data_2NYU
#
_model_server_result.job_id            CaOsLuGL-czu6VD7jiEFGQ 
_model_server_result.datetime_utc      '2024-11-26 10:24:02' 
_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          2nyu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    2NYU 
#
_exptl.entry_id    2NYU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              398.437 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYLMETHIONINE 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            2NYU 
_cell.length_a            102.022 
_cell.length_b            102.022 
_cell.length_c            37.068 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2NYU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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
? 2 C N N 
? 2 D N N 
#
_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                     2NYU 
_atom_sites.fract_transf_matrix[1][1]    0.009802 
_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]    0.009802 
_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]    0.026977 
_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 SAM A 1 201 5000 SAM SAM . 
D 2 SAM B 1 201 5001 SAM SAM . 
E 3 HOH A 1 202 1 HOH HOH . 
E 3 HOH A 2 203 2 HOH HOH . 
E 3 HOH A 3 204 3 HOH HOH . 
E 3 HOH A 4 205 4 HOH HOH . 
E 3 HOH A 5 206 6 HOH HOH . 
E 3 HOH A 6 207 9 HOH HOH . 
E 3 HOH A 7 208 12 HOH HOH . 
E 3 HOH A 8 209 13 HOH HOH . 
E 3 HOH A 9 210 14 HOH HOH . 
E 3 HOH A 10 211 15 HOH HOH . 
E 3 HOH A 11 212 17 HOH HOH . 
E 3 HOH A 12 213 18 HOH HOH . 
E 3 HOH A 13 214 19 HOH HOH . 
E 3 HOH A 14 215 20 HOH HOH . 
E 3 HOH A 15 216 21 HOH HOH . 
E 3 HOH A 16 217 24 HOH HOH . 
E 3 HOH A 17 218 25 HOH HOH . 
E 3 HOH A 18 219 26 HOH HOH . 
E 3 HOH A 19 220 31 HOH HOH . 
E 3 HOH A 20 221 36 HOH HOH . 
E 3 HOH A 21 222 38 HOH HOH . 
E 3 HOH A 22 223 39 HOH HOH . 
E 3 HOH A 23 224 42 HOH HOH . 
E 3 HOH A 24 225 43 HOH HOH . 
E 3 HOH A 25 226 44 HOH HOH . 
E 3 HOH A 26 227 45 HOH HOH . 
E 3 HOH A 27 228 47 HOH HOH . 
E 3 HOH A 28 229 48 HOH HOH . 
E 3 HOH A 29 230 49 HOH HOH . 
E 3 HOH A 30 231 50 HOH HOH . 
E 3 HOH A 31 232 53 HOH HOH . 
E 3 HOH A 32 233 54 HOH HOH . 
E 3 HOH A 33 234 55 HOH HOH . 
E 3 HOH A 34 235 57 HOH HOH . 
E 3 HOH A 35 236 58 HOH HOH . 
E 3 HOH A 36 237 61 HOH HOH . 
E 3 HOH A 37 238 64 HOH HOH . 
E 3 HOH A 38 239 65 HOH HOH . 
E 3 HOH A 39 240 67 HOH HOH . 
E 3 HOH A 40 241 68 HOH HOH . 
E 3 HOH A 41 242 69 HOH HOH . 
E 3 HOH A 42 243 70 HOH HOH . 
E 3 HOH A 43 244 71 HOH HOH . 
E 3 HOH A 44 245 72 HOH HOH . 
E 3 HOH A 45 246 75 HOH HOH . 
E 3 HOH A 46 247 76 HOH HOH . 
E 3 HOH A 47 248 77 HOH HOH . 
E 3 HOH A 48 249 78 HOH HOH . 
E 3 HOH A 49 250 79 HOH HOH . 
E 3 HOH A 50 251 82 HOH HOH . 
E 3 HOH A 51 252 83 HOH HOH . 
E 3 HOH A 52 253 84 HOH HOH . 
E 3 HOH A 53 254 85 HOH HOH . 
E 3 HOH A 54 255 86 HOH HOH . 
E 3 HOH A 55 256 87 HOH HOH . 
E 3 HOH A 56 257 88 HOH HOH . 
E 3 HOH A 57 258 94 HOH HOH . 
E 3 HOH A 58 259 97 HOH HOH . 
E 3 HOH A 59 260 102 HOH HOH . 
E 3 HOH A 60 261 103 HOH HOH . 
E 3 HOH A 61 262 104 HOH HOH . 
E 3 HOH A 62 263 106 HOH HOH . 
E 3 HOH A 63 264 108 HOH HOH . 
E 3 HOH A 64 265 110 HOH HOH . 
E 3 HOH A 65 266 111 HOH HOH . 
E 3 HOH A 66 267 113 HOH HOH . 
E 3 HOH A 67 268 114 HOH HOH . 
E 3 HOH A 68 269 115 HOH HOH . 
E 3 HOH A 69 270 117 HOH HOH . 
E 3 HOH A 70 271 118 HOH HOH . 
E 3 HOH A 71 272 119 HOH HOH . 
E 3 HOH A 72 273 121 HOH HOH . 
E 3 HOH A 73 274 122 HOH HOH . 
E 3 HOH A 74 275 128 HOH HOH . 
E 3 HOH A 75 276 129 HOH HOH . 
E 3 HOH A 76 277 131 HOH HOH . 
E 3 HOH A 77 278 132 HOH HOH . 
E 3 HOH A 78 279 134 HOH HOH . 
E 3 HOH A 79 280 136 HOH HOH . 
E 3 HOH A 80 281 140 HOH HOH . 
E 3 HOH A 81 282 141 HOH HOH . 
E 3 HOH A 82 283 143 HOH HOH . 
E 3 HOH A 83 284 145 HOH HOH . 
E 3 HOH A 84 285 147 HOH HOH . 
E 3 HOH A 85 286 148 HOH HOH . 
E 3 HOH A 86 287 150 HOH HOH . 
E 3 HOH A 87 288 151 HOH HOH . 
E 3 HOH A 88 289 152 HOH HOH . 
E 3 HOH A 89 290 153 HOH HOH . 
E 3 HOH A 90 291 158 HOH HOH . 
E 3 HOH A 91 292 162 HOH HOH . 
E 3 HOH A 92 293 163 HOH HOH . 
E 3 HOH A 93 294 169 HOH HOH . 
E 3 HOH A 94 295 170 HOH HOH . 
E 3 HOH A 95 296 171 HOH HOH . 
E 3 HOH A 96 297 172 HOH HOH . 
E 3 HOH A 97 298 173 HOH HOH . 
E 3 HOH A 98 299 174 HOH HOH . 
E 3 HOH A 99 300 176 HOH HOH . 
E 3 HOH A 100 301 181 HOH HOH . 
E 3 HOH A 101 302 183 HOH HOH . 
E 3 HOH A 102 303 184 HOH HOH . 
E 3 HOH A 103 304 186 HOH HOH . 
E 3 HOH A 104 305 187 HOH HOH . 
E 3 HOH A 105 306 189 HOH HOH . 
E 3 HOH A 106 307 192 HOH HOH . 
E 3 HOH A 107 308 193 HOH HOH . 
E 3 HOH A 108 309 194 HOH HOH . 
E 3 HOH A 109 310 196 HOH HOH . 
E 3 HOH A 110 311 199 HOH HOH . 
F 3 HOH B 1 202 5 HOH HOH . 
F 3 HOH B 2 203 7 HOH HOH . 
F 3 HOH B 3 204 8 HOH HOH . 
F 3 HOH B 4 205 10 HOH HOH . 
F 3 HOH B 5 206 11 HOH HOH . 
F 3 HOH B 6 207 16 HOH HOH . 
F 3 HOH B 7 208 22 HOH HOH . 
F 3 HOH B 8 209 23 HOH HOH . 
F 3 HOH B 9 210 27 HOH HOH . 
F 3 HOH B 10 211 28 HOH HOH . 
F 3 HOH B 11 212 29 HOH HOH . 
F 3 HOH B 12 213 30 HOH HOH . 
F 3 HOH B 13 214 32 HOH HOH . 
F 3 HOH B 14 215 33 HOH HOH . 
F 3 HOH B 15 216 34 HOH HOH . 
F 3 HOH B 16 217 35 HOH HOH . 
F 3 HOH B 17 218 37 HOH HOH . 
F 3 HOH B 18 219 40 HOH HOH . 
F 3 HOH B 19 220 41 HOH HOH . 
F 3 HOH B 20 221 46 HOH HOH . 
F 3 HOH B 21 222 51 HOH HOH . 
F 3 HOH B 22 223 52 HOH HOH . 
F 3 HOH B 23 224 56 HOH HOH . 
F 3 HOH B 24 225 59 HOH HOH . 
F 3 HOH B 25 226 60 HOH HOH . 
F 3 HOH B 26 227 62 HOH HOH . 
F 3 HOH B 27 228 63 HOH HOH . 
F 3 HOH B 28 229 66 HOH HOH . 
F 3 HOH B 29 230 73 HOH HOH . 
F 3 HOH B 30 231 74 HOH HOH . 
F 3 HOH B 31 232 80 HOH HOH . 
F 3 HOH B 32 233 81 HOH HOH . 
F 3 HOH B 33 234 89 HOH HOH . 
F 3 HOH B 34 235 90 HOH HOH . 
F 3 HOH B 35 236 91 HOH HOH . 
F 3 HOH B 36 237 92 HOH HOH . 
F 3 HOH B 37 238 93 HOH HOH . 
F 3 HOH B 38 239 95 HOH HOH . 
F 3 HOH B 39 240 96 HOH HOH . 
F 3 HOH B 40 241 98 HOH HOH . 
F 3 HOH B 41 242 99 HOH HOH . 
F 3 HOH B 42 243 100 HOH HOH . 
F 3 HOH B 43 244 101 HOH HOH . 
F 3 HOH B 44 245 105 HOH HOH . 
F 3 HOH B 45 246 107 HOH HOH . 
F 3 HOH B 46 247 109 HOH HOH . 
F 3 HOH B 47 248 112 HOH HOH . 
F 3 HOH B 48 249 116 HOH HOH . 
F 3 HOH B 49 250 120 HOH HOH . 
F 3 HOH B 50 251 123 HOH HOH . 
F 3 HOH B 51 252 124 HOH HOH . 
F 3 HOH B 52 253 125 HOH HOH . 
F 3 HOH B 53 254 126 HOH HOH . 
F 3 HOH B 54 255 127 HOH HOH . 
F 3 HOH B 55 256 130 HOH HOH . 
F 3 HOH B 56 257 133 HOH HOH . 
F 3 HOH B 57 258 135 HOH HOH . 
F 3 HOH B 58 259 137 HOH HOH . 
F 3 HOH B 59 260 138 HOH HOH . 
F 3 HOH B 60 261 139 HOH HOH . 
F 3 HOH B 61 262 142 HOH HOH . 
F 3 HOH B 62 263 144 HOH HOH . 
F 3 HOH B 63 264 146 HOH HOH . 
F 3 HOH B 64 265 149 HOH HOH . 
F 3 HOH B 65 266 154 HOH HOH . 
F 3 HOH B 66 267 155 HOH HOH . 
F 3 HOH B 67 268 156 HOH HOH . 
F 3 HOH B 68 269 157 HOH HOH . 
F 3 HOH B 69 270 159 HOH HOH . 
F 3 HOH B 70 271 160 HOH HOH . 
F 3 HOH B 71 272 161 HOH HOH . 
F 3 HOH B 72 273 164 HOH HOH . 
F 3 HOH B 73 274 165 HOH HOH . 
F 3 HOH B 74 275 166 HOH HOH . 
F 3 HOH B 75 276 167 HOH HOH . 
F 3 HOH B 76 277 168 HOH HOH . 
F 3 HOH B 77 278 175 HOH HOH . 
F 3 HOH B 78 279 177 HOH HOH . 
F 3 HOH B 79 280 178 HOH HOH . 
F 3 HOH B 80 281 179 HOH HOH . 
F 3 HOH B 81 282 180 HOH HOH . 
F 3 HOH B 82 283 182 HOH HOH . 
F 3 HOH B 83 284 185 HOH HOH . 
F 3 HOH B 84 285 188 HOH HOH . 
F 3 HOH B 85 286 190 HOH HOH . 
F 3 HOH B 86 287 191 HOH HOH . 
F 3 HOH B 87 288 195 HOH HOH . 
F 3 HOH B 88 289 197 HOH HOH . 
F 3 HOH B 89 290 198 HOH HOH . 
F 3 HOH B 90 291 200 HOH HOH . 
F 3 HOH B 91 292 201 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 2 17.996 25.664 1.913 1 27.45 ? N SAM 201 B 1 
HETATM 2 C CA SAM . . . D 2 19.32 26.303 1.95 1 27.1 ? CA SAM 201 B 1 
HETATM 3 C C SAM . . . D 2 19.4 27.394 0.924 1 28.1 ? C SAM 201 B 1 
HETATM 4 O O SAM . . . D 2 20.306 28.194 0.914 1 29.15 ? O SAM 201 B 1 
HETATM 5 O OXT SAM . . . D 2 18.518 27.451 0.015 1 30.55 ? OXT SAM 201 B 1 
HETATM 6 C CB SAM . . . D 2 20.362 25.2 1.731 1 25.71 ? CB SAM 201 B 1 
HETATM 7 C CG SAM . . . D 2 20.469 24.459 3.097 1 24.6 ? CG SAM 201 B 1 
HETATM 8 S SD SAM . . . D 2 21.907 23.34 3.238 1 30.72 ? SD SAM 201 B 1 
HETATM 9 C CE SAM . . . D 2 21.255 21.938 2.333 1 31.43 ? CE SAM 201 B 1 
HETATM 10 C C5' SAM . . . D 2 21.667 22.494 4.824 1 29.61 ? C5' SAM 201 B 1 
HETATM 11 C C4' SAM . . . D 2 21.93 23.383 6 1 24.88 ? C4' SAM 201 B 1 
HETATM 12 O O4' SAM . . . D 2 21.445 22.741 7.157 1 22.88 ? O4' SAM 201 B 1 
HETATM 13 C C3' SAM . . . D 2 23.448 23.59 6.272 1 24.57 ? C3' SAM 201 B 1 
HETATM 14 O O3' SAM . . . D 2 23.736 24.938 5.965 1 24.36 ? O3' SAM 201 B 1 
HETATM 15 C C2' SAM . . . D 2 23.567 23.226 7.746 1 25.05 ? C2' SAM 201 B 1 
HETATM 16 O O2' SAM . . . D 2 24.471 24.022 8.497 1 25.49 ? O2' SAM 201 B 1 
HETATM 17 C C1' SAM . . . D 2 22.119 23.309 8.247 1 23.9 ? C1' SAM 201 B 1 
HETATM 18 N N9 SAM . . . D 2 21.925 22.552 9.457 1 26.24 ? N9 SAM 201 B 1 
HETATM 19 C C8 SAM . . . D 2 22.137 21.227 9.671 1 26.87 ? C8 SAM 201 B 1 
HETATM 20 N N7 SAM . . . D 2 21.781 20.959 10.942 1 26.11 ? N7 SAM 201 B 1 
HETATM 21 C C5 SAM . . . D 2 21.354 22.086 11.501 1 24.95 ? C5 SAM 201 B 1 
HETATM 22 C C6 SAM . . . D 2 20.936 22.347 12.802 1 27.35 ? C6 SAM 201 B 1 
HETATM 23 N N6 SAM . . . D 2 20.887 21.335 13.706 1 28.01 ? N6 SAM 201 B 1 
HETATM 24 N N1 SAM . . . D 2 20.546 23.629 13.072 1 27.14 ? N1 SAM 201 B 1 
HETATM 25 C C2 SAM . . . D 2 20.649 24.631 12.134 1 27.86 ? C2 SAM 201 B 1 
HETATM 26 N N3 SAM . . . D 2 21.096 24.347 10.859 1 26.04 ? N3 SAM 201 B 1 
HETATM 27 C C4 SAM . . . D 2 21.435 23.09 10.594 1 23.99 ? C4 SAM 201 B 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#