM 4 O O SAM . . . D 4 -62.628 68.593 1.479 1 25.2 ? O SAM 7102 A 1 HETATM 5 O OXT SAM . . . D 4 -62.517 67.268 3.128 1 22.51 ? OXT SAM 7102 A 1 HETATM 6 C CB SAM . . . D 4 -60.815 67.116 -0.066 1 23.52 ? CB SAM 7102 A 1 HETATM 7 C CG SAM . . . D 4 -59.556 66.58 -0.717 1 24.2 ? CG SAM 7102 A 1 HETATM 8 S SD SAM . . . D 4 -59.522 66.944 -2.487 1 25.32 ? SD SAM 7102 A 1 HETATM 9 C CE SAM . . . D 4 -60.762 65.82 -3.111 1 26.73 ? CE SAM 7102 A 1 HETATM 10 C C5' SAM . . . D 4 -57.996 66.076 -2.929 1 24.14 ? C5' SAM 7102 A 1 HETATM 11 C C4' SAM . . . D 4 -56.76 66.694 -2.306 1 23.54 ? C4' SAM 7102 A 1 HETATM 12 O O4' SAM . . . D 4 -55.62 65.85 -2.574 1 23.3 ? O4' SAM 7102 A 1 HETATM 13 C C3' SAM . . . D 4 -56.379 68.087 -2.826 1 23.22 ? C3' SAM 7102 A 1 HETATM 14 O O3' SAM . . . D 4 -56.508 69.051 -1.787 1 22.88 ? O3' SAM 7102 A 1 HETATM 15 C C2' SAM . . . D 4 -54.923 67.934 -3.297 1 23.52 ? C2' SAM 7102 A 1 HETATM 16 O O2' SAM . . . D 4 -54.101 69.031 -2.963 1 22.7 ? O2' SAM 7102 A 1 HETATM 17 C C1' SAM . . . D 4 -54.487 66.679 -2.553 1 24.72 ? C1' SAM 7102 A 1 HETATM 18 N N9 SAM . . . D 4 -53.368 65.976 -3.164 1 26.94 ? N9 SAM 7102 A 1 HETATM 19 C C8 SAM . . . D 4 -53.29 65.509 -4.452 1 29.42 ? C8 SAM 7102 A 1 HETATM 20 N N7 SAM . . . D 4 -52.153 64.919 -4.723 1 30.84 ? N7 SAM 7102 A 1 HETATM 21 C C5 SAM . . . D 4 -51.433 64.997 -3.539 1 29.98 ? C5 SAM 7102 A 1 HETATM 22 C C6 SAM . . . D 4 -50.144 64.549 -3.18 1 29.35 ? C6 SAM 7102 A 1 HETATM 23 N N6 SAM . . . D 4 -49.32 63.915 -4.011 1 28.15 ? N6 SAM 7102 A 1 HETATM 24 N N1 SAM . . . D 4 -49.733 64.788 -1.912 1 28.09 ? N1 SAM 7102 A 1 HETATM 25 C C2 SAM . . . D 4 -50.565 65.432 -1.082 1 27.81 ? C2 SAM 7102 A 1 HETATM 26 N N3 SAM . . . D 4 -51.79 65.898 -1.308 1 27.11 ? N3 SAM 7102 A 1 HETATM 27 C C4 SAM . . . D 4 -52.174 65.647 -2.569 1 28.09 ? C4 SAM 7102 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #