data_3AP2 # _model_server_result.job_id 1ll6RFCS5Vh12d_-t5235A _model_server_result.datetime_utc '2024-11-15 04:16:02' _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 3ap2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1}' # _entry.id 3AP2 # _exptl.entry_id 3AP2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 3AP2 _cell.length_a 138.379 _cell.length_b 138.379 _cell.length_c 228.547 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AP2 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G,H,I,J,K _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 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 disulf ? disulf1 A SG CYS 74 A CYS 96 1_555 A SG CYS 134 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf2 A SG CYS 203 A CYS 225 1_555 A SG CYS 211 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf3 B SG CYS 74 B CYS 96 1_555 B SG CYS 134 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf4 B SG CYS 203 B CYS 225 1_555 B SG CYS 211 B CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 3AP2 _atom_sites.fract_transf_matrix[1][1] 0.007227 _atom_sites.fract_transf_matrix[1][2] 0.004172 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008344 _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] 0.004375 _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 E 3 A3P A 1 1 1 A3P A3P . F 3 A3P B 1 1 1 A3P A3P . G 4 GOL B 1 360 1 GOL GOL . H 5 PO4 T 1 1 1 PO4 PO4 . I 6 HOH A 1 3 3 HOH HOH . I 6 HOH A 2 4 4 HOH HOH . I 6 HOH A 3 7 7 HOH HOH . I 6 HOH A 4 8 8 HOH HOH . I 6 HOH A 5 9 9 HOH HOH . I 6 HOH A 6 10 10 HOH HOH . I 6 HOH A 7 11 11 HOH HOH . I 6 HOH A 8 14 14 HOH HOH . I 6 HOH A 9 16 16 HOH HOH . I 6 HOH A 10 17 17 HOH HOH . I 6 HOH A 11 18 18 HOH HOH . I 6 HOH A 12 360 1 HOH HOH . I 6 HOH A 13 361 25 HOH HOH . I 6 HOH A 14 362 27 HOH HOH . I 6 HOH A 15 363 30 HOH HOH . I 6 HOH A 16 364 31 HOH HOH . I 6 HOH A 17 365 32 HOH HOH . I 6 HOH A 18 366 33 HOH HOH . I 6 HOH A 19 367 38 HOH HOH . I 6 HOH A 20 368 40 HOH HOH . I 6 HOH A 21 369 45 HOH HOH . I 6 HOH A 22 370 46 HOH HOH . I 6 HOH A 23 371 48 HOH HOH . I 6 HOH A 24 372 49 HOH HOH . I 6 HOH A 25 373 50 HOH HOH . I 6 HOH A 26 374 52 HOH HOH . I 6 HOH A 27 375 54 HOH HOH . J 6 HOH B 1 2 2 HOH HOH . J 6 HOH B 2 5 5 HOH HOH . J 6 HOH B 3 6 6 HOH HOH . J 6 HOH B 4 12 12 HOH HOH . J 6 HOH B 5 13 13 HOH HOH . J 6 HOH B 6 15 15 HOH HOH . J 6 HOH B 7 19 19 HOH HOH . J 6 HOH B 8 20 20 HOH HOH . J 6 HOH B 9 21 21 HOH HOH . J 6 HOH B 10 22 22 HOH HOH . J 6 HOH B 11 361 24 HOH HOH . J 6 HOH B 12 362 26 HOH HOH . J 6 HOH B 13 363 28 HOH HOH . J 6 HOH B 14 364 34 HOH HOH . J 6 HOH B 15 365 35 HOH HOH . J 6 HOH B 16 366 36 HOH HOH . J 6 HOH B 17 367 37 HOH HOH . J 6 HOH B 18 368 39 HOH HOH . J 6 HOH B 19 369 41 HOH HOH . J 6 HOH B 20 370 42 HOH HOH . J 6 HOH B 21 371 43 HOH HOH . J 6 HOH B 22 372 44 HOH HOH . J 6 HOH B 23 373 47 HOH HOH . J 6 HOH B 24 374 51 HOH HOH . J 6 HOH B 25 375 53 HOH HOH . K 6 HOH S 1 23 23 HOH HOH . K 6 HOH S 2 29 29 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 P P1 A3P . . . E 3 -47.174 -13.741 -12.247 1 25.41 ? P1 A3P 1 A 1 HETATM 2 O O1P A3P . . . E 3 -47.401 -13.179 -10.892 1 29.82 ? O1P A3P 1 A 1 HETATM 3 O O2P A3P . . . E 3 -48.494 -14.282 -12.725 1 26.27 ? O2P A3P 1 A 1 HETATM 4 O O3P A3P . . . E 3 -46.466 -12.851 -13.221 1 24.52 ? O3P A3P 1 A 1 HETATM 5 P P2 A3P . . . E 3 -43.107 -17.359 -7.272 1 23.66 ? P2 A3P 1 A 1 HETATM 6 O O4P A3P . . . E 3 -43.635 -16.073 -6.698 1 28.23 ? O4P A3P 1 A 1 HETATM 7 O O5P A3P . . . E 3 -41.612 -17.527 -7.291 1 24.64 ? O5P A3P 1 A 1 HETATM 8 O O6P A3P . . . E 3 -43.948 -18.483 -6.753 1 23.09 ? O6P A3P 1 A 1 HETATM 9 O O5' A3P . . . E 3 -43.448 -17.138 -8.828 1 22.56 ? O5' A3P 1 A 1 HETATM 10 C C5' A3P . . . E 3 -44.774 -16.644 -9.108 1 23.83 ? C5' A3P 1 A 1 HETATM 11 C C4' A3P . . . E 3 -44.971 -16.688 -10.609 1 26.4 ? C4' A3P 1 A 1 HETATM 12 O O4' A3P . . . E 3 -45.008 -18.074 -11 1 27.06 ? O4' A3P 1 A 1 HETATM 13 C C3' A3P . . . E 3 -46.255 -15.989 -11.052 1 26.6 ? C3' A3P 1 A 1 HETATM 14 O O3' A3P . . . E 3 -46.085 -14.969 -12.051 1 26.86 ? O3' A3P 1 A 1 HETATM 15 C C2' A3P . . . E 3 -47.027 -17.162 -11.597 1 27.68 ? C2' A3P 1 A 1 HETATM 16 O O2' A3P . . . E 3 -47.954 -16.796 -12.619 1 29.6 ? O2' A3P 1 A 1 HETATM 17 C C1' A3P . . . E 3 -45.971 -18.202 -12.026 1 27.87 ? C1' A3P 1 A 1 HETATM 18 N N9 A3P . . . E 3 -46.75 -19.467 -12.1 1 28.49 ? N9 A3P 1 A 1 HETATM 19 C C8 A3P . . . E 3 -47.366 -20.089 -11.076 1 27 ? C8 A3P 1 A 1 HETATM 20 N N7 A3P . . . E 3 -48.07 -21.148 -11.515 1 28.28 ? N7 A3P 1 A 1 HETATM 21 C C5 A3P . . . E 3 -47.915 -21.204 -12.851 1 27.14 ? C5 A3P 1 A 1 HETATM 22 C C6 A3P . . . E 3 -48.393 -22.085 -13.907 1 27.34 ? C6 A3P 1 A 1 HETATM 23 N N6 A3P . . . E 3 -49.199 -23.127 -13.571 1 30.17 ? N6 A3P 1 A 1 HETATM 24 N N1 A3P . . . E 3 -48.012 -21.823 -15.181 1 28.19 ? N1 A3P 1 A 1 HETATM 25 C C2 A3P . . . E 3 -47.217 -20.763 -15.499 1 29.02 ? C2 A3P 1 A 1 HETATM 26 N N3 A3P . . . E 3 -46.743 -19.898 -14.58 1 27.75 ? N3 A3P 1 A 1 HETATM 27 C C4 A3P . . . E 3 -47.058 -20.086 -13.254 1 28.6 ? C4 A3P 1 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #