data_5YWC # _model_server_result.job_id 8vjiPLaEaf5ZjqMbPHz6mg _model_server_result.datetime_utc '2024-11-04 23:32:38' _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 5ywc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":2502}' # _entry.id 5YWC # _exptl.entry_id 5YWC _exptl.method 'ELECTRON MICROSCOPY' # _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 12 _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 5YWC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YWC _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 ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 J N N ? 3 K N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 S N N ? 3 T N N ? 3 U N N ? 3 X N N ? 3 Y N N ? 3 Z 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 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 E SG CYS 110 E CYS 110 1_555 E SG CYS 142 E CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 G SG CYS 110 G CYS 110 1_555 G SG CYS 142 G CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc1 B OG SER 720 B SER 720 1_555 L MG MG . B MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc2 B OE1 GLN 775 B GLN 775 1_555 L MG MG . B MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc3 J O2B ADP . B ADP 2501 1_555 L MG MG . B MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc4 J O3B ADP . B ADP 2501 1_555 L MG MG . B MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc5 K O2B ADP . B ADP 2502 1_555 M MG MG . B MG 2504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc6 D OG SER 720 D SER 720 1_555 Q MG MG . D MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc7 D OE1 GLN 775 D GLN 775 1_555 Q MG MG . D MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc8 O O2B ADP . D ADP 2501 1_555 Q MG MG . D MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc9 O O3B ADP . D ADP 2501 1_555 Q MG MG . D MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc10 P O2B ADP . D ADP 2502 1_555 R MG MG . D MG 2504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc11 F OG SER 720 F SER 720 1_555 V MG MG . F MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc12 F OE1 GLN 775 F GLN 775 1_555 V MG MG . F MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc13 T O2B ADP . F ADP 2501 1_555 V MG MG . F MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc14 T O3B ADP . F ADP 2501 1_555 V MG MG . F MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc15 U O2B ADP . F ADP 2502 1_555 W MG MG . F MG 2504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc16 H OG SER 720 H SER 720 1_555 AA MG MG . H MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc17 H OE1 GLN 775 H GLN 775 1_555 AA MG MG . H MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc18 Y O2B ADP . H ADP 2501 1_555 AA MG MG . H MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc19 Y O3B ADP . H ADP 2501 1_555 AA MG MG . H MG 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc20 Z O2B ADP . H ADP 2502 1_555 BA MG MG . H MG 2504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? # _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 5YWC _atom_sites.fract_transf_matrix[1][1] 0.003038 _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] 0.003038 _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] 0.003038 _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 3 ADP A 1 401 401 ADP ADP . J 3 ADP B 1 2501 2501 ADP ADP . K 3 ADP B 1 2502 2502 ADP ADP . L 4 MG B 1 2503 2503 MG MG . M 4 MG B 1 2504 2504 MG MG . N 3 ADP C 1 401 401 ADP ADP . O 3 ADP D 1 2501 2501 ADP ADP . P 3 ADP D 1 2502 2502 ADP ADP . Q 4 MG D 1 2503 2503 MG MG . R 4 MG D 1 2504 2504 MG MG . S 3 ADP E 1 401 401 ADP ADP . T 3 ADP F 1 2501 2501 ADP ADP . U 3 ADP F 1 2502 2502 ADP ADP . V 4 MG F 1 2503 2503 MG MG . W 4 MG F 1 2504 2504 MG MG . X 3 ADP G 1 401 401 ADP ADP . Y 3 ADP H 1 2501 2501 ADP ADP . Z 3 ADP H 1 2502 2502 ADP ADP . AA 4 MG H 1 2503 2503 MG MG . BA 4 MG H 1 2504 2504 MG MG . # 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 . . . K 3 106.355 113.163 125.825 1 382.27 ? PB ADP 2502 B 1 HETATM 2 O O1B ADP . . . K 3 106.348 113.222 124.316 1 378.81 ? O1B ADP 2502 B 1 HETATM 3 O O2B ADP . . . K 3 105.691 111.894 126.302 1 380.17 ? O2B ADP 2502 B 1 HETATM 4 O O3B ADP . . . K 3 107.774 113.228 126.34 1 381.92 ? O3B ADP 2502 B 1 HETATM 5 P PA ADP . . . K 3 105.298 114.644 127.961 1 401.48 ? PA ADP 2502 B 1 HETATM 6 O O1A ADP . . . K 3 104.21 113.702 128.421 1 396.69 ? O1A ADP 2502 B 1 HETATM 7 O O2A ADP . . . K 3 106.582 114.369 128.711 1 398.9 ? O2A ADP 2502 B 1 HETATM 8 O O3A ADP . . . K 3 105.537 114.434 126.383 1 388.39 ? O3A ADP 2502 B 1 HETATM 9 O O5' ADP . . . K 3 104.832 116.163 128.229 1 397.88 ? O5' ADP 2502 B 1 HETATM 10 C C5' ADP . . . K 3 105.377 117.233 127.46 1 394.58 ? C5' ADP 2502 B 1 HETATM 11 C C4' ADP . . . K 3 105.623 118.44 128.356 1 394.32 ? C4' ADP 2502 B 1 HETATM 12 O O4' ADP . . . K 3 105.098 118.187 129.662 1 397.83 ? O4' ADP 2502 B 1 HETATM 13 C C3' ADP . . . K 3 107.109 118.722 128.51 1 398.21 ? C3' ADP 2502 B 1 HETATM 14 O O3' ADP . . . K 3 107.375 120.072 128.123 1 405.51 ? O3' ADP 2502 B 1 HETATM 15 C C2' ADP . . . K 3 107.412 118.524 129.981 1 401.64 ? C2' ADP 2502 B 1 HETATM 16 O O2' ADP . . . K 3 108.215 119.599 130.475 1 402.92 ? O2' ADP 2502 B 1 HETATM 17 C C1' ADP . . . K 3 106.056 118.528 130.665 1 409.06 ? C1' ADP 2502 B 1 HETATM 18 N N9 ADP . . . K 3 106.015 117.521 131.754 1 428.85 ? N9 ADP 2502 B 1 HETATM 19 C C8 ADP . . . K 3 105.952 116.187 131.587 1 432.69 ? C8 ADP 2502 B 1 HETATM 20 N N7 ADP . . . K 3 105.923 115.545 132.781 1 435.26 ? N7 ADP 2502 B 1 HETATM 21 C C5 ADP . . . K 3 105.962 116.484 133.742 1 430.56 ? C5 ADP 2502 B 1 HETATM 22 C C6 ADP . . . K 3 105.962 116.492 135.22 1 433.79 ? C6 ADP 2502 B 1 HETATM 23 N N6 ADP . . . K 3 105.906 115.331 135.912 1 436.99 ? N6 ADP 2502 B 1 HETATM 24 N N1 ADP . . . K 3 106.014 117.687 135.846 1 447.49 ? N1 ADP 2502 B 1 HETATM 25 C C2 ADP . . . K 3 106.067 118.842 135.157 1 445.92 ? C2 ADP 2502 B 1 HETATM 26 N N3 ADP . . . K 3 106.072 118.91 133.814 1 444.68 ? N3 ADP 2502 B 1 HETATM 27 C C4 ADP . . . K 3 106.022 117.785 133.062 1 432.22 ? C4 ADP 2502 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 137 _model_server_stats.query_time_ms 515 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #