data_1IM2 # _model_server_result.job_id 8epVFWtuQfGzPPNGG1rqMA _model_server_result.datetime_utc '2024-11-28 12:03:40' _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 1im2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":450}' # _entry.id 1IM2 # _exptl.entry_id 1IM2 _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 1 _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 120 _cell.entry_id 1IM2 _cell.length_a 109.826 _cell.length_b 109.826 _cell.length_c 313.675 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1IM2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 y,-x+y,z 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 6_555 x-y,x,z 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A C GLU 3 A GLU 3 1_555 A N MSE 4 A MSE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C MSE 4 A MSE 4 1_555 A N THR 5 A THR 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C ARG 37 A ARG 37 1_555 A N MSE 38 A MSE 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C MSE 38 A MSE 38 1_555 A N GLN 39 A GLN 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C LEU 54 A LEU 54 1_555 A N MSE 55 A MSE 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C MSE 55 A MSE 55 1_555 A N ILE 56 A ILE 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale7 A C ALA 107 A ALA 107 1_555 A N MSE 108 A MSE 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 108 A MSE 108 1_555 A N LYS 109 A LYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 A C GLY 296 A GLY 296 1_555 A N MSE 297 A MSE 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 A C MSE 297 A MSE 297 1_555 A N VAL 298 A VAL 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 A C LEU 359 A LEU 359 1_555 A N MSE 360 A MSE 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale12 A C MSE 360 A MSE 360 1_555 A N ALA 361 A ALA 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale13 A C VAL 399 A VAL 399 1_555 A N MSE 400 A MSE 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale14 A C MSE 400 A MSE 400 1_555 A N GLU 401 A GLU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale15 A C LEU 403 A LEU 403 1_555 A N MSE 404 A MSE 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale16 A C MSE 404 A MSE 404 1_555 A N ASP 405 A ASP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale17 A C ASP 413 A ASP 413 1_555 A N MSE 414 A MSE 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale18 A C MSE 414 A MSE 414 1_555 A N ASN 415 A ASN 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _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 1IM2 _atom_sites.fract_transf_matrix[1][1] 0.009105 _atom_sites.fract_transf_matrix[1][2] 0.005257 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010514 _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] 0.003188 _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 B 2 SO4 A 1 600 600 SO4 SO4 . C 3 ADP A 1 450 450 ADP ADP . # 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 3 24.74 22.462 17.581 1 54.51 ? PB ADP 450 A 1 HETATM 2 O O1B ADP . . . C 3 24.43 23.645 16.73 1 56.04 ? O1B ADP 450 A 1 HETATM 3 O O2B ADP . . . C 3 23.479 21.774 18.187 1 53.19 ? O2B ADP 450 A 1 HETATM 4 O O3B ADP . . . C 3 25.607 21.426 16.909 1 66.49 ? O3B ADP 450 A 1 HETATM 5 P PA ADP . . . C 3 26.107 22.268 20.169 1 43.03 ? PA ADP 450 A 1 HETATM 6 O O1A ADP . . . C 3 24.944 21.49 20.686 1 43.77 ? O1A ADP 450 A 1 HETATM 7 O O2A ADP . . . C 3 26.747 23.295 21.02 1 41.34 ? O2A ADP 450 A 1 HETATM 8 O O3A ADP . . . C 3 25.529 22.982 18.812 1 49.07 ? O3A ADP 450 A 1 HETATM 9 O O5' ADP . . . C 3 27.189 21.192 19.688 1 37.03 ? O5' ADP 450 A 1 HETATM 10 C C5' ADP . . . C 3 28.422 21.669 19.168 1 35.63 ? C5' ADP 450 A 1 HETATM 11 C C4' ADP . . . C 3 29.657 21.064 19.821 1 34.94 ? C4' ADP 450 A 1 HETATM 12 O O4' ADP . . . C 3 30.755 21.879 19.275 1 33.87 ? O4' ADP 450 A 1 HETATM 13 C C3' ADP . . . C 3 29.823 21.203 21.341 1 35.35 ? C3' ADP 450 A 1 HETATM 14 O O3' ADP . . . C 3 30.735 20.196 21.85 1 32.59 ? O3' ADP 450 A 1 HETATM 15 C C2' ADP . . . C 3 30.512 22.612 21.539 1 35.93 ? C2' ADP 450 A 1 HETATM 16 O O2' ADP . . . C 3 31.48 22.632 22.632 1 39.05 ? O2' ADP 450 A 1 HETATM 17 C C1' ADP . . . C 3 31.289 22.817 20.214 1 34.1 ? C1' ADP 450 A 1 HETATM 18 N N9 ADP . . . C 3 31.019 24.23 19.65 1 33.32 ? N9 ADP 450 A 1 HETATM 19 C C8 ADP . . . C 3 30.284 24.543 18.585 1 33.78 ? C8 ADP 450 A 1 HETATM 20 N N7 ADP . . . C 3 30.22 25.801 18.36 1 32.83 ? N7 ADP 450 A 1 HETATM 21 C C5 ADP . . . C 3 30.973 26.38 19.366 1 33.01 ? C5 ADP 450 A 1 HETATM 22 C C6 ADP . . . C 3 31.321 27.742 19.71 1 33.4 ? C6 ADP 450 A 1 HETATM 23 N N6 ADP . . . C 3 30.898 28.816 18.985 1 35.11 ? N6 ADP 450 A 1 HETATM 24 N N1 ADP . . . C 3 32.108 27.944 20.81 1 34.63 ? N1 ADP 450 A 1 HETATM 25 C C2 ADP . . . C 3 32.531 26.887 21.526 1 35.16 ? C2 ADP 450 A 1 HETATM 26 N N3 ADP . . . C 3 32.257 25.582 21.278 1 33.56 ? N3 ADP 450 A 1 HETATM 27 C C4 ADP . . . C 3 31.474 25.399 20.185 1 33.19 ? C4 ADP 450 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #