data_3SJD # _model_server_result.job_id u813s6IIsmrwQjIvzNi7aA _model_server_result.datetime_utc '2024-12-21 13:12:21' _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 3sjd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 3SJD # _exptl.entry_id 3SJD _exptl.method 'X-RAY DIFFRACTION' # _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 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 3SJD _cell.length_a 149.64 _cell.length_b 209.75 _cell.length_c 133.24 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SJD _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 ? trimeric 3 author_defined_assembly 1 ? tetrameric 4 author_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,E,F,G,H,I,J 1 1 C,D,K,L,M 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 K 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 OG1 THR 32 A THR 32 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc2 A SG CYS 285 A CYS 285 1_555 J ZN ZN . B ZN 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc3 A SG CYS 288 A CYS 288 1_555 J ZN ZN . B ZN 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc4 F O2B ADP . A ADP 401 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc5 B OG1 THR 32 B THR 32 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc6 B SG CYS 288 B CYS 288 1_555 J ZN ZN . B ZN 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc7 H O2B ADP . B ADP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc8 C OG1 THR 32 C THR 32 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc9 C SG CYS 285 C CYS 285 1_555 M ZN ZN . C ZN 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc10 K O2B ADP . C ADP 401 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? # _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 3SJD _atom_sites.fract_transf_matrix[1][1] 0.006683 _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] 0.004768 _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] 0.007505 _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 F 3 ADP A 1 401 401 ADP ADP . G 4 MG A 1 402 402 MG MG . H 3 ADP B 1 401 401 ADP ADP . I 4 MG B 1 402 402 MG MG . J 5 ZN B 1 363 363 ZN ZN . K 3 ADP C 1 401 401 ADP ADP . L 4 MG C 1 402 402 MG MG . M 5 ZN C 1 363 363 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 . . . H 3 36.019 -50.528 -9.074 1 336.49 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . H 3 36.02 -51.325 -10.378 1 339.07 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . H 3 34.825 -51.243 -8.364 1 336.52 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . H 3 36.008 -49.074 -9.131 1 333.64 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . H 3 37.587 -52.379 -7.307 1 341.72 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . H 3 36.999 -52.091 -5.912 1 340.1 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . H 3 37.159 -53.565 -8.04 1 344.79 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . H 3 37.2 -51.151 -8.21 1 338.71 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . H 3 39.184 -52.254 -7.099 1 342.92 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . H 3 39.963 -52.628 -8.249 1 345.47 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . H 3 41.103 -53.582 -7.818 1 349.05 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . H 3 41.976 -52.952 -6.859 1 347.62 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . H 3 40.533 -54.828 -7.113 1 351.62 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . H 3 41.327 -55.944 -7.468 1 356.28 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . H 3 40.671 -54.495 -5.608 1 350.06 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . H 3 40.905 -55.617 -4.792 1 353.67 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . H 3 41.929 -53.6 -5.581 1 348.57 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . H 3 41.914 -52.509 -4.652 1 345.11 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . H 3 41.063 -51.395 -4.545 1 341.47 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . H 3 41.55 -50.473 -3.695 1 339.44 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . H 3 42.756 -50.996 -3.236 1 341.49 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . H 3 43.75 -50.55 -2.319 1 340.93 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . H 3 43.603 -49.339 -1.706 1 338 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . H 3 44.863 -51.313 -2.077 1 343.53 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . H 3 44.971 -52.482 -2.735 1 346.89 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . H 3 44.132 -53.052 -3.617 1 348.12 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . H 3 43.019 -52.281 -3.822 1 345.15 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #