data_8X4O
#
_model_server_result.job_id            gdVgcVW7a05UwTIb86Teug 
_model_server_result.datetime_utc      '2024-11-22 13:58:53' 
_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          8x4o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":301}' 
#
_entry.id    8X4O 
#
_exptl.entry_id    8X4O 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              297.334 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_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            8X4O 
_cell.length_a            125.539 
_cell.length_b            125.539 
_cell.length_c            37.14 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8X4O 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        143 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3' 
#
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,I 1 1 
B,F,G,H,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
? 2 C N N 
? 2 F 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
metalc ? metalc1 A ND1 HIS 231 A HIS 231 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc2 A NE2 HIS 286 A HIS 286 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc3 D ZN ZN . A ZN 302 3_555 B NE2 HIS 286 B HIS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc4 I O HOH . A HOH 405 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc5 B ND1 HIS 231 B HIS 231 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
#
_chem_comp.formula           'C11 H15 N5 O3 S' 
_chem_comp.formula_weight    297.334 
_chem_comp.id                MTA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_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
CS S5' MTA sing 233 n n 
CS HCS1 MTA sing 234 n n 
CS HCS2 MTA sing 235 n n 
CS HCS3 MTA sing 236 n n 
S5' C5' MTA sing 237 n n 
C5' C4' MTA sing 238 n n 
C5' "H5'1" MTA sing 239 n n 
C5' "H5'2" MTA sing 240 n n 
C4' O4' MTA sing 241 n n 
C4' C3' MTA sing 242 n n 
C4' H4' MTA sing 243 n n 
O4' C1' MTA sing 244 n n 
C2' O2' MTA sing 245 n n 
C2' C3' MTA sing 246 n n 
C2' C1' MTA sing 247 n n 
C2' H2' MTA sing 248 n n 
O2' HO2' MTA sing 249 n n 
C3' O3' MTA sing 250 n n 
C3' H3' MTA sing 251 n n 
O3' H3T MTA sing 252 n n 
C1' N9 MTA sing 253 n n 
C1' H1' MTA sing 254 n n 
N9 C8 MTA sing 255 n y 
N9 C4 MTA sing 256 n y 
C8 N7 MTA doub 257 n y 
C8 H8 MTA sing 258 n n 
N7 C5 MTA sing 259 n y 
C5 C6 MTA sing 260 n y 
C5 C4 MTA doub 261 n y 
C6 N6 MTA sing 262 n n 
C6 N1 MTA doub 263 n y 
N6 H61 MTA sing 264 n n 
N6 H62 MTA sing 265 n n 
N1 C2 MTA sing 266 n y 
C2 N3 MTA doub 267 n y 
C2 H2 MTA sing 268 n n 
N3 C4 MTA sing 269 n y 
#
_atom_sites.entry_id                     8X4O 
_atom_sites.fract_transf_matrix[1][1]    0.007966 
_atom_sites.fract_transf_matrix[1][2]    0.004599 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009198 
_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]    0.026925 
_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 MTA A 1 301 1 MTA MTA . 
D 3 ZN A 1 302 3 ZN ZN . 
E 4 EDO A 1 303 5 EDO EDO . 
F 2 MTA B 1 301 2 MTA MTA . 
G 3 ZN B 1 302 4 ZN ZN . 
H 4 EDO B 1 303 6 EDO EDO . 
I 5 HOH A 1 401 19 HOH HOH . 
I 5 HOH A 2 402 20 HOH HOH . 
I 5 HOH A 3 403 4 HOH HOH . 
I 5 HOH A 4 404 8 HOH HOH . 
I 5 HOH A 5 405 7 HOH HOH . 
I 5 HOH A 6 406 1 HOH HOH . 
I 5 HOH A 7 407 3 HOH HOH . 
I 5 HOH A 8 408 2 HOH HOH . 
J 5 HOH B 1 401 21 HOH HOH . 
J 5 HOH B 2 402 15 HOH HOH . 
J 5 HOH B 3 403 16 HOH HOH . 
J 5 HOH B 4 404 18 HOH HOH . 
J 5 HOH B 5 405 14 HOH HOH . 
J 5 HOH B 6 406 6 HOH HOH . 
J 5 HOH B 7 407 5 HOH HOH . 
J 5 HOH B 8 408 13 HOH HOH . 
J 5 HOH B 9 409 12 HOH HOH . 
J 5 HOH B 10 410 11 HOH HOH . 
J 5 HOH B 11 411 17 HOH HOH . 
J 5 HOH B 12 412 10 HOH HOH . 
J 5 HOH B 13 413 9 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 C CS MTA . . . F 2 17.104 -51.962 -1.37 1 115.03 ? CS MTA 301 B 1 
HETATM 2 S S5' MTA . . . F 2 18.308 -51.355 -2.563 1 111.37 ? S5' MTA 301 B 1 
HETATM 3 C C5' MTA . . . F 2 17.408 -51.589 -4.111 1 107.2 ? C5' MTA 301 B 1 
HETATM 4 C C4' MTA . . . F 2 17.152 -53.045 -4.421 1 117 ? C4' MTA 301 B 1 
HETATM 5 O O4' MTA . . . F 2 15.9 -53.179 -5.127 1 115.07 ? O4' MTA 301 B 1 
HETATM 6 C C2' MTA . . . F 2 17.4 -54.788 -6.045 1 121.99 ? C2' MTA 301 B 1 
HETATM 7 O O2' MTA . . . F 2 17.549 -56.014 -5.357 1 118.44 ? O2' MTA 301 B 1 
HETATM 8 C C3' MTA . . . F 2 18.193 -53.69 -5.328 1 127.5 ? C3' MTA 301 B 1 
HETATM 9 O O3' MTA . . . F 2 19.229 -54.243 -4.525 1 138.09 ? O3' MTA 301 B 1 
HETATM 10 C C1' MTA . . . F 2 15.961 -54.262 -6.027 1 103.27 ? C1' MTA 301 B 1 
HETATM 11 N N9 MTA . . . F 2 15.496 -53.781 -7.322 1 86.03 ? N9 MTA 301 B 1 
HETATM 12 C C8 MTA . . . F 2 16.153 -52.94 -8.187 1 81.15 ? C8 MTA 301 B 1 
HETATM 13 N N7 MTA . . . F 2 15.486 -52.696 -9.289 1 74.3 ? N7 MTA 301 B 1 
HETATM 14 C C5 MTA . . . F 2 14.315 -53.423 -9.139 1 69.64 ? C5 MTA 301 B 1 
HETATM 15 C C6 MTA . . . F 2 13.196 -53.588 -9.97 1 72.79 ? C6 MTA 301 B 1 
HETATM 16 N N6 MTA . . . F 2 13.075 -53.01 -11.163 1 86.09 ? N6 MTA 301 B 1 
HETATM 17 N N1 MTA . . . F 2 12.198 -54.387 -9.524 1 73.03 ? N1 MTA 301 B 1 
HETATM 18 C C2 MTA . . . F 2 12.336 -54.979 -8.33 1 74.27 ? C2 MTA 301 B 1 
HETATM 19 N N3 MTA . . . F 2 13.34 -54.895 -7.461 1 70.49 ? N3 MTA 301 B 1 
HETATM 20 C C4 MTA . . . F 2 14.31 -54.097 -7.932 1 74.65 ? C4 MTA 301 B 1 
#
_model_server_stats.io_time_ms              70 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           20 
#