data_2PAU # _model_server_result.job_id OyHp-rkolmo0kVlgXYA79Q _model_server_result.datetime_utc '2025-03-06 07:08:27' _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 2pau # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 2PAU # _exptl.entry_id 2PAU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 2PAU _cell.length_a 135.595 _cell.length_b 135.595 _cell.length_c 54.936 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PAU _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 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 dimeric 2 author_and_software_defined_assembly 1 PQS hexameric 6 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,B,C,D,E,F,G,H,I 1 1 A,B,C,D,E,F,G,H,I 2 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G 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 NE2 HIS 35 A HIS 33 1_555 C CO CO . A CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc2 A NE2 HIS 70 A HIS 68 1_555 C CO CO . A CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc3 A OD2 ASP 71 A ASP 69 1_555 C CO CO . A CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc4 A OD1 ASP 139 A ASP 137 1_555 C CO CO . A CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc5 C CO CO . A CO 201 1_555 D O1P D5M . A D5M 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc6 C CO CO . A CO 201 1_555 H O HOH . A HOH 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc7 B NE2 HIS 35 B HIS 33 1_555 F CO CO . B CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc8 B NE2 HIS 70 B HIS 68 1_555 F CO CO . B CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc9 B OD2 ASP 71 B ASP 69 1_555 F CO CO . B CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc10 B OD1 ASP 139 B ASP 137 1_555 F CO CO . B CO 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc11 F CO CO . B CO 201 1_555 G O1P D5M . B D5M 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? # _chem_comp.formula 'C10 H14 N5 O6 P' _chem_comp.formula_weight 331.222 _chem_comp.id D5M _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 O5' C5' D5M sing 83 n n O5' P D5M sing 84 n n C5' C4' D5M sing 85 n n C5' "H5'1" D5M sing 86 n n C5' "H5'2" D5M sing 87 n n C4' O4' D5M sing 88 n n C4' C3' D5M sing 89 n n C4' H4' D5M sing 90 n n O4' C1' D5M sing 91 n n C3' O3' D5M sing 92 n n C3' C2' D5M sing 93 n n C3' H1 D5M sing 94 n n O3' H3' D5M sing 95 n n C2' C1' D5M sing 96 n n C2' "H2'1" D5M sing 97 n n C2' "H2'2" D5M sing 98 n n C1' N9 D5M sing 99 n n C1' H1' D5M sing 100 n n N9 C8 D5M sing 101 n y N9 C4 D5M sing 102 n y C8 N7 D5M doub 103 n y C8 H8 D5M sing 104 n n N7 C5 D5M sing 105 n y C5 C6 D5M sing 106 n y C5 C4 D5M doub 107 n y C6 N6 D5M sing 108 n n C6 N1 D5M doub 109 n y N6 HN61 D5M sing 110 n n N6 HN62 D5M sing 111 n n N1 C2 D5M sing 112 n y C2 N3 D5M doub 113 n y C2 H2 D5M sing 114 n n N3 C4 D5M sing 115 n y P O1P D5M doub 116 n n P O3P D5M sing 117 n n P O2P D5M sing 118 n n O3P H3P D5M sing 119 n n O2P H2P D5M sing 120 n n # _atom_sites.entry_id 2PAU _atom_sites.fract_transf_matrix[1][1] 0.00738 _atom_sites.fract_transf_matrix[1][2] 0.00426 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00852 _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] 0.0182 _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 CO A 1 201 201 CO CO . D 3 D5M A 1 301 301 D5M D5M . E 4 PEG A 1 401 401 PEG PEG . F 2 CO B 1 201 201 CO CO . G 3 D5M B 1 301 301 D5M D5M . H 5 HOH A 1 402 3 HOH HOH . H 5 HOH A 2 403 5 HOH HOH . H 5 HOH A 3 404 6 HOH HOH . H 5 HOH A 4 405 7 HOH HOH . H 5 HOH A 5 406 8 HOH HOH . H 5 HOH A 6 407 9 HOH HOH . H 5 HOH A 7 408 11 HOH HOH . H 5 HOH A 8 409 15 HOH HOH . H 5 HOH A 9 410 16 HOH HOH . H 5 HOH A 10 411 18 HOH HOH . H 5 HOH A 11 412 22 HOH HOH . H 5 HOH A 12 413 23 HOH HOH . H 5 HOH A 13 414 28 HOH HOH . H 5 HOH A 14 415 29 HOH HOH . H 5 HOH A 15 416 30 HOH HOH . H 5 HOH A 16 417 31 HOH HOH . H 5 HOH A 17 418 32 HOH HOH . H 5 HOH A 18 419 34 HOH HOH . H 5 HOH A 19 420 35 HOH HOH . H 5 HOH A 20 421 36 HOH HOH . H 5 HOH A 21 422 38 HOH HOH . H 5 HOH A 22 423 41 HOH HOH . H 5 HOH A 23 424 43 HOH HOH . H 5 HOH A 24 425 46 HOH HOH . H 5 HOH A 25 426 47 HOH HOH . H 5 HOH A 26 427 49 HOH HOH . H 5 HOH A 27 428 51 HOH HOH . H 5 HOH A 28 429 54 HOH HOH . H 5 HOH A 29 430 56 HOH HOH . H 5 HOH A 30 431 58 HOH HOH . H 5 HOH A 31 432 61 HOH HOH . I 5 HOH B 1 302 1 HOH HOH . I 5 HOH B 2 303 2 HOH HOH . I 5 HOH B 3 304 4 HOH HOH . I 5 HOH B 4 305 10 HOH HOH . I 5 HOH B 5 306 12 HOH HOH . I 5 HOH B 6 307 13 HOH HOH . I 5 HOH B 7 308 14 HOH HOH . I 5 HOH B 8 309 17 HOH HOH . I 5 HOH B 9 310 19 HOH HOH . I 5 HOH B 10 311 20 HOH HOH . I 5 HOH B 11 312 21 HOH HOH . I 5 HOH B 12 313 24 HOH HOH . I 5 HOH B 13 314 25 HOH HOH . I 5 HOH B 14 315 33 HOH HOH . I 5 HOH B 15 316 37 HOH HOH . I 5 HOH B 16 317 40 HOH HOH . I 5 HOH B 17 318 42 HOH HOH . I 5 HOH B 18 319 44 HOH HOH . I 5 HOH B 19 320 45 HOH HOH . I 5 HOH B 20 321 48 HOH HOH . I 5 HOH B 21 322 52 HOH HOH . I 5 HOH B 22 323 57 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 O5' D5M . . . D 3 -20.663 6.755 30.26 0.7 52.53 ? O5' D5M 301 A 1 HETATM 2 C C5' D5M . . . D 3 -21.232 5.501 30.577 0.7 46.41 ? C5' D5M 301 A 1 HETATM 3 C C4' D5M . . . D 3 -20.253 4.34 30.384 0.7 44.85 ? C4' D5M 301 A 1 HETATM 4 O O4' D5M . . . D 3 -20.618 3.74 29.111 0.7 49.54 ? O4' D5M 301 A 1 HETATM 5 C C3' D5M . . . D 3 -18.756 4.62 30.213 0.7 43.81 ? C3' D5M 301 A 1 HETATM 6 O O3' D5M . . . D 3 -17.996 3.554 30.757 0.7 36.18 ? O3' D5M 301 A 1 HETATM 7 C C2' D5M . . . D 3 -18.498 4.593 28.712 0.7 45.5 ? C2' D5M 301 A 1 HETATM 8 C C1' D5M . . . D 3 -19.472 3.527 28.261 0.7 46.87 ? C1' D5M 301 A 1 HETATM 9 N N9 D5M . . . D 3 -19.895 3.552 26.797 0.7 48.6 ? N9 D5M 301 A 1 HETATM 10 C C8 D5M . . . D 3 -20.439 4.547 26.064 0.7 46.87 ? C8 D5M 301 A 1 HETATM 11 N N7 D5M . . . D 3 -20.686 4.056 24.814 0.7 47.78 ? N7 D5M 301 A 1 HETATM 12 C C5 D5M . . . D 3 -20.307 2.748 24.793 0.7 46.81 ? C5 D5M 301 A 1 HETATM 13 C C6 D5M . . . D 3 -20.31 1.745 23.825 0.7 47.4 ? C6 D5M 301 A 1 HETATM 14 N N6 D5M . . . D 3 -20.78 2.023 22.571 0.7 48.19 ? N6 D5M 301 A 1 HETATM 15 N N1 D5M . . . D 3 -19.841 0.494 24.124 0.7 47.31 ? N1 D5M 301 A 1 HETATM 16 C C2 D5M . . . D 3 -19.381 0.211 25.379 0.7 47.42 ? C2 D5M 301 A 1 HETATM 17 N N3 D5M . . . D 3 -19.364 1.172 26.325 0.7 45.61 ? N3 D5M 301 A 1 HETATM 18 C C4 D5M . . . D 3 -19.825 2.434 26.051 0.7 45.39 ? C4 D5M 301 A 1 HETATM 19 P P D5M . . . D 3 -21.421 8.149 29.84 0.7 57.57 ? P D5M 301 A 1 HETATM 20 O O1P D5M . . . D 3 -20.785 9.248 30.682 0.7 53.28 ? O1P D5M 301 A 1 HETATM 21 O O3P D5M . . . D 3 -20.957 8.258 28.398 0.7 54.89 ? O3P D5M 301 A 1 HETATM 22 O O2P D5M . . . D 3 -22.91 7.925 30.106 0.7 55.01 ? O2P D5M 301 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 22 #