data_1XXI # _model_server_result.job_id aVRJxjRgwNBJSjcDj7GQWw _model_server_result.datetime_utc '2024-12-26 15:15:09' _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 1xxi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":803}' # _entry.id 1XXI # _exptl.entry_id 1XXI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 1XXI _cell.length_a 98.208 _cell.length_b 106.574 _cell.length_c 535.829 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XXI _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 pentameric 5 author_and_software_defined_assembly 1 PISA pentameric 5 author_and_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,B,C,D,E,K,L,M,N,O,P,Q 1 1 F,G,H,I,J,R,S,T,U,V 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 ? 5 L N N ? 5 P N N ? 5 U 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 B SG CYS 64 B CYS 64 1_555 K ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc2 B SG CYS 73 B CYS 73 1_555 K ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc3 B SG CYS 76 B CYS 76 1_555 K ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc4 B SG CYS 79 B CYS 79 1_555 K ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc5 C SG CYS 64 C CYS 64 1_555 N ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc6 C SG CYS 73 C CYS 73 1_555 N ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc7 C SG CYS 76 C CYS 76 1_555 N ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc8 C SG CYS 79 C CYS 79 1_555 N ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc9 D SG CYS 64 D CYS 64 1_555 O ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc10 D SG CYS 73 D CYS 73 1_555 O ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc11 D SG CYS 76 D CYS 76 1_555 O ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc12 D SG CYS 79 D CYS 79 1_555 O ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc13 E SG CYS 50 E CYS 50 1_555 Q ZN ZN . E ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc14 E SG CYS 59 E CYS 59 1_555 Q ZN ZN . E ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc15 E SG CYS 62 E CYS 62 1_555 Q ZN ZN . E ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc16 E SG CYS 65 E CYS 65 1_555 Q ZN ZN . E ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc17 G SG CYS 64 G CYS 64 1_555 R ZN ZN . G ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc18 G SG CYS 73 G CYS 73 1_555 R ZN ZN . G ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc19 G SG CYS 76 G CYS 76 1_555 R ZN ZN . G ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc20 G SG CYS 79 G CYS 79 1_555 R ZN ZN . G ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc21 H SG CYS 64 H CYS 64 1_555 S ZN ZN . H ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc22 H SG CYS 73 H CYS 73 1_555 S ZN ZN . H ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc23 H SG CYS 76 H CYS 76 1_555 S ZN ZN . H ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc24 H SG CYS 79 H CYS 79 1_555 S ZN ZN . H ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc25 I SG CYS 64 I CYS 64 1_555 T ZN ZN . I ZN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc26 I SG CYS 73 I CYS 73 1_555 T ZN ZN . I ZN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc27 I SG CYS 76 I CYS 76 1_555 T ZN ZN . I ZN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc28 I SG CYS 79 I CYS 79 1_555 T ZN ZN . I ZN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc29 J SG CYS 50 J CYS 50 1_555 V ZN ZN . J ZN 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc30 J SG CYS 59 J CYS 59 1_555 V ZN ZN . J ZN 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc31 J SG CYS 62 J CYS 62 1_555 V ZN ZN . J ZN 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc32 J SG CYS 65 J CYS 65 1_555 V ZN ZN . J ZN 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? # _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 1XXI _atom_sites.fract_transf_matrix[1][1] 0.010182 _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] 0.009383 _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] 0.001866 _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 K 4 ZN B 1 403 403 ZN ZN . L 5 ADP B 1 802 802 ADP ADP . M 6 PO4 C 1 1300 1300 PO4 PO4 . N 4 ZN C 1 401 401 ZN ZN . O 4 ZN D 1 402 402 ZN ZN . P 5 ADP D 1 801 801 ADP ADP . Q 4 ZN E 1 404 404 ZN ZN . R 4 ZN G 1 407 407 ZN ZN . S 4 ZN H 1 405 405 ZN ZN . T 4 ZN I 1 406 406 ZN ZN . U 5 ADP I 1 803 803 ADP ADP . V 4 ZN J 1 408 408 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 . . . U 5 101.278 -7.492 104.872 1 203.78 ? PB ADP 803 I 1 HETATM 2 O O1B ADP . . . U 5 101.871 -6.274 105.452 1 203.78 ? O1B ADP 803 I 1 HETATM 3 O O2B ADP . . . U 5 100.807 -7.438 103.425 1 203.78 ? O2B ADP 803 I 1 HETATM 4 O O3B ADP . . . U 5 100.095 -7.925 105.812 1 203.78 ? O3B ADP 803 I 1 HETATM 5 P PA ADP . . . U 5 103.342 -9.064 106.122 1 203.78 ? PA ADP 803 I 1 HETATM 6 O O1A ADP . . . U 5 104.656 -8.989 105.438 1 203.78 ? O1A ADP 803 I 1 HETATM 7 O O2A ADP . . . U 5 103.296 -8.208 107.354 1 203.78 ? O2A ADP 803 I 1 HETATM 8 O O3A ADP . . . U 5 102.291 -8.619 105.002 1 203.78 ? O3A ADP 803 I 1 HETATM 9 O O5' ADP . . . U 5 102.879 -10.616 106.339 1 203.78 ? O5' ADP 803 I 1 HETATM 10 C C5' ADP . . . U 5 102.942 -11.178 107.705 1 203.78 ? C5' ADP 803 I 1 HETATM 11 C C4' ADP . . . U 5 103.578 -12.592 107.758 1 203.78 ? C4' ADP 803 I 1 HETATM 12 O O4' ADP . . . U 5 103.009 -13.368 106.629 1 203.78 ? O4' ADP 803 I 1 HETATM 13 C C3' ADP . . . U 5 105.097 -12.62 107.491 1 203.78 ? C3' ADP 803 I 1 HETATM 14 O O3' ADP . . . U 5 105.904 -12.43 108.617 1 203.78 ? O3' ADP 803 I 1 HETATM 15 C C2' ADP . . . U 5 105.288 -13.941 106.761 1 203.78 ? C2' ADP 803 I 1 HETATM 16 O O2' ADP . . . U 5 105.571 -15.074 107.577 1 203.78 ? O2' ADP 803 I 1 HETATM 17 C C1' ADP . . . U 5 104.046 -14.152 106.008 1 203.78 ? C1' ADP 803 I 1 HETATM 18 N N9 ADP . . . U 5 104.141 -13.717 104.541 1 203.78 ? N9 ADP 803 I 1 HETATM 19 C C8 ADP . . . U 5 103.3 -12.763 104.006 1 203.78 ? C8 ADP 803 I 1 HETATM 20 N N7 ADP . . . U 5 103.466 -12.477 102.742 1 203.78 ? N7 ADP 803 I 1 HETATM 21 C C5 ADP . . . U 5 104.489 -13.27 102.371 1 203.78 ? C5 ADP 803 I 1 HETATM 22 C C6 ADP . . . U 5 105.191 -13.477 101.105 1 203.78 ? C6 ADP 803 I 1 HETATM 23 N N6 ADP . . . U 5 104.906 -12.814 99.961 1 203.78 ? N6 ADP 803 I 1 HETATM 24 N N1 ADP . . . U 5 106.221 -14.398 101.086 1 203.78 ? N1 ADP 803 I 1 HETATM 25 C C2 ADP . . . U 5 106.557 -15.107 102.23 1 203.78 ? C2 ADP 803 I 1 HETATM 26 N N3 ADP . . . U 5 105.967 -14.999 103.461 1 203.78 ? N3 ADP 803 I 1 HETATM 27 C C4 ADP . . . U 5 104.93 -14.074 103.476 1 203.78 ? C4 ADP 803 I 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #