data_5L4G # _model_server_result.job_id JpUwgPUGYI51sEDJsVxGmg _model_server_result.datetime_utc '2024-10-18 16:26:09' _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 5l4g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"SA","auth_seq_id":501}' # _entry.id 5L4G # _exptl.entry_id 5L4G _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 23 _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 5L4G _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L4G _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 34-meric _pdbx_struct_assembly.oligomeric_count 34 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 23 _struct_asym.id SA _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 metalc ? metalc1 CA OG1 THR 223 H THR 223 1_555 JA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc2 IA O2G ATP . H ATP 501 1_555 JA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.788 ? metalc ? metalc3 IA O1B ATP . H ATP 501 1_555 JA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc4 DA OG1 THR 233 I THR 233 1_555 LA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc5 KA O1G ATP . I ATP 501 1_555 LA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc6 KA O2B ATP . I ATP 501 1_555 LA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc7 EA OG1 THR 213 K THR 213 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc8 MA O2G ATP . K ATP 501 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc9 MA O2B ATP . K ATP 501 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc10 FA OG1 THR 181 L THR 181 1_555 PA MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc11 OA O2G ATP . L ATP 401 1_555 PA MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc12 OA O2B ATP . L ATP 401 1_555 PA MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc13 GA OG1 THR 234 M THR 234 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc14 QA O2G ATP . M ATP 501 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc15 QA O2B ATP . M ATP 501 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc16 QA O3B ATP . M ATP 501 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? # _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 5L4G _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 IA 21 ATP H 1 501 439 ATP ATP . JA 22 MG H 1 502 601 MG MG . KA 21 ATP I 1 501 439 ATP ATP . LA 22 MG I 1 502 601 MG MG . MA 21 ATP K 1 501 439 ATP ATP . NA 22 MG K 1 502 601 MG MG . OA 21 ATP L 1 401 439 ATP ATP . PA 22 MG L 1 402 601 MG MG . QA 21 ATP M 1 501 439 ATP ATP . RA 22 MG M 1 502 601 MG MG . SA 23 ADP J 1 501 439 ADP ADP . # 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 . . . SA 23 165.207 304.03 251.47 1 123.92 ? PB ADP 501 J 1 HETATM 2 O O1B ADP . . . SA 23 165.635 304.129 250.016 1 84.86 ? O1B ADP 501 J 1 HETATM 3 O O2B ADP . . . SA 23 164.369 302.816 251.841 1 74.12 ? O2B ADP 501 J 1 HETATM 4 O O3B ADP . . . SA 23 166.359 304.266 252.423 1 135.02 ? O3B ADP 501 J 1 HETATM 5 P PA ADP . . . SA 23 163.807 306.427 250.631 1 136.15 ? PA ADP 501 J 1 HETATM 6 O O1A ADP . . . SA 23 164.774 306.31 249.462 1 92.94 ? O1A ADP 501 J 1 HETATM 7 O O2A ADP . . . SA 23 162.3 306.36 250.438 1 109.76 ? O2A ADP 501 J 1 HETATM 8 O O3A ADP . . . SA 23 164.224 305.307 251.734 1 117.75 ? O3A ADP 501 J 1 HETATM 9 O O5' ADP . . . SA 23 164.115 307.793 251.423 1 101.72 ? O5' ADP 501 J 1 HETATM 10 C C5' ADP . . . SA 23 163.678 308.016 252.763 1 110.9 ? C5' ADP 501 J 1 HETATM 11 C C4' ADP . . . SA 23 163.22 309.463 252.844 1 115.29 ? C4' ADP 501 J 1 HETATM 12 O O4' ADP . . . SA 23 164.281 310.406 252.611 1 121.21 ? O4' ADP 501 J 1 HETATM 13 C C3' ADP . . . SA 23 162.204 309.777 251.766 1 118.31 ? C3' ADP 501 J 1 HETATM 14 O O3' ADP . . . SA 23 160.905 309.28 252.112 1 128.23 ? O3' ADP 501 J 1 HETATM 15 C C2' ADP . . . SA 23 162.314 311.287 251.677 1 118.24 ? C2' ADP 501 J 1 HETATM 16 O O2' ADP . . . SA 23 161.596 311.95 252.725 1 125.64 ? O2' ADP 501 J 1 HETATM 17 C C1' ADP . . . SA 23 163.804 311.55 251.876 1 109.4 ? C1' ADP 501 J 1 HETATM 18 N N9 ADP . . . SA 23 164.514 311.672 250.568 1 68.27 ? N9 ADP 501 J 1 HETATM 19 C C8 ADP . . . SA 23 165.566 310.93 250.168 1 71.84 ? C8 ADP 501 J 1 HETATM 20 N N7 ADP . . . SA 23 165.987 311.286 248.926 1 64.3 ? N7 ADP 501 J 1 HETATM 21 C C5 ADP . . . SA 23 165.191 312.276 248.513 1 65.14 ? C5 ADP 501 J 1 HETATM 22 C C6 ADP . . . SA 23 165.072 313.104 247.301 1 75.02 ? C6 ADP 501 J 1 HETATM 23 N N6 ADP . . . SA 23 165.907 312.947 246.25 1 67.49 ? N6 ADP 501 J 1 HETATM 24 N N1 ADP . . . SA 23 164.099 314.026 247.276 1 89.36 ? N1 ADP 501 J 1 HETATM 25 C C2 ADP . . . SA 23 163.255 314.208 248.309 1 91.44 ? C2 ADP 501 J 1 HETATM 26 N N3 ADP . . . SA 23 163.306 313.487 249.44 1 65.94 ? N3 ADP 501 J 1 HETATM 27 C C4 ADP . . . SA 23 164.233 312.529 249.596 1 65.16 ? C4 ADP 501 J 1 HETATM 28 H "H5'1" ADP . . . SA 23 164.406 307.858 253.385 1 109.74 ? "H5'1" ADP 501 J 1 HETATM 29 H "H5'2" ADP . . . SA 23 162.946 307.419 252.982 1 109.74 ? "H5'2" ADP 501 J 1 HETATM 30 H H4' ADP . . . SA 23 162.818 309.62 253.712 1 113.13 ? H4' ADP 501 J 1 HETATM 31 H H3' ADP . . . SA 23 162.501 309.388 250.928 1 115.6 ? H3' ADP 501 J 1 HETATM 32 H HO3' ADP . . . SA 23 160.321 309.685 251.664 1 125.8 ? HO3' ADP 501 J 1 HETATM 33 H H2' ADP . . . SA 23 162.033 311.595 250.801 1 114.5 ? H2' ADP 501 J 1 HETATM 34 H HO2' ADP . . . SA 23 160.968 311.458 252.99 1 121.62 ? HO2' ADP 501 J 1 HETATM 35 H H1' ADP . . . SA 23 163.918 312.359 252.399 1 105.67 ? H1' ADP 501 J 1 HETATM 36 H H8 ADP . . . SA 23 165.973 310.23 250.702 1 68.32 ? H8 ADP 501 J 1 HETATM 37 H HN61 ADP . . . SA 23 165.822 313.446 245.555 1 61.73 ? HN61 ADP 501 J 1 HETATM 38 H HN62 ADP . . . SA 23 166.527 312.352 246.279 1 61.73 ? HN62 ADP 501 J 1 HETATM 39 H H2 ADP . . . SA 23 162.572 314.892 248.23 1 85.03 ? H2 ADP 501 J 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 175 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #