data_4YNP
#
_model_server_result.job_id            o05ZUBF3O4mSYwfxd8wzeg 
_model_server_result.datetime_utc      '2024-11-21 17:07:12' 
_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          4ynp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":2304}' 
#
_entry.id    4YNP 
#
_exptl.entry_id    4YNP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              398.437 
_entity.id                          3 
_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            4YNP 
_cell.length_a            59.262 
_cell.length_b            59.262 
_cell.length_c            233.924 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YNP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_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,D,E,F 1 1 
B,G,H,I,J 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
? 3 F 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
disulf ? disulf1 B SG CYS 55 B CYS 2117 1_555 B SG CYS 60 B CYS 2122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 B SG CYS 55 B CYS 2117 1_555 B SG CYS 66 B CYS 2128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? 
disulf ? disulf3 B SG CYS 60 B CYS 2122 1_555 B SG CYS 66 B CYS 2128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc1 A SG CYS 29 A CYS 2091 1_555 E ZN ZN . A ZN 2303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc2 A SG CYS 31 A CYS 2093 1_555 E ZN ZN . A ZN 2303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc3 A SG CYS 42 A CYS 2104 1_555 D ZN ZN . A ZN 2302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc4 A SG CYS 42 A CYS 2104 1_555 E ZN ZN . A ZN 2303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc5 A SG CYS 46 A CYS 2108 1_555 E ZN ZN . A ZN 2303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc6 A SG CYS 55 A CYS 2117 1_555 D ZN ZN . A ZN 2302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc7 A SG CYS 60 A CYS 2122 1_555 D ZN ZN . A ZN 2302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc8 A SG CYS 66 A CYS 2128 1_555 D ZN ZN . A ZN 2302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc9 A SG CYS 158 A CYS 2220 1_555 C ZN ZN . A ZN 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
metalc ? metalc10 A SG CYS 206 A CYS 2268 1_555 C ZN ZN . A ZN 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
metalc ? metalc11 A SG CYS 208 A CYS 2270 1_555 C ZN ZN . A ZN 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? 
metalc ? metalc12 A SG CYS 213 A CYS 2275 1_555 C ZN ZN . A ZN 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? 
metalc ? metalc13 B SG CYS 42 B CYS 2104 1_555 I ZN ZN . B ZN 2303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc14 B SG CYS 46 B CYS 2108 1_555 I ZN ZN . B ZN 2303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc15 B SG CYS 55 B CYS 2117 1_555 H ZN ZN . B ZN 2302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc16 B SG CYS 60 B CYS 2122 1_555 H ZN ZN . B ZN 2302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc17 B SG CYS 158 B CYS 2220 1_555 G ZN ZN . B ZN 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc18 B SG CYS 206 B CYS 2268 1_555 G ZN ZN . B ZN 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc19 B SG CYS 208 B CYS 2270 1_555 G ZN ZN . B ZN 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc20 B SG CYS 213 B CYS 2275 1_555 G ZN ZN . B ZN 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
#
_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 275 n n 
N HN1 SAM sing 276 n n 
N HN2 SAM sing 277 n n 
CA C SAM sing 278 n n 
CA CB SAM sing 279 n n 
CA HA SAM sing 280 n n 
C O SAM doub 281 n n 
C OXT SAM sing 282 n n 
CB CG SAM sing 283 n n 
CB HB1 SAM sing 284 n n 
CB HB2 SAM sing 285 n n 
CG SD SAM sing 286 n n 
CG HG1 SAM sing 287 n n 
CG HG2 SAM sing 288 n n 
SD CE SAM sing 289 n n 
SD C5' SAM sing 290 n n 
CE HE1 SAM sing 291 n n 
CE HE2 SAM sing 292 n n 
CE HE3 SAM sing 293 n n 
C5' C4' SAM sing 294 n n 
C5' "H5'1" SAM sing 295 n n 
C5' "H5'2" SAM sing 296 n n 
C4' O4' SAM sing 297 n n 
C4' C3' SAM sing 298 n n 
C4' H4' SAM sing 299 n n 
O4' C1' SAM sing 300 n n 
C3' O3' SAM sing 301 n n 
C3' C2' SAM sing 302 n n 
C3' H3' SAM sing 303 n n 
O3' HO3' SAM sing 304 n n 
C2' O2' SAM sing 305 n n 
C2' C1' SAM sing 306 n n 
C2' H2' SAM sing 307 n n 
O2' HO2' SAM sing 308 n n 
C1' N9 SAM sing 309 n n 
C1' H1' SAM sing 310 n n 
N9 C8 SAM sing 311 n y 
N9 C4 SAM sing 312 n y 
C8 N7 SAM doub 313 n y 
C8 H8 SAM sing 314 n n 
N7 C5 SAM sing 315 n y 
C5 C6 SAM sing 316 n y 
C5 C4 SAM doub 317 n y 
C6 N6 SAM sing 318 n n 
C6 N1 SAM doub 319 n y 
N6 HN61 SAM sing 320 n n 
N6 HN62 SAM sing 321 n n 
N1 C2 SAM sing 322 n y 
C2 N3 SAM doub 323 n y 
C2 H2 SAM sing 324 n n 
N3 C4 SAM sing 325 n y 
#
_atom_sites.entry_id                     4YNP 
_atom_sites.fract_transf_matrix[1][1]    0.016874 
_atom_sites.fract_transf_matrix[1][2]    0.009742 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019485 
_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]    0.004275 
_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 ZN A 1 2301 1 ZN ZN . 
D 2 ZN A 1 2302 2 ZN ZN . 
E 2 ZN A 1 2303 4 ZN ZN . 
F 3 SAM A 1 2304 7 SAM SAM . 
G 2 ZN B 1 2301 3 ZN ZN . 
H 2 ZN B 1 2302 5 ZN ZN . 
I 2 ZN B 1 2303 6 ZN ZN . 
J 3 SAM B 1 2304 8 SAM SAM . 
#
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 . . . J 3 40.837 5.135 21.102 1 56.61 ? N SAM 2304 B 1 
HETATM 2 C CA SAM . . . J 3 40.548 4.726 19.694 1 56.62 ? CA SAM 2304 B 1 
HETATM 3 C C SAM . . . J 3 39.075 4.933 19.349 1 56.59 ? C SAM 2304 B 1 
HETATM 4 O O SAM . . . J 3 38.55 4.33 18.41 1 56.56 ? O SAM 2304 B 1 
HETATM 5 O OXT SAM . . . J 3 38.378 5.712 20.001 1 56.47 ? OXT SAM 2304 B 1 
HETATM 6 C CB SAM . . . J 3 40.982 3.286 19.438 1 56.52 ? CB SAM 2304 B 1 
HETATM 7 C CG SAM . . . J 3 42.481 3.102 19.24 1 56.66 ? CG SAM 2304 B 1 
HETATM 8 S SD SAM . . . J 3 43.014 3.545 17.569 1 56.76 ? SD SAM 2304 B 1 
HETATM 9 C CE SAM . . . J 3 44.033 2.122 17.113 1 56.9 ? CE SAM 2304 B 1 
HETATM 10 C C5' SAM . . . J 3 44.276 4.806 17.878 1 57.57 ? C5' SAM 2304 B 1 
HETATM 11 C C4' SAM . . . J 3 43.664 6.185 18.1 1 58.2 ? C4' SAM 2304 B 1 
HETATM 12 O O4' SAM . . . J 3 43.194 6.303 19.433 1 58.36 ? O4' SAM 2304 B 1 
HETATM 13 C C3' SAM . . . J 3 44.661 7.31 17.874 1 58.36 ? C3' SAM 2304 B 1 
HETATM 14 O O3' SAM . . . J 3 44.482 7.898 16.607 1 58.49 ? O3' SAM 2304 B 1 
HETATM 15 C C2' SAM . . . J 3 44.37 8.297 18.986 1 58.57 ? C2' SAM 2304 B 1 
HETATM 16 O O2' SAM . . . J 3 43.487 9.302 18.549 1 58.89 ? O2' SAM 2304 B 1 
HETATM 17 C C1' SAM . . . J 3 43.69 7.468 20.066 1 58.55 ? C1' SAM 2304 B 1 
HETATM 18 N N9 SAM . . . J 3 44.686 7.111 21.1 1 58.35 ? N9 SAM 2304 B 1 
HETATM 19 C C8 SAM . . . J 3 45.155 5.851 21.372 1 58.29 ? C8 SAM 2304 B 1 
HETATM 20 N N7 SAM . . . J 3 46.055 5.93 22.374 1 58.25 ? N7 SAM 2304 B 1 
HETATM 21 C C5 SAM . . . J 3 46.18 7.22 22.748 1 58.13 ? C5 SAM 2304 B 1 
HETATM 22 C C6 SAM . . . J 3 46.961 7.844 23.717 1 57.92 ? C6 SAM 2304 B 1 
HETATM 23 N N6 SAM . . . J 3 47.78 7.129 24.481 1 57.63 ? N6 SAM 2304 B 1 
HETATM 24 N N1 SAM . . . J 3 46.878 9.213 23.881 1 57.96 ? N1 SAM 2304 B 1 
HETATM 25 C C2 SAM . . . J 3 46.022 9.956 23.084 1 58.01 ? C2 SAM 2304 B 1 
HETATM 26 N N3 SAM . . . J 3 45.251 9.327 22.123 1 58.03 ? N3 SAM 2304 B 1 
HETATM 27 C C4 SAM . . . J 3 45.325 7.979 21.955 1 58.1 ? C4 SAM 2304 B 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#