data_3DD5 # _model_server_result.job_id C0HECa2JKwd1mzPBTeG7Gg _model_server_result.datetime_utc '2024-11-15 01:20:12' _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 3dd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":407}' # _entry.id 3DD5 # _exptl.entry_id 3DD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 138.102 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIETHYL PHOSPHONATE' _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.57 _cell.angle_gamma 90 _cell.entry_id 3DD5 _cell.length_a 73.47 _cell.length_b 117.37 _cell.length_c 95.24 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 ? monomeric 1 author_defined_assembly 6 ? monomeric 1 author_defined_assembly 7 ? monomeric 1 author_defined_assembly 8 PISA tetrameric 4 software_defined_assembly 9 PISA tetrameric 4 software_defined_assembly 10 PISA dimeric 2 software_defined_assembly 11 PISA dimeric 2 software_defined_assembly 12 PISA dimeric 2 software_defined_assembly 13 PISA dimeric 2 software_defined_assembly 14 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,I,Q 1 1 B,J 2 1 C,K,R 3 1 D,L,S 4 1 E,M 5 1 F,N 6 1 G,O 7 1 H,P,T 8 1 B,J 9 2 C,K,R 9 3 A,F,I,N,Q 9 1 D,L,S 10 1 G,O 10 4 E,M 10 5 H,P,T 10 6 A,I,Q 11 1 B,J 11 2 C,K,R 12 1 F,N 12 7 D,L,S 13 1 E,M 13 5 G,O 14 1 H,P,T 14 2 # 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_546 -x,y-1/2,-z+1 -1 0 0 0 1 0 0 0 -1 -22.346462 -58.685 92.581279 3 'crystal symmetry operation' 2_646 -x+1,y-1/2,-z+1 -1 0 0 0 1 0 0 0 -1 51.123538 -58.685 92.581279 4 'crystal symmetry operation' 1_454 x-1,y,z-1 1 0 0 0 1 0 0 0 1 -51.123538 0 -92.581279 5 'crystal symmetry operation' 2_545 -x,y-1/2,-z -1 0 0 0 1 0 0 0 -1 0 -58.685 0 6 'crystal symmetry operation' 2_445 -x-1,y-1/2,-z -1 0 0 0 1 0 0 0 -1 -73.47 -58.685 0 7 'crystal symmetry operation' 2_656 -x+1,y+1/2,-z+1 -1 0 0 0 1 0 0 0 -1 51.123538 58.685 92.581279 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P 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 23 A CYS 46 1_555 A SG CYS 102 A CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 164 A CYS 187 1_555 A SG CYS 171 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? disulf ? disulf3 B SG CYS 23 B CYS 46 1_555 B SG CYS 102 B CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf4 B SG CYS 164 B CYS 187 1_555 B SG CYS 171 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? disulf ? disulf5 C SG CYS 23 C CYS 46 1_555 C SG CYS 102 C CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf6 C SG CYS 164 C CYS 187 1_555 C SG CYS 171 C CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? disulf ? disulf7 D SG CYS 23 D CYS 46 1_555 D SG CYS 102 D CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf8 D SG CYS 164 D CYS 187 1_555 D SG CYS 171 D CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? disulf ? disulf9 E SG CYS 23 E CYS 46 1_555 E SG CYS 102 E CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf10 E SG CYS 164 E CYS 187 1_555 E SG CYS 171 E CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? disulf ? disulf11 F SG CYS 23 F CYS 46 1_555 F SG CYS 102 F CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? disulf ? disulf12 F SG CYS 164 F CYS 187 1_555 F SG CYS 171 F CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? disulf ? disulf13 G SG CYS 23 G CYS 46 1_555 G SG CYS 102 G CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf14 G SG CYS 164 G CYS 187 1_555 G SG CYS 171 G CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? disulf ? disulf15 H SG CYS 23 H CYS 46 1_555 H SG CYS 102 H CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf16 H SG CYS 164 H CYS 187 1_555 H SG CYS 171 H CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? covale ? covale1 A OG SER 113 A SER 136 1_555 I P DEP . A DEP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? covale ? covale2 B OG SER 113 B SER 136 1_555 J P DEP . B DEP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? covale ? covale3 C OG SER 113 C SER 136 1_555 K P DEP . C DEP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? covale ? covale4 D OG SER 113 D SER 136 1_555 L P DEP . D DEP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? covale ? covale5 E OG SER 113 E SER 136 1_555 M P DEP . E DEP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? covale ? covale6 F OG SER 113 F SER 136 1_555 N P DEP . F DEP 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.744 ? covale ? covale7 G OG SER 113 G SER 136 1_555 O P DEP . G DEP 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? covale ? covale8 H OG SER 113 H SER 136 1_555 P P DEP . H DEP 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.731 ? # _chem_comp.formula 'C4 H11 O3 P' _chem_comp.formula_weight 138.102 _chem_comp.id DEP _chem_comp.mon_nstd_flag . _chem_comp.name 'DIETHYL PHOSPHONATE' _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 C1 C2 DEP sing 83 n n C1 O1 DEP sing 84 n n C1 H11 DEP sing 85 n n C1 H12 DEP sing 86 n n C2 H21 DEP sing 87 n n C2 H22 DEP sing 88 n n C2 H23 DEP sing 89 n n C3 C4 DEP sing 90 n n C3 O2 DEP sing 91 n n C3 H31 DEP sing 92 n n C3 H32 DEP sing 93 n n C4 H41 DEP sing 94 n n C4 H42 DEP sing 95 n n C4 H43 DEP sing 96 n n O1 P DEP sing 97 n n O2 P DEP sing 98 n n O3 P DEP doub 99 n n HP1 P DEP sing 100 n n # _atom_sites.entry_id 3DD5 _atom_sites.fract_transf_matrix[1][1] 0.01361 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003286 _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] 0.010801 _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 I 2 DEP A 1 401 401 DEP DEP . J 2 DEP B 1 402 402 DEP DEP . K 2 DEP C 1 403 403 DEP DEP . L 2 DEP D 1 404 404 DEP DEP . M 2 DEP E 1 405 405 DEP DEP . N 2 DEP F 1 406 406 DEP DEP . O 2 DEP G 1 407 407 DEP DEP . P 2 DEP H 1 408 408 DEP DEP . Q 3 HOH A 1 2 2 HOH HOH . R 3 HOH C 1 3 3 HOH HOH . S 3 HOH D 1 4 4 HOH HOH . T 3 HOH H 1 1 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 C C1 DEP . . . O 2 -0.964 -34.246 84.2 1 20.31 ? C1 DEP 407 G 1 HETATM 2 C C2 DEP . . . O 2 0.183 -34.283 85.195 1 20.31 ? C2 DEP 407 G 1 HETATM 3 C C3 DEP . . . O 2 -1.103 -35.136 80.126 1 20.31 ? C3 DEP 407 G 1 HETATM 4 C C4 DEP . . . O 2 -2.497 -34.981 79.577 1 20.31 ? C4 DEP 407 G 1 HETATM 5 O O1 DEP . . . O 2 -0.89 -33.075 83.396 1 20.31 ? O1 DEP 407 G 1 HETATM 6 O O2 DEP . . . O 2 -1.141 -34.701 81.477 1 20.31 ? O2 DEP 407 G 1 HETATM 7 O O3 DEP . . . O 2 0.586 -32.771 81.281 1 20.31 ? O3 DEP 407 G 1 HETATM 8 P P DEP . . . O 2 -0.852 -33.158 81.793 1 20.31 ? P DEP 407 G 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 8 #