data_3KDR # _model_server_result.job_id lFenOnTcRIFugByZ0-_0pA _model_server_result.datetime_utc '2024-11-07 23:32:41' _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 3kdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 3KDR # _exptl.entry_id 3KDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 94.971 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHATE ION' _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 3KDR _cell.length_a 340.068 _cell.length_b 340.068 _cell.length_c 340.068 _cell.Z_PDB 288 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 209 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'F 4 3 2' # 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 dodecameric 12 author_and_software_defined_assembly 1 PISA 72-meric 72 software_defined_assembly 2 PISA 72-meric 72 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1,2,3,4 A,B,C,D,E,F,G,H,I,J 2 1,2,5,6,7,8,3,4,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24 A,B,C,D,E,F,G,H,I,J 3 1,2,25,26,27,28,29,30,31,32,33,34,35,36,3,4,37,38,39,40,41,42,43,44 # 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 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 15_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 16_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 340.068 6 'crystal symmetry operation' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 340.068 7 'crystal symmetry operation' 13_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 340.068 8 'crystal symmetry operation' 14_556 -y,-x,-z+1 0 -1 0 -1 0 0 0 0 -1 0 0 340.068 9 'crystal symmetry operation' 33_545 y,z-1/2,x+1/2 0 1 0 0 0 1 1 0 0 0 -170.034 170.034 10 'crystal symmetry operation' 34_545 -y,z-1/2,-x+1/2 0 -1 0 0 0 1 -1 0 0 0 -170.034 170.034 11 'crystal symmetry operation' 35_555 y,-z+1/2,-x+1/2 0 1 0 0 0 -1 -1 0 0 0 170.034 170.034 12 'crystal symmetry operation' 36_555 -y,-z+1/2,x+1/2 0 -1 0 0 0 -1 1 0 0 0 170.034 170.034 13 'crystal symmetry operation' 41_545 x,z-1/2,-y+1/2 1 0 0 0 0 1 0 -1 0 0 -170.034 170.034 14 'crystal symmetry operation' 42_545 -x,z-1/2,y+1/2 -1 0 0 0 0 1 0 1 0 0 -170.034 170.034 15 'crystal symmetry operation' 43_555 -x,-z+1/2,-y+1/2 -1 0 0 0 0 -1 0 -1 0 0 170.034 170.034 16 'crystal symmetry operation' 44_555 x,-z+1/2,y+1/2 1 0 0 0 0 -1 0 1 0 0 170.034 170.034 17 'crystal symmetry operation' 53_455 z-1/2,x,y+1/2 0 0 1 1 0 0 0 1 0 -170.034 0 170.034 18 'crystal symmetry operation' 54_455 z-1/2,-x,-y+1/2 0 0 1 -1 0 0 0 -1 0 -170.034 0 170.034 19 'crystal symmetry operation' 55_555 -z+1/2,-x,y+1/2 0 0 -1 -1 0 0 0 1 0 170.034 0 170.034 20 'crystal symmetry operation' 56_555 -z+1/2,x,-y+1/2 0 0 -1 1 0 0 0 -1 0 170.034 0 170.034 21 'crystal symmetry operation' 69_455 z-1/2,y,-x+1/2 0 0 1 0 1 0 -1 0 0 -170.034 0 170.034 22 'crystal symmetry operation' 70_455 z-1/2,-y,x+1/2 0 0 1 0 -1 0 1 0 0 -170.034 0 170.034 23 'crystal symmetry operation' 71_555 -z+1/2,y,x+1/2 0 0 -1 0 1 0 1 0 0 170.034 0 170.034 24 'crystal symmetry operation' 72_555 -z+1/2,-y,-x+1/2 0 0 -1 0 -1 0 -1 0 0 170.034 0 170.034 25 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 26 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 27 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 28 'crystal symmetry operation' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 29 'crystal symmetry operation' 7_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 30 'crystal symmetry operation' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 31 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 32 'crystal symmetry operation' 10_555 -y,z,-x 0 -1 0 0 0 1 -1 0 0 0 0 0 33 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 34 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 35 'crystal symmetry operation' 13_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 36 'crystal symmetry operation' 14_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 37 'crystal symmetry operation' 17_555 x,z,-y 1 0 0 0 0 1 0 -1 0 0 0 0 38 'crystal symmetry operation' 18_555 -x,z,y -1 0 0 0 0 1 0 1 0 0 0 0 39 'crystal symmetry operation' 19_555 -x,-z,-y -1 0 0 0 0 -1 0 -1 0 0 0 0 40 'crystal symmetry operation' 20_555 x,-z,y 1 0 0 0 0 -1 0 1 0 0 0 0 41 'crystal symmetry operation' 21_555 z,y,-x 0 0 1 0 1 0 -1 0 0 0 0 0 42 'crystal symmetry operation' 22_555 z,-y,x 0 0 1 0 -1 0 1 0 0 0 0 0 43 'crystal symmetry operation' 23_555 -z,y,x 0 0 -1 0 1 0 1 0 0 0 0 0 44 'crystal symmetry operation' 24_555 -z,-y,-x 0 0 -1 0 -1 0 -1 0 0 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 ? 2 D N N ? 2 H 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 covale ? covale1 A C MSE 57 A MSE 96 1_555 A N GLN 58 A GLN 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MSE 64 A MSE 103 1_555 A N LEU 65 A LEU 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 A C MSE 117 A MSE 156 1_555 A N GLU 118 A GLU 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale4 A C MSE 205 A MSE 244 1_555 A N ALA 206 A ALA 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C MSE 226 A MSE 265 1_555 A N ASN 227 A ASN 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 A C MSE 251 A MSE 290 1_555 A N ILE 252 A ILE 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale7 A C MSE 263 A MSE 302 1_555 A N SER 264 A SER 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C MSE 275 A MSE 314 1_555 A N HIS 276 A HIS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale9 B C MSE 57 B MSE 96 1_555 B N GLN 58 B GLN 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale10 B C MSE 64 B MSE 103 1_555 B N LEU 65 B LEU 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale11 B C MSE 117 B MSE 156 1_555 B N GLU 118 B GLU 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 B C MSE 205 B MSE 244 1_555 B N ALA 206 B ALA 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale13 B C MSE 226 B MSE 265 1_555 B N ASN 227 B ASN 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale14 B C MSE 251 B MSE 290 1_555 B N ILE 252 B ILE 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale15 B C MSE 263 B MSE 302 1_555 B N SER 264 B SER 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale16 B C MSE 275 B MSE 314 1_555 B N HIS 276 B HIS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale17 C C MSE 57 C MSE 96 1_555 C N GLN 58 C GLN 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale18 C C MSE 64 C MSE 103 1_555 C N LEU 65 C LEU 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.309 ? covale ? covale19 C C MSE 117 C MSE 156 1_555 C N GLU 118 C GLU 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale20 C C MSE 205 C MSE 244 1_555 C N ALA 206 C ALA 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale21 C C MSE 226 C MSE 265 1_555 C N ASN 227 C ASN 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale22 C C MSE 251 C MSE 290 1_555 C N ILE 252 C ILE 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale23 C C MSE 263 C MSE 302 1_555 C N SER 264 C SER 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale24 C C MSE 275 C MSE 314 1_555 C N HIS 276 C HIS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale25 A C THR 56 A THR 95 1_555 A N MSE 57 A MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale26 A C ARG 63 A ARG 102 1_555 A N MSE 64 A MSE 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale27 A C PRO 116 A PRO 155 1_555 A N MSE 117 A MSE 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale28 A C GLU 204 A GLU 243 1_555 A N MSE 205 A MSE 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale29 A C ALA 225 A ALA 264 1_555 A N MSE 226 A MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale30 A C ARG 250 A ARG 289 1_555 A N MSE 251 A MSE 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale31 A C LEU 262 A LEU 301 1_555 A N MSE 263 A MSE 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale32 A C ASP 274 A ASP 313 1_555 A N MSE 275 A MSE 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale33 B C THR 56 B THR 95 1_555 B N MSE 57 B MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale34 B C ARG 63 B ARG 102 1_555 B N MSE 64 B MSE 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale35 B C PRO 116 B PRO 155 1_555 B N MSE 117 B MSE 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.304 ? covale ? covale36 B C GLU 204 B GLU 243 1_555 B N MSE 205 B MSE 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale37 B C ALA 225 B ALA 264 1_555 B N MSE 226 B MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.308 ? covale ? covale38 B C ARG 250 B ARG 289 1_555 B N MSE 251 B MSE 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? covale ? covale39 B C LEU 262 B LEU 301 1_555 B N MSE 263 B MSE 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale40 B C ASP 274 B ASP 313 1_555 B N MSE 275 B MSE 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale41 C C THR 56 C THR 95 1_555 C N MSE 57 C MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale42 C C ARG 63 C ARG 102 1_555 C N MSE 64 C MSE 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale43 C C PRO 116 C PRO 155 1_555 C N MSE 117 C MSE 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale44 C C GLU 204 C GLU 243 1_555 C N MSE 205 C MSE 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale45 C C ALA 225 C ALA 264 1_555 C N MSE 226 C MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale46 C C ARG 250 C ARG 289 1_555 C N MSE 251 C MSE 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale47 C C LEU 262 C LEU 301 1_555 C N MSE 263 C MSE 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? covale ? covale48 C C ASP 274 C ASP 313 1_555 C N MSE 275 C MSE 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _chem_comp.formula 'O4 P -3' _chem_comp.formula_weight 94.971 _chem_comp.id PO4 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHATE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3KDR _atom_sites.fract_transf_matrix[1][1] 0.002941 _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] 0.002941 _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] 0.002941 _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 D 2 PO4 A 1 1 1 PO4 PO4 . E 3 GOL A 1 350 1 GOL GOL . F 4 SO4 B 1 4 4 SO4 SO4 . G 3 GOL B 1 2 2 GOL GOL . H 2 PO4 C 1 2 2 PO4 PO4 . I 4 SO4 C 1 3 3 SO4 SO4 . J 5 HOH A 1 351 1 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 P PO4 . . . D 2 44.567 10.8 86.175 1 83.81 ? P PO4 1 A 1 HETATM 2 O O1 PO4 . . . D 2 45.942 11.273 85.686 1 79.9 ? O1 PO4 1 A 1 HETATM 3 O O2 PO4 . . . D 2 43.412 11.756 85.746 1 78 ? O2 PO4 1 A 1 HETATM 4 O O3 PO4 . . . D 2 44.262 9.439 85.596 1 82.71 ? O3 PO4 1 A 1 HETATM 5 O O4 PO4 . . . D 2 44.702 10.579 87.687 1 81.79 ? O4 PO4 1 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 5 #