data_4JAS # _model_server_result.job_id 1gb5ZOmYjeKTY65lRlYzZw _model_server_result.datetime_utc '2024-11-27 19:56:27' _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 4jas # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4JAS # _exptl.entry_id 4JAS _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-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 4JAS _cell.length_a 75.71 _cell.length_b 85.309 _cell.length_c 185.595 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JAS _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_465 -x-1,-y+1,z -1 0 0 0 -1 0 0 0 1 -75.71 85.309 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 99 A CYS 330 1_555 A SG CYS 128 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 B C LEU 52 B LEU 52 1_555 B N BFD 53 B BFD 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 B C BFD 53 B BFD 53 1_555 B N ILE 54 B ILE 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A OD1 ASN 149 A ASN 380 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc2 C O1A ADP . A ADP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc3 C O3B ADP . A ADP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc4 B OD1 ASP 10 B ASP 10 1_555 E MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc5 B OD2 BFD 53 B BFD 53 1_555 E MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc6 B O MET 55 B MET 55 1_555 E MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc7 E MG MG . B MG 201 1_555 G O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc8 E MG MG . B MG 201 1_555 G O HOH . B HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? # _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 4JAS _atom_sites.fract_transf_matrix[1][1] 0.013208 _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] 0.011722 _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] 0.005388 _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 3 ADP A 1 501 500 ADP ADP . D 4 MG A 1 502 2 MG MG . E 4 MG B 1 201 1 MG MG . F 5 HOH A 1 601 3 HOH HOH . F 5 HOH A 2 602 4 HOH HOH . F 5 HOH A 3 603 6 HOH HOH . F 5 HOH A 4 604 10 HOH HOH . F 5 HOH A 5 605 11 HOH HOH . F 5 HOH A 6 606 12 HOH HOH . F 5 HOH A 7 607 13 HOH HOH . G 5 HOH B 1 301 1 HOH HOH . G 5 HOH B 2 302 2 HOH HOH . G 5 HOH B 3 303 5 HOH HOH . G 5 HOH B 4 304 7 HOH HOH . G 5 HOH B 5 305 8 HOH HOH . G 5 HOH B 6 306 9 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 PB ADP . . . C 3 -24.76 36.29 41.689 1 55.12 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . C 3 -26.012 36.308 40.832 1 54 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . C 3 -24.301 37.635 42.196 1 52.44 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . C 3 -23.646 35.452 41.11 1 56.05 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . C 3 -24.981 33.975 43.378 1 52.07 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . C 3 -24.597 33.202 42.137 1 51.1 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . C 3 -26.161 33.508 44.195 1 53.52 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . C 3 -25.213 35.541 43.045 1 53.89 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . C 3 -23.733 34.062 44.385 1 53.14 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . C 3 -23.854 34.857 45.562 1 54.79 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . C 3 -22.592 35.678 45.802 1 57.19 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . C 3 -21.541 34.825 46.256 1 59 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . C 3 -22.031 36.374 44.569 1 57.2 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . C 3 -22.576 37.68 44.379 1 56.92 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . C 3 -20.548 36.456 44.854 1 57.86 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . C 3 -20.254 37.645 45.592 1 57.36 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . C 3 -20.277 35.251 45.734 1 58.31 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . C 3 -19.679 34.149 44.941 1 57.39 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . C 3 -20.357 33.131 44.381 1 56.72 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . C 3 -19.524 32.282 43.732 1 58.07 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . C 3 -18.273 32.758 43.875 1 58.02 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . C 3 -16.916 32.352 43.433 1 56.54 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . C 3 -16.734 31.235 42.691 1 55.44 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . C 3 -15.872 33.138 43.796 1 57.18 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . C 3 -16.038 34.257 44.534 1 56.78 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . C 3 -17.24 34.688 44.965 1 58.32 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . C 3 -18.377 33.994 44.674 1 58.72 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #