data_9JD2
#
_model_server_result.job_id            pyl2xpQyh2wMzd20LVAiOQ 
_model_server_result.datetime_utc      '2024-11-22 10:18:45' 
_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          9jd2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    9JD2 
#
_exptl.entry_id    9JD2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              297.334 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_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            9JD2 
_cell.length_a            79.048 
_cell.length_b            79.048 
_cell.length_c            233.48 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9JD2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -39.524 -68.457576 0 
3 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 39.524 -68.457576 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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
disulf ? disulf1 A SG CYS 143 A CYS 143 1_555 A SG CYS 210 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf2 A SG CYS 205 A CYS 205 1_555 A SG CYS 266 A CYS 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf3 A SG CYS 264 A CYS 264 1_555 A SG CYS 267 A CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
#
_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 237 n n 
CS HCS1 MTA sing 238 n n 
CS HCS2 MTA sing 239 n n 
CS HCS3 MTA sing 240 n n 
S5' C5' MTA sing 241 n n 
C5' C4' MTA sing 242 n n 
C5' "H5'1" MTA sing 243 n n 
C5' "H5'2" MTA sing 244 n n 
C4' O4' MTA sing 245 n n 
C4' C3' MTA sing 246 n n 
C4' H4' MTA sing 247 n n 
O4' C1' MTA sing 248 n n 
C2' O2' MTA sing 249 n n 
C2' C3' MTA sing 250 n n 
C2' C1' MTA sing 251 n n 
C2' H2' MTA sing 252 n n 
O2' HO2' MTA sing 253 n n 
C3' O3' MTA sing 254 n n 
C3' H3' MTA sing 255 n n 
O3' H3T MTA sing 256 n n 
C1' N9 MTA sing 257 n n 
C1' H1' MTA sing 258 n n 
N9 C8 MTA sing 259 n y 
N9 C4 MTA sing 260 n y 
C8 N7 MTA doub 261 n y 
C8 H8 MTA sing 262 n n 
N7 C5 MTA sing 263 n y 
C5 C6 MTA sing 264 n y 
C5 C4 MTA doub 265 n y 
C6 N6 MTA sing 266 n n 
C6 N1 MTA doub 267 n y 
N6 H61 MTA sing 268 n n 
N6 H62 MTA sing 269 n n 
N1 C2 MTA sing 270 n y 
C2 N3 MTA doub 271 n y 
C2 H2 MTA sing 272 n n 
N3 C4 MTA sing 273 n y 
#
_atom_sites.entry_id                     9JD2 
_atom_sites.fract_transf_matrix[1][1]    0.012651 
_atom_sites.fract_transf_matrix[1][2]    0.007304 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014608 
_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]    0.004283 
_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
B 2 PO4 A 1 400 400 PO4 PO4 . 
C 3 MTA A 1 401 401 MTA MTA . 
D 4 HOH A 1 501 29 HOH HOH . 
D 4 HOH A 2 502 24 HOH HOH . 
D 4 HOH A 3 503 44 HOH HOH . 
D 4 HOH A 4 504 42 HOH HOH . 
D 4 HOH A 5 505 43 HOH HOH . 
D 4 HOH A 6 506 33 HOH HOH . 
D 4 HOH A 7 507 46 HOH HOH . 
D 4 HOH A 8 508 41 HOH HOH . 
D 4 HOH A 9 509 21 HOH HOH . 
D 4 HOH A 10 510 25 HOH HOH . 
D 4 HOH A 11 511 38 HOH HOH . 
D 4 HOH A 12 512 16 HOH HOH . 
D 4 HOH A 13 513 30 HOH HOH . 
D 4 HOH A 14 514 22 HOH HOH . 
D 4 HOH A 15 515 12 HOH HOH . 
D 4 HOH A 16 516 47 HOH HOH . 
D 4 HOH A 17 517 31 HOH HOH . 
D 4 HOH A 18 518 39 HOH HOH . 
D 4 HOH A 19 519 32 HOH HOH . 
D 4 HOH A 20 520 8 HOH HOH . 
D 4 HOH A 21 521 17 HOH HOH . 
D 4 HOH A 22 522 45 HOH HOH . 
D 4 HOH A 23 523 14 HOH HOH . 
D 4 HOH A 24 524 15 HOH HOH . 
D 4 HOH A 25 525 7 HOH HOH . 
D 4 HOH A 26 526 19 HOH HOH . 
D 4 HOH A 27 527 37 HOH HOH . 
D 4 HOH A 28 528 11 HOH HOH . 
D 4 HOH A 29 529 20 HOH HOH . 
D 4 HOH A 30 530 4 HOH HOH . 
D 4 HOH A 31 531 18 HOH HOH . 
D 4 HOH A 32 532 13 HOH HOH . 
D 4 HOH A 33 533 23 HOH HOH . 
D 4 HOH A 34 534 3 HOH HOH . 
D 4 HOH A 35 535 5 HOH HOH . 
D 4 HOH A 36 536 1 HOH HOH . 
D 4 HOH A 37 537 9 HOH HOH . 
D 4 HOH A 38 538 10 HOH HOH . 
D 4 HOH A 39 539 26 HOH HOH . 
D 4 HOH A 40 540 34 HOH HOH . 
D 4 HOH A 41 541 35 HOH HOH . 
D 4 HOH A 42 542 6 HOH HOH . 
D 4 HOH A 43 543 2 HOH HOH . 
D 4 HOH A 44 544 36 HOH HOH . 
D 4 HOH A 45 545 27 HOH HOH . 
D 4 HOH A 46 546 28 HOH HOH . 
D 4 HOH A 47 547 40 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 . . . C 3 5.49 -23.873 -21.737 1 32.58 ? CS MTA 401 A 1 
HETATM 2 S S5' MTA . . . C 3 4.236 -24.684 -20.725 1 28.75 ? S5' MTA 401 A 1 
HETATM 3 C C5' MTA . . . C 3 4.555 -26.414 -21.099 1 26.34 ? C5' MTA 401 A 1 
HETATM 4 C C4' MTA . . . C 3 5.829 -27.017 -20.566 1 22.15 ? C4' MTA 401 A 1 
HETATM 5 O O4' MTA . . . C 3 5.816 -26.917 -19.132 1 23.73 ? O4' MTA 401 A 1 
HETATM 6 C C2' MTA . . . C 3 6.386 -29.153 -19.518 1 20.37 ? C2' MTA 401 A 1 
HETATM 7 O O2' MTA . . . C 3 7.531 -29.97 -19.606 1 20.28 ? O2' MTA 401 A 1 
HETATM 8 C C3' MTA . . . C 3 5.93 -28.521 -20.859 1 21.21 ? C3' MTA 401 A 1 
HETATM 9 O O3' MTA . . . C 3 6.742 -28.739 -22.019 1 20.18 ? O3' MTA 401 A 1 
HETATM 10 C C1' MTA . . . C 3 6.611 -27.963 -18.576 1 21.91 ? C1' MTA 401 A 1 
HETATM 11 N N9 MTA . . . C 3 6.079 -28.02 -17.219 1 20.32 ? N9 MTA 401 A 1 
HETATM 12 C C8 MTA . . . C 3 6.188 -26.941 -16.372 1 20.1 ? C8 MTA 401 A 1 
HETATM 13 N N7 MTA . . . C 3 5.428 -27.013 -15.311 1 18.41 ? N7 MTA 401 A 1 
HETATM 14 C C5 MTA . . . C 3 4.741 -28.208 -15.481 1 17.37 ? C5 MTA 401 A 1 
HETATM 15 C C6 MTA . . . C 3 3.769 -28.858 -14.709 1 18.46 ? C6 MTA 401 A 1 
HETATM 16 N N6 MTA . . . C 3 3.297 -28.369 -13.558 1 20.53 ? N6 MTA 401 A 1 
HETATM 17 N N1 MTA . . . C 3 3.262 -30.028 -15.185 1 16.64 ? N1 MTA 401 A 1 
HETATM 18 C C2 MTA . . . C 3 3.764 -30.531 -16.308 1 16.56 ? C2 MTA 401 A 1 
HETATM 19 N N3 MTA . . . C 3 4.663 -29.997 -17.116 1 16.79 ? N3 MTA 401 A 1 
HETATM 20 C C4 MTA . . . C 3 5.118 -28.829 -16.66 1 17.68 ? C4 MTA 401 A 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          18 
_model_server_stats.element_count           20 
#