data_6EYC # _model_server_result.job_id E2D2fuPd3T4NKT2zXW9iBA _model_server_result.datetime_utc '2025-01-18 00:08:53' _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 6eyc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":2002}' # _entry.id 6EYC # _exptl.entry_id 6EYC _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 6EYC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EYC _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 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 ? 8 H N N ? 8 I N N ? 8 J N N ? 8 L N N ? 8 N N N ? 8 P 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 A SG CYS 341 2 CYS 341 1_555 G ZN ZN . 2 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc2 A SG CYS 344 2 CYS 344 1_555 G ZN ZN . 2 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc3 A SG CYS 364 2 CYS 364 1_555 G ZN ZN . 2 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc4 A SG CYS 367 2 CYS 367 1_555 G ZN ZN . 2 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc5 C SG CYS 349 4 CYS 349 1_555 K ZN ZN . 4 ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc6 C SG CYS 352 4 CYS 352 1_555 K ZN ZN . 4 ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc7 C SG CYS 371 4 CYS 371 1_555 K ZN ZN . 4 ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc8 D SG CYS 183 5 CYS 183 1_555 M ZN ZN . 5 ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc9 D SG CYS 186 5 CYS 186 1_555 M ZN ZN . 5 ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc10 D SG CYS 211 5 CYS 211 1_555 M ZN ZN . 5 ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc11 D SG CYS 236 5 CYS 236 1_555 M ZN ZN . 5 ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.977 ? metalc ? metalc12 E SG CYS 314 6 CYS 314 1_555 O ZN ZN . 6 ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc13 E SG CYS 333 6 CYS 333 1_555 O ZN ZN . 6 ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc14 E SG CYS 338 6 CYS 338 1_555 O ZN ZN . 6 ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? metalc ? metalc15 F SG CYS 262 7 CYS 262 1_555 Q ZN ZN . 7 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc16 F SG CYS 265 7 CYS 265 1_555 Q ZN ZN . 7 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc17 F SG CYS 284 7 CYS 284 1_555 Q ZN ZN . 7 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? # _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 6EYC _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 G 7 ZN 2 1 901 1 ZN ZN . H 8 ADP 2 1 902 2001 ADP ADP . I 8 ADP 3 1 2001 2001 ADP ADP . J 8 ADP 3 1 2002 2001 ADP ADP . K 7 ZN 4 1 1001 2 ZN ZN . L 8 ADP 4 1 1002 2001 ADP ADP . M 7 ZN 5 1 801 3 ZN ZN . N 8 ADP 5 1 802 2001 ADP ADP . O 7 ZN 6 1 1101 5 ZN ZN . P 8 ADP 6 1 1102 2001 ADP ADP . Q 7 ZN 7 1 901 4 ZN ZN . # 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 . . . J 8 187.367 268.484 222.759 1 61.57 ? PB ADP 2002 3 1 HETATM 2 O O1B ADP . . . J 8 187.593 267.645 221.525 1 61.57 ? O1B ADP 2002 3 1 HETATM 3 O O2B ADP . . . J 8 185.932 268.892 222.979 1 61.57 ? O2B ADP 2002 3 1 HETATM 4 O O3B ADP . . . J 8 188.342 269.615 222.969 1 61.57 ? O3B ADP 2002 3 1 HETATM 5 P PA ADP . . . J 8 186.675 267.645 225.242 1 61.57 ? PA ADP 2002 3 1 HETATM 6 O O1A ADP . . . J 8 185.373 267.001 224.843 1 61.57 ? O1A ADP 2002 3 1 HETATM 7 O O2A ADP . . . J 8 186.678 269.105 225.616 1 61.57 ? O2A ADP 2002 3 1 HETATM 8 O O3A ADP . . . J 8 187.659 267.49 223.989 1 61.57 ? O3A ADP 2002 3 1 HETATM 9 O O5' ADP . . . J 8 187.264 266.807 226.486 1 61.57 ? O5' ADP 2002 3 1 HETATM 10 C C5' ADP . . . J 8 186.405 266.678 227.623 1 61.57 ? C5' ADP 2002 3 1 HETATM 11 C C4' ADP . . . J 8 187.045 266.01 228.838 1 61.57 ? C4' ADP 2002 3 1 HETATM 12 O O4' ADP . . . J 8 187.132 266.949 229.914 1 61.57 ? O4' ADP 2002 3 1 HETATM 13 C C3' ADP . . . J 8 186.177 264.865 229.327 1 61.57 ? C3' ADP 2002 3 1 HETATM 14 O O3' ADP . . . J 8 186.992 263.723 229.605 1 61.57 ? O3' ADP 2002 3 1 HETATM 15 C C2' ADP . . . J 8 185.534 265.346 230.61 1 61.57 ? C2' ADP 2002 3 1 HETATM 16 O O2' ADP . . . J 8 185.667 264.343 231.618 1 61.57 ? O2' ADP 2002 3 1 HETATM 17 C C1' ADP . . . J 8 186.282 266.603 231.013 1 61.57 ? C1' ADP 2002 3 1 HETATM 18 N N9 ADP . . . J 8 185.327 267.721 231.191 1 61.57 ? N9 ADP 2002 3 1 HETATM 19 C C8 ADP . . . J 8 185.43 268.88 230.531 1 61.57 ? C8 ADP 2002 3 1 HETATM 20 N N7 ADP . . . J 8 184.443 269.739 230.867 1 61.57 ? N7 ADP 2002 3 1 HETATM 21 C C5 ADP . . . J 8 183.679 269.126 231.777 1 61.57 ? C5 ADP 2002 3 1 HETATM 22 C C6 ADP . . . J 8 182.469 269.493 232.534 1 61.57 ? C6 ADP 2002 3 1 HETATM 23 N N6 ADP . . . J 8 181.903 270.71 232.361 1 61.57 ? N6 ADP 2002 3 1 HETATM 24 N N1 ADP . . . J 8 181.967 268.579 233.392 1 61.57 ? N1 ADP 2002 3 1 HETATM 25 C C2 ADP . . . J 8 182.551 267.375 233.547 1 61.57 ? C2 ADP 2002 3 1 HETATM 26 N N3 ADP . . . J 8 183.653 266.975 232.885 1 61.57 ? N3 ADP 2002 3 1 HETATM 27 C C4 ADP . . . J 8 184.262 267.795 231.998 1 61.57 ? C4 ADP 2002 3 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 78 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 27 #