data_6RDU # _model_server_result.job_id c7NSUP3oPO3ZFbOE8NVxJw _model_server_result.datetime_utc '2024-12-26 20:23:38' _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 6rdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"OA","auth_seq_id":601}' # _entry.id 6RDU # _exptl.entry_id 6RDU _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 22 _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 6RDU _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RDU _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 31-meric _pdbx_struct_assembly.oligomeric_count 31 _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 _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 ? 22 MA N N ? 22 OA 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 U NE2 HIS 248 M HIS 248 1_555 FA ZN ZN . M ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc2 Z OG1 THR 232 T THR 232 1_555 HA MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc3 GA O2B ATP . T ATP 1001 1_555 HA MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc4 AA OG1 THR 232 U THR 232 1_555 JA MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc5 IA O1G ATP . U ATP 1001 1_555 JA MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc6 IA O3G ATP . U ATP 1001 1_555 JA MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc7 IA O2B ATP . U ATP 1001 1_555 JA MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc8 BA OG1 THR 232 V THR 232 1_555 LA MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc9 KA O1G ATP . V ATP 1001 1_555 LA MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc10 CA OG1 THR 190 X THR 190 1_555 NA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc11 MA O2B ADP . X ADP 601 1_555 NA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc12 DA OG1 THR 190 Y THR 190 1_555 PA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc13 OA O3B ADP . Y ADP 601 1_555 PA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? # _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 6RDU _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 FA 19 ZN M 1 600 600 ZN ZN . GA 20 ATP T 1 1001 1001 ATP ATP . HA 21 MG T 1 1002 1002 MG MG . IA 20 ATP U 1 1001 1001 ATP ATP . JA 21 MG U 1 1002 1002 MG MG . KA 20 ATP V 1 1001 1001 ATP ATP . LA 21 MG V 1 1002 1002 MG MG . MA 22 ADP X 1 601 1028 ADP ADP . NA 21 MG X 1 602 1029 MG MG . OA 22 ADP Y 1 601 1028 ADP ADP . PA 21 MG Y 1 602 1029 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 . . . OA 22 143.563 276.042 270.582 1 48.78 ? PB ADP 601 Y 1 HETATM 2 O O1B ADP . . . OA 22 142.498 275.683 269.593 1 48.78 ? O1B ADP 601 Y 1 HETATM 3 O O2B ADP . . . OA 22 144.263 274.838 271.132 1 48.78 ? O2B ADP 601 Y 1 HETATM 4 O O3B ADP . . . OA 22 143.151 277.047 271.619 1 48.78 ? O3B ADP 601 Y 1 HETATM 5 P PA ADP . . . OA 22 145.493 278.029 270.23 1 48.78 ? PA ADP 601 Y 1 HETATM 6 O O1A ADP . . . OA 22 144.78 279.308 269.927 1 48.78 ? O1A ADP 601 Y 1 HETATM 7 O O2A ADP . . . OA 22 145.931 277.691 271.618 1 48.78 ? O2A ADP 601 Y 1 HETATM 8 O O3A ADP . . . OA 22 144.635 276.804 269.668 1 48.78 ? O3A ADP 601 Y 1 HETATM 9 O O5' ADP . . . OA 22 146.791 277.992 269.304 1 48.78 ? O5' ADP 601 Y 1 HETATM 10 C C5' ADP . . . OA 22 147.803 277.04 269.578 1 48.78 ? C5' ADP 601 Y 1 HETATM 11 C C4' ADP . . . OA 22 149.136 277.436 268.965 1 48.78 ? C4' ADP 601 Y 1 HETATM 12 O O4' ADP . . . OA 22 149.081 277.425 267.538 1 48.78 ? O4' ADP 601 Y 1 HETATM 13 C C3' ADP . . . OA 22 149.574 278.84 269.318 1 48.78 ? C3' ADP 601 Y 1 HETATM 14 O O3' ADP . . . OA 22 150.169 278.954 270.608 1 48.78 ? O3' ADP 601 Y 1 HETATM 15 C C2' ADP . . . OA 22 150.58 279.068 268.222 1 48.78 ? C2' ADP 601 Y 1 HETATM 16 O O2' ADP . . . OA 22 151.763 278.343 268.54 1 48.78 ? O2' ADP 601 Y 1 HETATM 17 C C1' ADP . . . OA 22 149.939 278.434 267.013 1 48.78 ? C1' ADP 601 Y 1 HETATM 18 N N9 ADP . . . OA 22 149.131 279.497 266.374 1 48.78 ? N9 ADP 601 Y 1 HETATM 19 C C8 ADP . . . OA 22 147.799 279.616 266.427 1 48.78 ? C8 ADP 601 Y 1 HETATM 20 N N7 ADP . . . OA 22 147.365 280.7 265.757 1 48.78 ? N7 ADP 601 Y 1 HETATM 21 C C5 ADP . . . OA 22 148.442 281.3 265.249 1 48.78 ? C5 ADP 601 Y 1 HETATM 22 C C6 ADP . . . OA 22 148.685 282.495 264.424 1 48.78 ? C6 ADP 601 Y 1 HETATM 23 N N6 ADP . . . OA 22 147.656 283.263 264.017 1 48.78 ? N6 ADP 601 Y 1 HETATM 24 N N1 ADP . . . OA 22 149.956 282.786 264.101 1 48.78 ? N1 ADP 601 Y 1 HETATM 25 C C2 ADP . . . OA 22 150.975 282.013 264.504 1 48.78 ? C2 ADP 601 Y 1 HETATM 26 N N3 ADP . . . OA 22 150.828 280.913 265.254 1 48.78 ? N3 ADP 601 Y 1 HETATM 27 C C4 ADP . . . OA 22 149.603 280.508 265.652 1 48.78 ? C4 ADP 601 Y 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 75 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #