data_7DRM # _model_server_result.job_id wNNGjhYvl5pjUPxDneM6rw _model_server_result.datetime_utc '2024-12-03 14:19:25' _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 7drm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 7DRM # _exptl.entry_id 7DRM _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.16 _cell.angle_gamma 90 _cell.entry_id 7DRM _cell.length_a 92.432 _cell.length_b 91.294 _cell.length_c 100.308 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DRM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,E,G,H,I,M,N 1 1 C,D,F,J,K,L,O,P 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 ? 3 G N N ? 3 J 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 OD2 ASP 289 A ASP 269 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc2 A OE2 GLU 302 A GLU 282 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.788 ? metalc ? metalc3 A OE1 GLU 302 A GLU 282 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc4 G O1B ADP . A ADP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc5 G O1A ADP . A ADP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc6 G O1B ADP . A ADP 401 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc7 C OD2 ASP 289 C ASP 269 1_555 K MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc8 C OE2 GLU 302 C GLU 282 1_555 K MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc9 C OD1 ASN 304 C ASN 284 1_555 L MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? metalc ? metalc10 J O2A ADP . C ADP 401 1_555 K MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc11 J O1B ADP . C ADP 401 1_555 L MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? # _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 7DRM _atom_sites.fract_transf_matrix[1][1] 0.010819 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002133 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010954 _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] 0.010161 _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 G 3 ADP A 1 401 401 ADP ADP . H 4 MG A 1 402 402 MG MG . I 4 MG A 1 403 1 MG MG . J 3 ADP C 1 401 401 ADP ADP . K 4 MG C 1 402 402 MG MG . L 4 MG C 1 403 2 MG MG . M 5 HOH A 1 501 2 HOH HOH . N 5 HOH B 1 401 3 HOH HOH . N 5 HOH B 2 402 6 HOH HOH . N 5 HOH B 3 403 7 HOH HOH . N 5 HOH B 4 404 5 HOH HOH . O 5 HOH C 1 501 13 HOH HOH . O 5 HOH C 2 502 11 HOH HOH . O 5 HOH C 3 503 12 HOH HOH . O 5 HOH C 4 504 9 HOH HOH . O 5 HOH C 5 505 8 HOH HOH . O 5 HOH C 6 506 10 HOH HOH . O 5 HOH C 7 507 14 HOH HOH . P 5 HOH D 1 401 16 HOH HOH . P 5 HOH D 2 402 15 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 . . . J 3 -22.974 27.382 1.147 1 85.48 ? PB ADP 401 C 1 HETATM 2 O O1B ADP . . . J 3 -23.666 27.946 -0.067 1 78.3 ? O1B ADP 401 C 1 HETATM 3 O O2B ADP . . . J 3 -22.718 28.369 2.246 1 79.28 ? O2B ADP 401 C 1 HETATM 4 O O3B ADP . . . J 3 -23.585 26.114 1.667 1 100.92 ? O3B ADP 401 C 1 HETATM 5 P PA ADP . . . J 3 -20.403 27.906 0.099 1 69.97 ? PA ADP 401 C 1 HETATM 6 O O1A ADP . . . J 3 -19.727 27.268 -1.073 1 74.63 ? O1A ADP 401 C 1 HETATM 7 O O2A ADP . . . J 3 -20.969 29.293 0.002 1 72.41 ? O2A ADP 401 C 1 HETATM 8 O O3A ADP . . . J 3 -21.524 26.906 0.648 1 80.4 ? O3A ADP 401 C 1 HETATM 9 O O5' ADP . . . J 3 -19.341 27.931 1.281 1 67.36 ? O5' ADP 401 C 1 HETATM 10 C C5' ADP . . . J 3 -19.426 28.987 2.22 1 79.61 ? C5' ADP 401 C 1 HETATM 11 C C4' ADP . . . J 3 -18.052 29.553 2.507 1 79.76 ? C4' ADP 401 C 1 HETATM 12 O O4' ADP . . . J 3 -17.094 28.509 2.598 1 80.56 ? O4' ADP 401 C 1 HETATM 13 C C3' ADP . . . J 3 -17.604 30.427 1.373 1 79.59 ? C3' ADP 401 C 1 HETATM 14 O O3' ADP . . . J 3 -17.87 31.782 1.691 1 91.96 ? O3' ADP 401 C 1 HETATM 15 C C2' ADP . . . J 3 -16.125 30.229 1.351 1 81.03 ? C2' ADP 401 C 1 HETATM 16 O O2' ADP . . . J 3 -15.59 31.247 2.182 1 92.52 ? O2' ADP 401 C 1 HETATM 17 C C1' ADP . . . J 3 -15.871 28.889 1.994 1 77.96 ? C1' ADP 401 C 1 HETATM 18 N N9 ADP . . . J 3 -15.492 27.911 0.952 1 77.39 ? N9 ADP 401 C 1 HETATM 19 C C8 ADP . . . J 3 -16.306 27.161 0.195 1 76.37 ? C8 ADP 401 C 1 HETATM 20 N N7 ADP . . . J 3 -15.603 26.382 -0.656 1 72.34 ? N7 ADP 401 C 1 HETATM 21 C C5 ADP . . . J 3 -14.308 26.635 -0.441 1 66.36 ? C5 ADP 401 C 1 HETATM 22 C C6 ADP . . . J 3 -13.029 26.165 -0.989 1 66.5 ? C6 ADP 401 C 1 HETATM 23 N N6 ADP . . . J 3 -12.986 25.244 -1.964 1 67.54 ? N6 ADP 401 C 1 HETATM 24 N N1 ADP . . . J 3 -11.906 26.682 -0.484 1 68.1 ? N1 ADP 401 C 1 HETATM 25 C C2 ADP . . . J 3 -11.929 27.601 0.486 1 70.75 ? C2 ADP 401 C 1 HETATM 26 N N3 ADP . . . J 3 -13.047 28.076 1.032 1 72.56 ? N3 ADP 401 C 1 HETATM 27 C C4 ADP . . . J 3 -14.246 27.639 0.614 1 71.58 ? C4 ADP 401 C 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #