data_7NYB
#
_model_server_result.job_id            PahBqeYDsQF6CoYUFpQ0Cw 
_model_server_result.datetime_utc      '2025-02-05 06:41:55' 
_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          7nyb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    7NYB 
#
_exptl.entry_id    7NYB 
_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         120 
_cell.entry_id            7NYB 
_cell.length_a            178.19 
_cell.length_b            178.19 
_cell.length_c            37.01 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7NYB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_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 
_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
? 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 264 n n 
N HN1 SAM sing 265 n n 
N HN2 SAM sing 266 n n 
CA C SAM sing 267 n n 
CA CB SAM sing 268 n n 
CA HA SAM sing 269 n n 
C O SAM doub 270 n n 
C OXT SAM sing 271 n n 
CB CG SAM sing 272 n n 
CB HB1 SAM sing 273 n n 
CB HB2 SAM sing 274 n n 
CG SD SAM sing 275 n n 
CG HG1 SAM sing 276 n n 
CG HG2 SAM sing 277 n n 
SD CE SAM sing 278 n n 
SD C5' SAM sing 279 n n 
CE HE1 SAM sing 280 n n 
CE HE2 SAM sing 281 n n 
CE HE3 SAM sing 282 n n 
C5' C4' SAM sing 283 n n 
C5' "H5'1" SAM sing 284 n n 
C5' "H5'2" SAM sing 285 n n 
C4' O4' SAM sing 286 n n 
C4' C3' SAM sing 287 n n 
C4' H4' SAM sing 288 n n 
O4' C1' SAM sing 289 n n 
C3' O3' SAM sing 290 n n 
C3' C2' SAM sing 291 n n 
C3' H3' SAM sing 292 n n 
O3' HO3' SAM sing 293 n n 
C2' O2' SAM sing 294 n n 
C2' C1' SAM sing 295 n n 
C2' H2' SAM sing 296 n n 
O2' HO2' SAM sing 297 n n 
C1' N9 SAM sing 298 n n 
C1' H1' SAM sing 299 n n 
N9 C8 SAM sing 300 n y 
N9 C4 SAM sing 301 n y 
C8 N7 SAM doub 302 n y 
C8 H8 SAM sing 303 n n 
N7 C5 SAM sing 304 n y 
C5 C6 SAM sing 305 n y 
C5 C4 SAM doub 306 n y 
C6 N6 SAM sing 307 n n 
C6 N1 SAM doub 308 n y 
N6 HN61 SAM sing 309 n n 
N6 HN62 SAM sing 310 n n 
N1 C2 SAM sing 311 n y 
C2 N3 SAM doub 312 n y 
C2 H2 SAM sing 313 n n 
N3 C4 SAM sing 314 n y 
#
_atom_sites.entry_id                     7NYB 
_atom_sites.fract_transf_matrix[1][1]    0.005612 
_atom_sites.fract_transf_matrix[1][2]    0.00324 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00648 
_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]    0.02702 
_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 1 301 301 SAM SAM . 
D 2 SAM B 1 301 301 SAM SAM . 
E 3 HOH A 1 401 45 HOH HOH . 
E 3 HOH A 2 402 21 HOH HOH . 
E 3 HOH A 3 403 40 HOH HOH . 
E 3 HOH A 4 404 4 HOH HOH . 
E 3 HOH A 5 405 42 HOH HOH . 
E 3 HOH A 6 406 35 HOH HOH . 
E 3 HOH A 7 407 39 HOH HOH . 
E 3 HOH A 8 408 37 HOH HOH . 
E 3 HOH A 9 409 26 HOH HOH . 
E 3 HOH A 10 410 34 HOH HOH . 
E 3 HOH A 11 411 36 HOH HOH . 
E 3 HOH A 12 412 41 HOH HOH . 
E 3 HOH A 13 413 3 HOH HOH . 
E 3 HOH A 14 414 38 HOH HOH . 
E 3 HOH A 15 415 44 HOH HOH . 
E 3 HOH A 16 416 33 HOH HOH . 
E 3 HOH A 17 417 12 HOH HOH . 
E 3 HOH A 18 418 24 HOH HOH . 
E 3 HOH A 19 419 10 HOH HOH . 
E 3 HOH A 20 420 2 HOH HOH . 
E 3 HOH A 21 421 8 HOH HOH . 
E 3 HOH A 22 422 13 HOH HOH . 
E 3 HOH A 23 423 43 HOH HOH . 
E 3 HOH A 24 424 32 HOH HOH . 
F 3 HOH B 1 401 25 HOH HOH . 
F 3 HOH B 2 402 6 HOH HOH . 
F 3 HOH B 3 403 28 HOH HOH . 
F 3 HOH B 4 404 31 HOH HOH . 
F 3 HOH B 5 405 30 HOH HOH . 
F 3 HOH B 6 406 9 HOH HOH . 
F 3 HOH B 7 407 46 HOH HOH . 
F 3 HOH B 8 408 47 HOH HOH . 
F 3 HOH B 9 409 11 HOH HOH . 
F 3 HOH B 10 410 14 HOH HOH . 
F 3 HOH B 11 411 17 HOH HOH . 
F 3 HOH B 12 412 18 HOH HOH . 
F 3 HOH B 13 413 19 HOH HOH . 
F 3 HOH B 14 414 5 HOH HOH . 
F 3 HOH B 15 415 23 HOH HOH . 
F 3 HOH B 16 416 29 HOH HOH . 
F 3 HOH B 17 417 20 HOH HOH . 
F 3 HOH B 18 418 15 HOH HOH . 
F 3 HOH B 19 419 27 HOH HOH . 
F 3 HOH B 20 420 16 HOH HOH . 
F 3 HOH B 21 421 22 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 31.012 -21.623 9.201 1 63.65 ? N SAM 301 B 1 
HETATM 2 C CA SAM . . . D 2 31.677 -22.044 10.46 1 71.28 ? CA SAM 301 B 1 
HETATM 3 C C SAM . . . D 2 31.674 -20.867 11.446 1 72.49 ? C SAM 301 B 1 
HETATM 4 O O SAM . . . D 2 31.564 -19.72 10.994 1 70.05 ? O SAM 301 B 1 
HETATM 5 O OXT SAM . . . D 2 31.775 -21.063 12.664 1 63.38 ? OXT SAM 301 B 1 
HETATM 6 C CB SAM . . . D 2 33.109 -22.525 10.198 1 73.11 ? CB SAM 301 B 1 
HETATM 7 C CG SAM . . . D 2 34.082 -21.472 9.662 1 72.63 ? CG SAM 301 B 1 
HETATM 8 S SD SAM . . . D 2 35.659 -22.285 9.238 1 76.1 ? SD SAM 301 B 1 
HETATM 9 C CE SAM . . . D 2 36.867 -20.987 9.382 1 77.31 ? CE SAM 301 B 1 
HETATM 10 C C5' SAM . . . D 2 35.421 -22.406 7.44 1 87.27 ? C5' SAM 301 B 1 
HETATM 11 C C4' SAM . . . D 2 35.017 -23.804 7.01 1 83.92 ? C4' SAM 301 B 1 
HETATM 12 O O4' SAM . . . D 2 34.913 -23.869 5.57 1 86.51 ? O4' SAM 301 B 1 
HETATM 13 C C3' SAM . . . D 2 35.995 -24.913 7.4 1 86.35 ? C3' SAM 301 B 1 
HETATM 14 O O3' SAM . . . D 2 35.312 -25.865 8.197 1 83.64 ? O3' SAM 301 B 1 
HETATM 15 C C2' SAM . . . D 2 36.458 -25.512 6.065 1 88.74 ? C2' SAM 301 B 1 
HETATM 16 O O2' SAM . . . D 2 36.762 -26.895 6.135 1 92.09 ? O2' SAM 301 B 1 
HETATM 17 C C1' SAM . . . D 2 35.253 -25.179 5.195 1 83.84 ? C1' SAM 301 B 1 
HETATM 18 N N9 SAM . . . D 2 35.522 -25.205 3.766 1 85.47 ? N9 SAM 301 B 1 
HETATM 19 C C8 SAM . . . D 2 36.438 -24.441 3.088 1 81.19 ? C8 SAM 301 B 1 
HETATM 20 N N7 SAM . . . D 2 36.456 -24.681 1.8 1 80.14 ? N7 SAM 301 B 1 
HETATM 21 C C5 SAM . . . D 2 35.499 -25.671 1.618 1 71.55 ? C5 SAM 301 B 1 
HETATM 22 C C6 SAM . . . D 2 35.049 -26.357 0.474 1 71.65 ? C6 SAM 301 B 1 
HETATM 23 N N6 SAM . . . D 2 35.533 -26.147 -0.749 1 71.41 ? N6 SAM 301 B 1 
HETATM 24 N N1 SAM . . . D 2 34.083 -27.291 0.642 1 71.22 ? N1 SAM 301 B 1 
HETATM 25 C C2 SAM . . . D 2 33.601 -27.496 1.873 1 77.86 ? C2 SAM 301 B 1 
HETATM 26 N N3 SAM . . . D 2 33.946 -26.915 3.02 1 81.14 ? N3 SAM 301 B 1 
HETATM 27 C C4 SAM . . . D 2 34.914 -26.002 2.825 1 79.94 ? C4 SAM 301 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#