data_5LIH # _model_server_result.job_id khkHSb3OzafvjxTZcQ_h0A _model_server_result.datetime_utc '2025-01-02 21:12:44' _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 5lih # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 5LIH # _exptl.entry_id 5LIH _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 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 90 _cell.entry_id 5LIH _cell.length_a 78.98 _cell.length_b 84.23 _cell.length_c 111.83 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LIH _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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 software_defined_assembly 1 PISA dimeric 2 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,C,E,F,G,H,I,J,K,R,T 1 1 B,D,L,M,N,O,P,Q,S 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 ? 3 E N N ? 3 L 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 covale ? covale1 A C SER 164 A SER 411 1_555 A N TPO 165 A TPO 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C TPO 165 A TPO 412 1_555 A N PHE 166 A PHE 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C LEU 316 A LEU 563 1_555 A N TPO 317 A TPO 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C TPO 317 A TPO 564 1_555 A N PRO 318 A PRO 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale5 B C SER 164 B SER 411 1_555 B N TPO 165 B TPO 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 B C TPO 165 B TPO 412 1_555 B N PHE 166 B PHE 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 B C LEU 316 B LEU 563 1_555 B N TPO 317 B TPO 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 B C TPO 317 B TPO 564 1_555 B N PRO 318 B PRO 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? metalc ? metalc1 A NE2 HIS 107 A HIS 354 1_555 K MN MN . A MN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc2 A OD1 ASN 136 A ASN 383 1_555 G MN MN . A MN 603 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc3 A OD1 ASN 136 A ASN 383 1_555 G MN MN . A MN 603 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc4 A OD1 ASP 149 A ASP 396 1_555 H MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc5 A OD2 ASP 149 A ASP 396 1_555 H MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc6 E O1A ADP . A ADP 601 1_555 G MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? metalc ? metalc7 E O2B ADP . A ADP 601 1_555 H MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc8 G MN MN . A MN 603 1_555 I F1 AF3 . A AF3 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc9 H MN MN . A MN 604 1_555 I F3 AF3 . A AF3 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc10 B OD1 ASN 136 B ASN 383 1_555 N MN MN . B MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc11 B OD2 ASP 149 B ASP 396 1_555 N MN MN . B MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc12 B OD1 ASP 149 B ASP 396 1_555 O MN MN . B MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc13 B OD2 ASP 149 B ASP 396 1_555 O MN MN . B MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc14 L O1A ADP . B ADP 601 1_555 N MN MN . B MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc15 L O3B ADP . B ADP 601 1_555 O MN MN . B MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc16 N MN MN . B MN 603 1_555 P F1 AF3 . B AF3 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc17 O MN MN . B MN 604 1_555 P F3 AF3 . B AF3 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc18 O MN MN . B MN 604 1_555 S O HOH . B HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? # _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 5LIH _atom_sites.fract_transf_matrix[1][1] 0.012661 _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] 0.011872 _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] 0.008942 _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 ADP A 1 601 2 ADP ADP . F 4 AF3 A 1 602 2 AF3 AF3 . G 5 MN A 1 603 1 MN MN . H 5 MN A 1 604 2 MN MN . I 4 AF3 A 1 605 3 AF3 AF3 . J 6 SCN A 1 606 2 SCN SCN . K 5 MN A 1 607 1 MN MN . L 3 ADP B 1 601 1 ADP ADP . M 4 AF3 B 1 602 1 AF3 AF3 . N 5 MN B 1 603 1 MN MN . O 5 MN B 1 604 2 MN MN . P 4 AF3 B 1 605 3 AF3 AF3 . Q 6 SCN B 1 606 3 SCN SCN . R 7 HOH A 1 701 1 HOH HOH . R 7 HOH A 2 702 20 HOH HOH . R 7 HOH A 3 703 16 HOH HOH . R 7 HOH A 4 704 14 HOH HOH . R 7 HOH A 5 705 24 HOH HOH . R 7 HOH A 6 706 19 HOH HOH . R 7 HOH A 7 707 18 HOH HOH . R 7 HOH A 8 708 15 HOH HOH . R 7 HOH A 9 709 6 HOH HOH . R 7 HOH A 10 710 22 HOH HOH . R 7 HOH A 11 711 35 HOH HOH . R 7 HOH A 12 712 5 HOH HOH . R 7 HOH A 13 713 2 HOH HOH . S 7 HOH B 1 701 21 HOH HOH . S 7 HOH B 2 702 9 HOH HOH . S 7 HOH B 3 703 10 HOH HOH . S 7 HOH B 4 704 26 HOH HOH . S 7 HOH B 5 705 31 HOH HOH . S 7 HOH B 6 706 12 HOH HOH . S 7 HOH B 7 707 34 HOH HOH . S 7 HOH B 8 708 11 HOH HOH . S 7 HOH B 9 709 23 HOH HOH . S 7 HOH B 10 710 25 HOH HOH . T 7 HOH F 1 101 3 HOH HOH . T 7 HOH F 2 102 33 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 . . . E 3 39.364 13.601 38.753 1 44.97 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . E 3 38.367 13.989 37.69 1 40.76 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . E 3 40.731 14.212 38.567 1 43.8 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . E 3 39.39 12.123 39.06 1 58.64 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . E 3 38.152 15.731 40.246 1 33.87 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . E 3 37.892 16.302 38.874 1 33.52 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . E 3 38.972 16.523 41.237 1 34.31 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . E 3 38.836 14.271 40.125 1 36.36 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . E 3 36.734 15.42 40.942 1 31.45 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . E 3 35.639 14.938 40.169 1 36.24 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . E 3 34.36 15.63 40.624 1 31.34 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . E 3 34.399 15.893 42.029 1 29.1 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . E 3 34.157 16.969 39.936 1 29.97 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . E 3 33.247 16.847 38.841 1 28.75 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . E 3 33.577 17.873 41.003 1 36.96 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . E 3 32.178 18.047 40.772 1 26.09 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . E 3 33.783 17.149 42.324 1 33.17 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . E 3 34.679 17.96 43.188 1 37.25 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . E 3 36.026 17.915 43.182 1 46.4 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . E 3 36.552 18.78 44.086 1 28.59 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . E 3 35.523 19.401 44.692 1 27.51 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . E 3 35.372 20.431 45.746 1 27.85 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . E 3 36.455 20.982 46.344 1 29.37 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . E 3 34.119 20.803 46.088 1 27.17 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . E 3 33.035 20.261 45.499 1 26.12 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . E 3 33.097 19.321 44.536 1 25.67 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . E 3 34.292 18.858 44.096 1 26.36 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #