data_5LU4 # _model_server_result.job_id 4vJl7fDEJTF9ATG4cymR8w _model_server_result.datetime_utc '2024-11-27 18:12:05' _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 5lu4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":901}' # _entry.id 5LU4 # _exptl.entry_id 5LU4 _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 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 5LU4 _cell.length_a 74.159 _cell.length_b 126.515 _cell.length_c 218.998 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LU4 _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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 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,C,D,E,F,J 1 1 B,G,H,I,K 1 2 B,G,H,I,K 2 1 A,C,D,E,F,J 2 3 # 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' 2_995 -x+9/2,-y+4,z+1/2 -1 0 0 0 -1 0 0 0 1 333.7155 506.06 109.499 3 'crystal symmetry operation' 2_994 -x+9/2,-y+4,z-1/2 -1 0 0 0 -1 0 0 0 1 333.7155 506.06 -109.499 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 G 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 OE1 GLU 324 A GLU 324 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc2 A OE2 GLU 324 A GLU 324 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc3 A OE1 GLN 336 A GLN 336 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc4 A OD2 ASP 622 A ASP 622 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc5 A OE2 GLU 748 A GLU 748 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc6 A OD2 ASP 772 A ASP 772 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc7 C O2B ADP . A ADP 901 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc8 C O3A ADP . A ADP 901 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc9 C O5' ADP . A ADP 901 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? metalc ? metalc10 E OXT PYR . A PYR 903 1_555 F MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc11 B OE1 GLU 324 B GLU 324 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc12 B OE2 GLU 324 B GLU 324 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc13 B OE1 GLN 336 B GLN 336 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc14 B OD2 ASP 622 B ASP 622 1_555 I MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc15 B OE2 GLU 748 B GLU 748 1_555 I MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc16 B OD2 ASP 772 B ASP 772 1_555 I MG MG . B MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc17 G O1B ADP . B ADP 901 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc18 G O2B ADP . B ADP 901 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc19 G O3A ADP . B ADP 901 1_555 H MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? # _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 5LU4 _atom_sites.fract_transf_matrix[1][1] 0.013485 _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] 0.007904 _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] 0.004566 _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 1 901 873 ADP ADP . D 3 MG A 1 902 874 MG MG . E 4 PYR A 1 903 875 PYR PYR . F 3 MG A 1 904 876 MG MG . G 2 ADP B 1 901 873 ADP ADP . H 3 MG B 1 902 874 MG MG . I 3 MG B 1 903 875 MG MG . J 5 HOH A 1 1001 878 HOH HOH . K 5 HOH B 1 1001 876 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 2 173.706 271.429 215.896 1 110.43 ? PB ADP 901 A 1 HETATM 2 O O1B ADP . . . C 2 172.283 270.838 215.874 1 99.9 ? O1B ADP 901 A 1 HETATM 3 O O2B ADP . . . C 2 174.82 270.362 215.927 1 75.56 ? O2B ADP 901 A 1 HETATM 4 O O3B ADP . . . C 2 173.832 272.29 217.173 1 72.6 ? O3B ADP 901 A 1 HETATM 5 P PA ADP . . . C 2 172.842 272.911 213.29 1 46.38 ? PA ADP 901 A 1 HETATM 6 O O1A ADP . . . C 2 172.771 274.365 213.008 1 35.13 ? O1A ADP 901 A 1 HETATM 7 O O2A ADP . . . C 2 171.642 272.076 213.692 1 57.12 ? O2A ADP 901 A 1 HETATM 8 O O3A ADP . . . C 2 173.922 272.364 214.444 1 74.53 ? O3A ADP 901 A 1 HETATM 9 O O5' ADP . . . C 2 172.937 272.277 211.889 1 38.97 ? O5' ADP 901 A 1 HETATM 10 C C5' ADP . . . C 2 172.047 272.594 210.856 1 34.45 ? C5' ADP 901 A 1 HETATM 11 C C4' ADP . . . C 2 172.329 271.604 209.712 1 38.55 ? C4' ADP 901 A 1 HETATM 12 O O4' ADP . . . C 2 172.562 272.318 208.496 1 40.4 ? O4' ADP 901 A 1 HETATM 13 C C3' ADP . . . C 2 173.65 270.864 209.82 1 44.13 ? C3' ADP 901 A 1 HETATM 14 O O3' ADP . . . C 2 173.661 269.782 208.933 1 45.14 ? O3' ADP 901 A 1 HETATM 15 C C2' ADP . . . C 2 174.667 271.922 209.387 1 40.74 ? C2' ADP 901 A 1 HETATM 16 O O2' ADP . . . C 2 175.903 271.367 209.043 1 53.23 ? O2' ADP 901 A 1 HETATM 17 C C1' ADP . . . C 2 173.968 272.571 208.229 1 33.24 ? C1' ADP 901 A 1 HETATM 18 N N9 ADP . . . C 2 174.151 274.039 208.13 1 24.71 ? N9 ADP 901 A 1 HETATM 19 C C8 ADP . . . C 2 173.962 275.004 209.056 1 25.01 ? C8 ADP 901 A 1 HETATM 20 N N7 ADP . . . C 2 174.117 276.274 208.461 1 24.32 ? N7 ADP 901 A 1 HETATM 21 C C5 ADP . . . C 2 174.416 276.05 207.191 1 18.92 ? C5 ADP 901 A 1 HETATM 22 C C6 ADP . . . C 2 174.765 276.859 206.098 1 23.04 ? C6 ADP 901 A 1 HETATM 23 N N6 ADP . . . C 2 174.812 278.179 206.215 1 28.11 ? N6 ADP 901 A 1 HETATM 24 N N1 ADP . . . C 2 175.007 276.344 204.916 1 27.93 ? N1 ADP 901 A 1 HETATM 25 C C2 ADP . . . C 2 174.962 275.01 204.838 1 29.79 ? C2 ADP 901 A 1 HETATM 26 N N3 ADP . . . C 2 174.644 274.192 205.84 1 25.17 ? N3 ADP 901 A 1 HETATM 27 C C4 ADP . . . C 2 174.388 274.658 207.008 1 19.99 ? C4 ADP 901 A 1 # _model_server_stats.io_time_ms 135 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #