data_4PY0 # _model_server_result.job_id '_WtbW6m5CrLyDAhv_l5XAg' _model_server_result.datetime_utc '2024-11-20 07:27:56' _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 4py0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1201}' # _entry.id 4PY0 # _exptl.entry_id 4PY0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 553.273 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate)" _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 95.5 _cell.angle_gamma 90 _cell.entry_id 4PY0 _cell.length_a 75.65 _cell.length_b 65.11 _cell.length_c 100.74 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PY0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 106 A CYS 97 1_555 A SG CYS 184 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? # _chem_comp.formula 'C11 H18 N5 O13 P3 S' _chem_comp.formula_weight 553.273 _chem_comp.id 6AT _chem_comp.mon_nstd_flag . _chem_comp.name "2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2-methylthio-adenosine-5'-triphosphate" # 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 CAA S2 6AT sing 1 n n S2 C2 6AT sing 2 n n N1 C2 6AT doub 3 n y N1 C6 6AT sing 4 n y C2 N3 6AT sing 5 n y N6 C6 6AT sing 6 n n C6 C5 6AT doub 7 n y N3 C4 6AT doub 8 n y C5 C4 6AT sing 9 n y C5 N7 6AT sing 10 n y C4 N9 6AT sing 11 n y N7 C8 6AT doub 12 n y N9 C8 6AT sing 13 n y N9 C1' 6AT sing 14 n n O4' C1' 6AT sing 15 n n O4' C4' 6AT sing 16 n n C1' C2' 6AT sing 17 n n C4' C5' 6AT sing 18 n n C4' C3' 6AT sing 19 n n O5' C5' 6AT sing 20 n n O5' PBF 6AT sing 21 n n C2' O2' 6AT sing 22 n n C2' C3' 6AT sing 23 n n OAD PBF 6AT doub 24 n n C3' O3' 6AT sing 25 n n PBF OAT 6AT sing 26 n n PBF OAJ 6AT sing 27 n n OAK PBG 6AT doub 28 n n OAT PBG 6AT sing 29 n n PBG OAE 6AT sing 30 n n PBG OAS 6AT sing 31 n n OAS PBE 6AT sing 32 n n OAH PBE 6AT doub 33 n n PBE OAC 6AT sing 34 n n PBE OAI 6AT sing 35 n n OAI H1 6AT sing 36 n n OAC H2 6AT sing 37 n n OAE H3 6AT sing 38 n n OAJ H4 6AT sing 39 n n C5' H5 6AT sing 40 n n C5' H6 6AT sing 41 n n C4' H7 6AT sing 42 n n C3' H8 6AT sing 43 n n O3' H9 6AT sing 44 n n C2' H10 6AT sing 45 n n O2' H11 6AT sing 46 n n C1' H12 6AT sing 47 n n C8 H13 6AT sing 48 n n CAA H14 6AT sing 49 n n CAA H15 6AT sing 50 n n CAA H16 6AT sing 51 n n N6 H17 6AT sing 52 n n N6 H18 6AT sing 53 n n # _atom_sites.entry_id 4PY0 _atom_sites.fract_transf_matrix[1][1] 0.013219 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001273 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015359 _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] 0.009972 _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 6AT A 1 1201 1 6AT DRG . C 3 OLC A 1 1202 4 OLC OLC . D 3 OLC A 1 1203 5 OLC OLC . E 4 HOH A 1 1301 1 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 OAI 6AT . . . B 2 -15.253 -8.614 18.681 1 83.2 ? OAI 6AT 1201 A 1 HETATM 2 P PBE 6AT . . . B 2 -15.967 -7.455 17.805 1 82.82 ? PBE 6AT 1201 A 1 HETATM 3 O OAH 6AT . . . B 2 -17.415 -7.741 17.788 1 83.71 ? OAH 6AT 1201 A 1 HETATM 4 O OAC 6AT . . . B 2 -15.478 -6.136 18.276 1 83.02 ? OAC 6AT 1201 A 1 HETATM 5 O OAS 6AT . . . B 2 -15.417 -7.693 16.309 1 79.35 ? OAS 6AT 1201 A 1 HETATM 6 P PBG 6AT . . . B 2 -16.009 -6.797 15.11 1 75.95 ? PBG 6AT 1201 A 1 HETATM 7 O OAK 6AT . . . B 2 -14.889 -6.804 13.966 1 76.13 ? OAK 6AT 1201 A 1 HETATM 8 O OAE 6AT . . . B 2 -16.323 -5.412 15.525 1 76.06 ? OAE 6AT 1201 A 1 HETATM 9 O OAT 6AT . . . B 2 -17.328 -7.568 14.565 1 72.86 ? OAT 6AT 1201 A 1 HETATM 10 P PBF 6AT . . . B 2 -17.329 -8.89 13.622 1 70.11 ? PBF 6AT 1201 A 1 HETATM 11 O OAJ 6AT . . . B 2 -17.621 -10.136 14.592 1 69.82 ? OAJ 6AT 1201 A 1 HETATM 12 O OAD 6AT . . . B 2 -16.099 -9.083 12.828 1 70.33 ? OAD 6AT 1201 A 1 HETATM 13 O O5' 6AT . . . B 2 -18.623 -8.793 12.662 1 68.72 ? O5' 6AT 1201 A 1 HETATM 14 C C5' 6AT . . . B 2 -19.741 -7.948 12.961 1 67.58 ? C5' 6AT 1201 A 1 HETATM 15 C C4' 6AT . . . B 2 -21.026 -8.528 12.351 1 66.55 ? C4' 6AT 1201 A 1 HETATM 16 O O4' 6AT . . . B 2 -20.801 -9.226 11.098 1 65.97 ? O4' 6AT 1201 A 1 HETATM 17 C C3' 6AT . . . B 2 -21.699 -9.49 13.314 1 66.03 ? C3' 6AT 1201 A 1 HETATM 18 O O3' 6AT . . . B 2 -23.119 -9.237 13.328 1 66.15 ? O3' 6AT 1201 A 1 HETATM 19 C C2' 6AT . . . B 2 -21.387 -10.852 12.729 1 65.38 ? C2' 6AT 1201 A 1 HETATM 20 O O2' 6AT . . . B 2 -22.443 -11.789 12.972 1 65.15 ? O2' 6AT 1201 A 1 HETATM 21 C C1' 6AT . . . B 2 -21.232 -10.599 11.235 1 65.1 ? C1' 6AT 1201 A 1 HETATM 22 N N9 6AT . . . B 2 -20.192 -11.473 10.602 1 64.02 ? N9 6AT 1201 A 1 HETATM 23 C C8 6AT . . . B 2 -18.988 -11.769 11.094 1 63.69 ? C8 6AT 1201 A 1 HETATM 24 N N7 6AT . . . B 2 -18.361 -12.556 10.229 1 63.42 ? N7 6AT 1201 A 1 HETATM 25 C C5 6AT . . . B 2 -19.159 -12.727 9.178 1 63.2 ? C5 6AT 1201 A 1 HETATM 26 C C4 6AT . . . B 2 -20.294 -12.051 9.404 1 63.39 ? C4 6AT 1201 A 1 HETATM 27 N N3 6AT . . . B 2 -21.281 -12.058 8.479 1 62.93 ? N3 6AT 1201 A 1 HETATM 28 C C2 6AT . . . B 2 -21.138 -12.75 7.331 1 62.82 ? C2 6AT 1201 A 1 HETATM 29 S S2 6AT . . . B 2 -22.466 -12.737 6.137 1 62.93 ? S2 6AT 1201 A 1 HETATM 30 C CAA 6AT . . . B 2 -21.719 -13.469 4.692 1 62.93 ? CAA 6AT 1201 A 1 HETATM 31 N N1 6AT . . . B 2 -19.99 -13.427 7.109 1 62.66 ? N1 6AT 1201 A 1 HETATM 32 C C6 6AT . . . B 2 -19.014 -13.412 8.036 1 62.81 ? C6 6AT 1201 A 1 HETATM 33 N N6 6AT . . . B 2 -17.866 -14.067 7.861 1 62.76 ? N6 6AT 1201 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #