data_1DFL # _model_server_result.job_id oYYQdXUFqyvSuoy8ncGhPA _model_server_result.datetime_utc '2024-10-18 14:29:58' _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 1dfl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":2999}' # _entry.id 1DFL # _exptl.entry_id 1DFL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 100.2 _cell.angle_gamma 90 _cell.entry_id 1DFL _cell.length_a 53.032 _cell.length_b 243.475 _cell.length_c 124.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DFL _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 ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_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,G,H,I,J,K 1 1 D,E,F,L,M,N,O,P 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 ? 6 I N N ? 6 N 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 G MG MG . A MG 1997 1_555 H O1 VO4 . A VO4 1998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc2 G MG MG . A MG 1997 1_555 I O1B ADP . A ADP 1999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc3 H V VO4 . A VO4 1998 1_555 I O3B ADP . A ADP 1999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc4 B O PHE 23 Y PHE 34 1_555 J MG MG . Y MG 1996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc5 C O ASP 17 Z ASP 19 1_555 K CA CA . Z CA 1995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc6 C O ASP 20 Z ASP 22 1_555 K CA CA . Z CA 1995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.378 ? metalc ? metalc7 C O GLY 21 Z GLY 23 1_555 K CA CA . Z CA 1995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc8 C O ALA 25 Z ALA 27 1_555 K CA CA . Z CA 1995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc9 L MG MG . B MG 2997 1_555 M O1 VO4 . B VO4 2998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc10 L MG MG . B MG 2997 1_555 N O1B ADP . B ADP 2999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc11 M V VO4 . B VO4 2998 1_555 N O3B ADP . B ADP 2999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc12 E O PHE 23 W PHE 34 1_555 O MG MG . W MG 2996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc13 F O ASP 17 X ASP 19 1_555 P CA CA . X CA 2995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc14 F O ASP 20 X ASP 22 1_555 P CA CA . X CA 2995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.38 ? metalc ? metalc15 F O GLY 21 X GLY 23 1_555 P CA CA . X CA 2995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc16 F O ALA 25 X ALA 27 1_555 P CA CA . X CA 2995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1DFL _atom_sites.fract_transf_matrix[1][1] 0.018857 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003392 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004107 _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] 0.008151 _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 G 4 MG A 1 1997 1997 MG MG . H 5 VO4 A 1 1998 1998 VO4 VO4 . I 6 ADP A 1 1999 1999 ADP ADP . J 4 MG Y 1 1996 1996 MG MG . K 7 CA Z 1 1995 1995 CA CA . L 4 MG B 1 2997 2997 MG MG . M 5 VO4 B 1 2998 2998 VO4 VO4 . N 6 ADP B 1 2999 2999 ADP ADP . O 4 MG W 1 2996 2996 MG MG . P 7 CA X 1 2995 2995 CA CA . # 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 PB ADP . . . N 6 19.192 12.951 112.192 1 30 ? PB ADP 2999 B 1 HETATM 2 O O1B ADP . . . N 6 19.046 13.132 113.654 1 30 ? O1B ADP 2999 B 1 HETATM 3 O O2B ADP . . . N 6 19.939 11.7 111.854 1 30 ? O2B ADP 2999 B 1 HETATM 4 O O3B ADP . . . N 6 19.656 14.126 111.427 1 30 ? O3B ADP 2999 B 1 HETATM 5 P PA ADP . . . N 6 16.286 12.648 112.433 1 30 ? PA ADP 2999 B 1 HETATM 6 O O1A ADP . . . N 6 16.335 11.627 113.471 1 30 ? O1A ADP 2999 B 1 HETATM 7 O O2A ADP . . . N 6 15.902 14 112.987 1 30 ? O2A ADP 2999 B 1 HETATM 8 O O3A ADP . . . N 6 17.672 12.732 111.641 1 30 ? O3A ADP 2999 B 1 HETATM 9 O O5' ADP . . . N 6 15.22 12.235 111.3 1 30 ? O5' ADP 2999 B 1 HETATM 10 C C5' ADP . . . N 6 14.891 13.184 110.282 1 30 ? C5' ADP 2999 B 1 HETATM 11 C C4' ADP . . . N 6 13.405 12.975 110 1 30 ? C4' ADP 2999 B 1 HETATM 12 O O4' ADP . . . N 6 13.236 11.617 109.451 1 30 ? O4' ADP 2999 B 1 HETATM 13 C C3' ADP . . . N 6 12.573 12.991 111.284 1 30 ? C3' ADP 2999 B 1 HETATM 14 O O3' ADP . . . N 6 12.222 14.333 111.662 1 30 ? O3' ADP 2999 B 1 HETATM 15 C C2' ADP . . . N 6 11.375 12.163 110.789 1 30 ? C2' ADP 2999 B 1 HETATM 16 O O2' ADP . . . N 6 10.558 12.986 109.913 1 30 ? O2' ADP 2999 B 1 HETATM 17 C C1' ADP . . . N 6 12.05 11.092 109.944 1 30 ? C1' ADP 2999 B 1 HETATM 18 N N9 ADP . . . N 6 12.346 9.898 110.697 1 30 ? N9 ADP 2999 B 1 HETATM 19 C C8 ADP . . . N 6 13.549 9.375 111.046 1 30 ? C8 ADP 2999 B 1 HETATM 20 N N7 ADP . . . N 6 13.472 8.166 111.609 1 30 ? N7 ADP 2999 B 1 HETATM 21 C C5 ADP . . . N 6 12.103 7.943 111.63 1 30 ? C5 ADP 2999 B 1 HETATM 22 C C6 ADP . . . N 6 11.35 6.843 112.091 1 30 ? C6 ADP 2999 B 1 HETATM 23 N N6 ADP . . . N 6 11.863 5.748 112.651 1 30 ? N6 ADP 2999 B 1 HETATM 24 N N1 ADP . . . N 6 9.996 6.978 112.021 1 30 ? N1 ADP 2999 B 1 HETATM 25 C C2 ADP . . . N 6 9.428 8.089 111.454 1 30 ? C2 ADP 2999 B 1 HETATM 26 N N3 ADP . . . N 6 10.039 9.132 110.962 1 30 ? N3 ADP 2999 B 1 HETATM 27 C C4 ADP . . . N 6 11.389 9.017 111.129 1 30 ? C4 ADP 2999 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #