data_3AP3 # _model_server_result.job_id DQd2AxWLFuGGMyeLINfFZA _model_server_result.datetime_utc '2024-11-26 23:11:49' _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 3ap3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1}' # _entry.id 3AP3 # _exptl.entry_id 3AP3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 3AP3 _cell.length_a 71.432 _cell.length_b 81.326 _cell.length_c 226.659 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AP3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # 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 PISA dimeric 2 author_and_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,E,F 1 1 C,D,G,H 2 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 A SG CYS 203 A CYS 225 1_555 A SG CYS 211 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 B SG CYS 74 B CYS 96 1_555 B SG CYS 134 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf4 B SG CYS 203 B CYS 225 1_555 B SG CYS 211 B CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 C SG CYS 74 C CYS 96 1_555 C SG CYS 134 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 C SG CYS 203 C CYS 225 1_555 C SG CYS 211 C CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 D SG CYS 74 D CYS 96 1_555 D SG CYS 134 D CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf8 D SG CYS 203 D CYS 225 1_555 D SG CYS 211 D CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _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 3AP3 _atom_sites.fract_transf_matrix[1][1] 0.013999 _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] 0.012296 _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] 0.004412 _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 2 A3P A 1 1 1 A3P A3P . F 2 A3P B 1 1 1 A3P A3P . G 2 A3P C 1 1 1 A3P A3P . H 2 A3P D 1 1 1 A3P A3P . # 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 2 -10.931 -7.212 13.571 1 56.35 ? P1 A3P 1 A 1 HETATM 2 O O1P A3P . . . E 2 -10.976 -6.526 12.218 1 54.53 ? O1P A3P 1 A 1 HETATM 3 O O2P A3P . . . E 2 -10.028 -6.588 14.633 1 54.96 ? O2P A3P 1 A 1 HETATM 4 O O3P A3P . . . E 2 -12.284 -7.545 14.182 1 55.72 ? O3P A3P 1 A 1 HETATM 5 P P2 A3P . . . E 2 -7.907 -11.7 8.766 1 53.9 ? P2 A3P 1 A 1 HETATM 6 O O4P A3P . . . E 2 -8.282 -10.556 7.819 1 52.38 ? O4P A3P 1 A 1 HETATM 7 O O5P A3P . . . E 2 -8.543 -13.001 8.327 1 53.96 ? O5P A3P 1 A 1 HETATM 8 O O6P A3P . . . E 2 -6.495 -11.8 9.341 1 54.79 ? O6P A3P 1 A 1 HETATM 9 O O5' A3P . . . E 2 -8.574 -11.362 10.176 1 52.47 ? O5' A3P 1 A 1 HETATM 10 C C5' A3P . . . E 2 -8.836 -10.016 10.514 1 52.09 ? C5' A3P 1 A 1 HETATM 11 C C4' A3P . . . E 2 -8.599 -9.918 12.001 1 52.32 ? C4' A3P 1 A 1 HETATM 12 O O4' A3P . . . E 2 -7.207 -10.064 12.293 1 51.45 ? O4' A3P 1 A 1 HETATM 13 C C3' A3P . . . E 2 -8.965 -8.55 12.548 1 51.79 ? C3' A3P 1 A 1 HETATM 14 O O3' A3P . . . E 2 -10.238 -8.615 13.17 1 53.63 ? O3' A3P 1 A 1 HETATM 15 C C2' A3P . . . E 2 -7.854 -8.241 13.541 1 49.97 ? C2' A3P 1 A 1 HETATM 16 O O2' A3P . . . E 2 -8.319 -7.882 14.834 1 46.43 ? O2' A3P 1 A 1 HETATM 17 C C1' A3P . . . E 2 -7.194 -9.584 13.635 1 51.07 ? C1' A3P 1 A 1 HETATM 18 N N9 A3P . . . E 2 -5.826 -9.474 14.162 1 53.34 ? N9 A3P 1 A 1 HETATM 19 C C8 A3P . . . E 2 -4.712 -9.2 13.448 1 54.26 ? C8 A3P 1 A 1 HETATM 20 N N7 A3P . . . E 2 -3.607 -9.2 14.245 1 53.97 ? N7 A3P 1 A 1 HETATM 21 C C5 A3P . . . E 2 -4.031 -9.478 15.478 1 53.61 ? C5 A3P 1 A 1 HETATM 22 C C6 A3P . . . E 2 -3.383 -9.615 16.778 1 54.78 ? C6 A3P 1 A 1 HETATM 23 N N6 A3P . . . E 2 -2.034 -9.448 16.852 1 54.58 ? N6 A3P 1 A 1 HETATM 24 N N1 A3P . . . E 2 -4.189 -9.915 17.848 1 56.36 ? N1 A3P 1 A 1 HETATM 25 C C2 A3P . . . E 2 -5.536 -10.077 17.754 1 54.97 ? C2 A3P 1 A 1 HETATM 26 N N3 A3P . . . E 2 -6.18 -9.956 16.58 1 54.19 ? N3 A3P 1 A 1 HETATM 27 C C4 A3P . . . E 2 -5.491 -9.668 15.44 1 53.69 ? C4 A3P 1 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #