data_4PXZ
#
_model_server_result.job_id            0ZHQFcrtXwH8uDRm9aLkMA 
_model_server_result.datetime_utc      '2024-11-16 22:44:19' 
_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          4pxz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1201}' 
#
_entry.id    4PXZ 
#
_exptl.entry_id    4PXZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              473.293 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)" 
_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         90 
_cell.entry_id            4PXZ 
_cell.length_a            65.11 
_cell.length_b            104.17 
_cell.length_c            169.43 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PXZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,G,H 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 26 A CYS 17 1_555 A SG CYS 385 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 106 A CYS 97 1_555 A SG CYS 184 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
#
_chem_comp.formula           'C11 H17 N5 O10 P2 S' 
_chem_comp.formula_weight    473.293 
_chem_comp.id                6AD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "2-methylthio-adenosine-5'-diphosphate" 
#
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
C11 S1 6AD sing 1 n n 
S1 C2 6AD sing 2 n n 
N1 C2 6AD doub 3 n y 
N1 C6 6AD sing 4 n y 
C2 N3 6AD sing 5 n y 
N6 C6 6AD sing 6 n n 
C6 C5 6AD doub 7 n y 
N3 C4 6AD doub 8 n y 
C5 C4 6AD sing 9 n y 
C5 N7 6AD sing 10 n y 
C4 N9 6AD sing 11 n y 
N7 C8 6AD doub 12 n y 
N9 C8 6AD sing 13 n y 
N9 C1' 6AD sing 14 n n 
O4' C1' 6AD sing 15 n n 
O4' C4' 6AD sing 16 n n 
C1' C2' 6AD sing 17 n n 
C4' C5' 6AD sing 18 n n 
C4' C3' 6AD sing 19 n n 
O1A PA 6AD doub 20 n n 
C2' O2' 6AD sing 21 n n 
C2' C3' 6AD sing 22 n n 
C5' O5' 6AD sing 23 n n 
O3' C3' 6AD sing 24 n n 
O5' PA 6AD sing 25 n n 
PA O2A 6AD sing 26 n n 
PA O3A 6AD sing 27 n n 
O1B PB 6AD doub 28 n n 
O3A PB 6AD sing 29 n n 
O3B PB 6AD sing 30 n n 
PB O2B 6AD sing 31 n n 
O2B H1 6AD sing 32 n n 
O3B H2 6AD sing 33 n n 
O2A H3 6AD sing 34 n n 
C5' H4 6AD sing 35 n n 
C5' H5 6AD sing 36 n n 
C4' H6 6AD sing 37 n n 
C3' H7 6AD sing 38 n n 
O3' H8 6AD sing 39 n n 
C2' H9 6AD sing 40 n n 
O2' H10 6AD sing 41 n n 
C1' H11 6AD sing 42 n n 
C8 H12 6AD sing 43 n n 
C11 H13 6AD sing 44 n n 
C11 H14 6AD sing 45 n n 
C11 H15 6AD sing 46 n n 
N6 H16 6AD sing 47 n n 
N6 H17 6AD sing 48 n n 
#
_atom_sites.entry_id                     4PXZ 
_atom_sites.fract_transf_matrix[1][1]    0.015359 
_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]    0.0096 
_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]    0.005902 
_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 6AD A 1 1201 1 6AD RES . 
C 3 CLR A 1 1202 1 CLR CLR . 
D 4 OLC A 1 1203 3 OLC OLC . 
E 4 OLC A 1 1204 4 OLC OLC . 
F 4 OLC A 1 1205 5 OLC OLC . 
G 5 PEG A 1 1206 6 PEG PEG . 
H 6 HOH A 1 1301 1 HOH HOH . 
H 6 HOH A 2 1302 2 HOH HOH . 
H 6 HOH A 3 1303 4 HOH HOH . 
H 6 HOH A 4 1304 5 HOH HOH . 
H 6 HOH A 5 1305 8 HOH HOH . 
H 6 HOH A 6 1306 9 HOH HOH . 
H 6 HOH A 7 1307 10 HOH HOH . 
H 6 HOH A 8 1308 11 HOH HOH . 
H 6 HOH A 9 1309 12 HOH HOH . 
H 6 HOH A 10 1310 13 HOH HOH . 
H 6 HOH A 11 1311 14 HOH HOH . 
H 6 HOH A 12 1312 15 HOH HOH . 
H 6 HOH A 13 1313 16 HOH HOH . 
H 6 HOH A 14 1314 17 HOH HOH . 
H 6 HOH A 15 1315 18 HOH HOH . 
H 6 HOH A 16 1316 21 HOH HOH . 
H 6 HOH A 17 1317 22 HOH HOH . 
H 6 HOH A 18 1318 1318 HOH HOH . 
H 6 HOH A 19 1319 24 HOH HOH . 
H 6 HOH A 20 1320 25 HOH HOH . 
H 6 HOH A 21 1321 26 HOH HOH . 
H 6 HOH A 22 1322 27 HOH HOH . 
H 6 HOH A 23 1323 28 HOH HOH . 
H 6 HOH A 24 1324 29 HOH HOH . 
H 6 HOH A 25 1325 30 HOH HOH . 
H 6 HOH A 26 1326 31 HOH HOH . 
H 6 HOH A 27 1327 32 HOH HOH . 
H 6 HOH A 28 1328 33 HOH HOH . 
H 6 HOH A 29 1329 34 HOH HOH . 
H 6 HOH A 30 1330 35 HOH HOH . 
H 6 HOH A 31 1331 36 HOH HOH . 
H 6 HOH A 32 1332 37 HOH HOH . 
H 6 HOH A 33 1333 38 HOH HOH . 
H 6 HOH A 34 1334 39 HOH HOH . 
H 6 HOH A 35 1335 41 HOH HOH . 
H 6 HOH A 36 1336 42 HOH HOH . 
H 6 HOH A 37 1337 43 HOH HOH . 
H 6 HOH A 38 1338 44 HOH HOH . 
H 6 HOH A 39 1339 45 HOH HOH . 
H 6 HOH A 40 1340 47 HOH HOH . 
H 6 HOH A 41 1341 48 HOH HOH . 
H 6 HOH A 42 1342 49 HOH HOH . 
H 6 HOH A 43 1343 50 HOH HOH . 
H 6 HOH A 44 1344 51 HOH HOH . 
H 6 HOH A 45 1345 52 HOH HOH . 
H 6 HOH A 46 1346 53 HOH HOH . 
H 6 HOH A 47 1347 54 HOH HOH . 
H 6 HOH A 48 1348 57 HOH HOH . 
H 6 HOH A 49 1349 59 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 O O2B 6AD . . . B 2 16.181 1.025 59.445 1 46.32 ? O2B 6AD 1201 A 1 
HETATM 2 P PB 6AD . . . B 2 16.569 0.984 57.87 1 44.17 ? PB 6AD 1201 A 1 
HETATM 3 O O3B 6AD . . . B 2 18.003 0.277 57.772 1 44.38 ? O3B 6AD 1201 A 1 
HETATM 4 O O1B 6AD . . . B 2 16.571 2.339 57.263 1 44.13 ? O1B 6AD 1201 A 1 
HETATM 5 O O3A 6AD . . . B 2 15.481 -0.035 57.297 1 42.76 ? O3A 6AD 1201 A 1 
HETATM 6 P PA 6AD . . . B 2 15.599 -0.994 55.991 1 39.7 ? PA 6AD 1201 A 1 
HETATM 7 O O2A 6AD . . . B 2 15.94 -2.388 56.356 1 36.9 ? O2A 6AD 1201 A 1 
HETATM 8 O O1A 6AD . . . B 2 16.343 -0.306 54.904 1 40.02 ? O1A 6AD 1201 A 1 
HETATM 9 O O5' 6AD . . . B 2 14.034 -1.053 55.675 1 37.87 ? O5' 6AD 1201 A 1 
HETATM 10 C C5' 6AD . . . B 2 13.267 0.075 55.188 1 37.83 ? C5' 6AD 1201 A 1 
HETATM 11 C C4' 6AD . . . B 2 11.889 -0.406 54.659 1 37.65 ? C4' 6AD 1201 A 1 
HETATM 12 O O4' 6AD . . . B 2 12.011 -1.113 53.382 1 38.41 ? O4' 6AD 1201 A 1 
HETATM 13 C C3' 6AD . . . B 2 11.197 -1.374 55.631 1 38.94 ? C3' 6AD 1201 A 1 
HETATM 14 O O3' 6AD . . . B 2 9.769 -1.226 55.606 1 42.59 ? O3' 6AD 1201 A 1 
HETATM 15 C C2' 6AD . . . B 2 11.582 -2.723 55.107 1 39.2 ? C2' 6AD 1201 A 1 
HETATM 16 O O2' 6AD . . . B 2 10.634 -3.727 55.422 1 41.16 ? O2' 6AD 1201 A 1 
HETATM 17 C C1' 6AD . . . B 2 11.687 -2.525 53.603 1 40.3 ? C1' 6AD 1201 A 1 
HETATM 18 N N9 6AD . . . B 2 12.703 -3.449 53.002 1 43.64 ? N9 6AD 1201 A 1 
HETATM 19 C C8 6AD . . . B 2 13.886 -3.813 53.502 1 43.83 ? C8 6AD 1201 A 1 
HETATM 20 N N7 6AD . . . B 2 14.434 -4.713 52.697 1 46.33 ? N7 6AD 1201 A 1 
HETATM 21 C C5 6AD . . . B 2 13.612 -4.895 51.659 1 49.95 ? C5 6AD 1201 A 1 
HETATM 22 C C4 6AD . . . B 2 12.518 -4.136 51.88 1 47.93 ? C4 6AD 1201 A 1 
HETATM 23 N N3 6AD . . . B 2 11.505 -4.135 50.996 1 49.08 ? N3 6AD 1201 A 1 
HETATM 24 C C2 6AD . . . B 2 11.566 -4.903 49.892 1 51.58 ? C2 6AD 1201 A 1 
HETATM 25 S S1 6AD . . . B 2 10.191 -4.864 48.788 1 51.59 ? S1 6AD 1201 A 1 
HETATM 26 C C11 6AD . . . B 2 10.293 -6.409 47.909 1 51.19 ? C11 6AD 1201 A 1 
HETATM 27 N N1 6AD . . . B 2 12.677 -5.636 49.644 1 51.89 ? N1 6AD 1201 A 1 
HETATM 28 C C6 6AD . . . B 2 13.688 -5.642 50.532 1 49.64 ? C6 6AD 1201 A 1 
HETATM 29 N N6 6AD . . . B 2 14.761 -6.416 50.348 1 46.28 ? N6 6AD 1201 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           29 
#