data_4RKZ # _model_server_result.job_id ogL9PBc2ozfcX2Yt6VJM1g _model_server_result.datetime_utc '2024-12-05 00:17:16' _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 4rkz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4RKZ # _exptl.entry_id 4RKZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 122.95 _cell.angle_gamma 90 _cell.entry_id 4RKZ _cell.length_a 146.37 _cell.length_b 61.06 _cell.length_c 103.55 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RKZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,J 1 1 B,F,G,H,I,K 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 62 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 43 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 62 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 43 _struct_conn.ptnr2_symmetry 1_555 _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 2.036 _struct_conn.pdbx_value_order ? # _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 27 n n PB O2B ADP sing 28 n n PB O3B ADP sing 29 n n PB O3A ADP sing 30 n n O2B HOB2 ADP sing 31 n n O3B HOB3 ADP sing 32 n n PA O1A ADP doub 33 n n PA O2A ADP sing 34 n n PA O3A ADP sing 35 n n PA O5' ADP sing 36 n n O2A HOA2 ADP sing 37 n n O5' C5' ADP sing 38 n n C5' C4' ADP sing 39 n n C5' "H5'1" ADP sing 40 n n C5' "H5'2" ADP sing 41 n n C4' O4' ADP sing 42 n n C4' C3' ADP sing 43 n n C4' H4' ADP sing 44 n n O4' C1' ADP sing 45 n n C3' O3' ADP sing 46 n n C3' C2' ADP sing 47 n n C3' H3' ADP sing 48 n n O3' HO3' ADP sing 49 n n C2' O2' ADP sing 50 n n C2' C1' ADP sing 51 n n C2' H2' ADP sing 52 n n O2' HO2' ADP sing 53 n n C1' N9 ADP sing 54 n n C1' H1' ADP sing 55 n n N9 C8 ADP sing 56 n y N9 C4 ADP sing 57 n y C8 N7 ADP doub 58 n y C8 H8 ADP sing 59 n n N7 C5 ADP sing 60 n y C5 C6 ADP sing 61 n y C5 C4 ADP doub 62 n y C6 N6 ADP sing 63 n n C6 N1 ADP doub 64 n y N6 HN61 ADP sing 65 n n N6 HN62 ADP sing 66 n n N1 C2 ADP sing 67 n y C2 N3 ADP doub 68 n y C2 H2 ADP sing 69 n n N3 C4 ADP sing 70 n y # _atom_sites.entry_id 4RKZ _atom_sites.fract_transf_matrix[1][1] 0.006832 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004428 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016377 _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] 0.011508 _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 C 2 ADP A 1 401 1 ADP ADP . D 3 3S4 A 1 402 1 3S4 M3P . E 4 SO4 A 1 403 4 SO4 SO4 . F 3 3S4 B 1 401 2 3S4 M3P . G 4 SO4 B 1 402 1 SO4 SO4 . H 4 SO4 B 1 403 2 SO4 SO4 . I 4 SO4 B 1 404 3 SO4 SO4 . J 5 HOH A 1 501 1 HOH HOH . J 5 HOH A 2 502 2 HOH HOH . J 5 HOH A 3 503 5 HOH HOH . J 5 HOH A 4 504 13 HOH HOH . J 5 HOH A 5 505 14 HOH HOH . J 5 HOH A 6 506 16 HOH HOH . J 5 HOH A 7 507 17 HOH HOH . J 5 HOH A 8 508 18 HOH HOH . J 5 HOH A 9 509 20 HOH HOH . J 5 HOH A 10 510 23 HOH HOH . J 5 HOH A 11 511 26 HOH HOH . J 5 HOH A 12 512 27 HOH HOH . J 5 HOH A 13 513 28 HOH HOH . J 5 HOH A 14 514 29 HOH HOH . J 5 HOH A 15 515 31 HOH HOH . J 5 HOH A 16 516 32 HOH HOH . J 5 HOH A 17 517 33 HOH HOH . J 5 HOH A 18 518 34 HOH HOH . J 5 HOH A 19 519 35 HOH HOH . J 5 HOH A 20 520 37 HOH HOH . J 5 HOH A 21 521 43 HOH HOH . J 5 HOH A 22 522 44 HOH HOH . J 5 HOH A 23 523 48 HOH HOH . J 5 HOH A 24 524 50 HOH HOH . J 5 HOH A 25 525 51 HOH HOH . K 5 HOH B 1 501 3 HOH HOH . K 5 HOH B 2 502 4 HOH HOH . K 5 HOH B 3 503 6 HOH HOH . K 5 HOH B 4 504 7 HOH HOH . K 5 HOH B 5 505 8 HOH HOH . K 5 HOH B 6 506 11 HOH HOH . K 5 HOH B 7 507 12 HOH HOH . K 5 HOH B 8 508 25 HOH HOH . K 5 HOH B 9 509 38 HOH HOH . K 5 HOH B 10 510 39 HOH HOH . K 5 HOH B 11 511 40 HOH HOH . K 5 HOH B 12 512 42 HOH HOH . K 5 HOH B 13 513 49 HOH HOH . K 5 HOH B 14 514 55 HOH HOH . K 5 HOH B 15 515 56 HOH HOH . # 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 . . . C 2 46.948 24.672 8.858 0.78 74.45 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . C 2 46.05 23.911 7.911 0.78 60.96 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . C 2 46.457 24.743 10.288 0.78 58.64 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . C 2 48.42 24.35 8.717 0.78 66.21 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . C 2 47.129 26.562 6.798 0.78 83.85 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . C 2 47.747 25.378 6.093 0.78 78.62 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . C 2 47.807 27.91 6.744 0.78 79.95 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . C 2 46.811 26.184 8.33 0.78 72.45 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . C 2 45.634 26.745 6.232 0.78 75.42 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . C 2 44.727 27.63 6.886 0.78 75.05 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . C 2 43.663 28.066 5.888 0.78 77.15 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . C 2 43.008 26.929 5.318 0.78 78.32 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . C 2 42.57 28.905 6.528 0.78 80.62 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . C 2 42.872 30.301 6.454 0.78 86.6 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . C 2 41.333 28.565 5.721 0.78 81.71 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . C 2 41.132 29.549 4.703 0.78 84.76 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . C 2 41.63 27.219 5.077 0.78 77.61 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . C 2 40.788 26.213 5.76 0.78 70.64 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . C 2 40.827 25.96 7.082 0.78 68.49 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . C 2 39.934 25.001 7.424 0.78 65.61 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . C 2 39.299 24.629 6.299 0.78 66.13 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . C 2 38.234 23.66 5.954 0.78 59.73 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . C 2 37.672 22.888 6.916 0.78 57.56 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . C 2 37.852 23.577 4.659 0.78 63.11 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . C 2 38.415 24.345 3.706 0.78 64.7 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . C 2 39.384 25.25 3.946 0.78 71.73 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . C 2 39.859 25.436 5.202 0.78 70.03 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #