data_7ODM # _model_server_result.job_id 1h0KovctJogQGG4BLTLMxQ _model_server_result.datetime_utc '2024-11-22 18:27:34' _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 7odm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7ODM # _exptl.entry_id 7ODM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.331 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{S})-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]azanium' _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 90 _cell.entry_id 7ODM _cell.length_a 112.611 _cell.length_b 112.611 _cell.length_c 103.646 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ODM _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 # 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' 5_554 -x+1/2,y,-z-1/4 -1 0 0 0 1 0 0 0 -1 56.3055 0 -25.9115 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H18 N3 O6 S 1' _chem_comp.formula_weight 308.331 _chem_comp.id VDW _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{S})-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]azanium' _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 SG2 CB2 VDW sing 376 n n CB2 CA2 VDW sing 377 n n CA2 N2 VDW sing 378 n n CA2 C2 VDW sing 379 n n N2 CD1 VDW sing 380 n n O11 C1 VDW doub 381 n n CG1 CD1 VDW sing 382 n n CG1 CB1 VDW sing 383 n n O12 C1 VDW sing 384 n n CD1 OE1 VDW doub 385 n n C1 CA1 VDW sing 386 n n N1 CA1 VDW sing 387 n n C2 N3 VDW sing 388 n n C2 O2 VDW doub 389 n n N3 CA3 VDW sing 390 n n CA1 CB1 VDW sing 391 n n CA3 C3 VDW sing 392 n n C3 O31 VDW doub 393 n n C3 O32 VDW sing 394 n n N1 HN13 VDW sing 395 n n N1 HN11 VDW sing 396 n n N1 HN12 VDW sing 397 n n CA1 HA1 VDW sing 398 n n O12 H1 VDW sing 399 n n CB1 HB13 VDW sing 400 n n CB1 HB12 VDW sing 401 n n CG1 HG13 VDW sing 402 n n CG1 HG12 VDW sing 403 n n N2 HN2 VDW sing 404 n n CA2 HA2 VDW sing 405 n n CB2 HB23 VDW sing 406 n n CB2 HB22 VDW sing 407 n n SG2 HSG VDW sing 408 n n N3 HN3 VDW sing 409 n n CA3 HA31 VDW sing 410 n n CA3 HA32 VDW sing 411 n n O32 H2 VDW sing 412 n n # _atom_sites.entry_id 7ODM _atom_sites.fract_transf_matrix[1][1] 0.00888 _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] 0.00888 _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] 0.009648 _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 VDW AAA 1 301 1 VDW GSH . C 3 HOH AAA 1 401 5 HOH HOH . C 3 HOH AAA 2 402 10 HOH HOH . C 3 HOH AAA 3 403 2 HOH HOH . C 3 HOH AAA 4 404 12 HOH HOH . C 3 HOH AAA 5 405 15 HOH HOH . C 3 HOH AAA 6 406 26 HOH HOH . C 3 HOH AAA 7 407 24 HOH HOH . C 3 HOH AAA 8 408 20 HOH HOH . C 3 HOH AAA 9 409 1 HOH HOH . C 3 HOH AAA 10 410 4 HOH HOH . C 3 HOH AAA 11 411 17 HOH HOH . C 3 HOH AAA 12 412 7 HOH HOH . C 3 HOH AAA 13 413 14 HOH HOH . C 3 HOH AAA 14 414 21 HOH HOH . C 3 HOH AAA 15 415 11 HOH HOH . C 3 HOH AAA 16 416 23 HOH HOH . C 3 HOH AAA 17 417 6 HOH HOH . C 3 HOH AAA 18 418 22 HOH HOH . C 3 HOH AAA 19 419 9 HOH HOH . C 3 HOH AAA 20 420 16 HOH HOH . C 3 HOH AAA 21 421 18 HOH HOH . C 3 HOH AAA 22 422 25 HOH HOH . C 3 HOH AAA 23 423 13 HOH HOH . C 3 HOH AAA 24 424 19 HOH HOH . C 3 HOH AAA 25 425 3 HOH HOH . C 3 HOH AAA 26 426 8 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 N N1 VDW . . . B 2 21.055 4.775 -12.506 0.7 70.56 0 N1 VDW 301 AAA 1 HETATM 2 C CA1 VDW . . . B 2 19.602 4.624 -12.807 0.7 68.38 0 CA1 VDW 301 AAA 1 HETATM 3 C C1 VDW . . . B 2 19.38 3.391 -13.706 0.7 65.32 0 C1 VDW 301 AAA 1 HETATM 4 O O11 VDW . . . B 2 20.405 2.782 -14.108 0.7 58.74 0 O11 VDW 301 AAA 1 HETATM 5 O O12 VDW . . . B 2 18.193 3.056 -13.959 0.7 52.77 0 O12 VDW 301 AAA 1 HETATM 6 C CB1 VDW . . . B 2 19.102 5.93 -13.43 0.7 72.57 0 CB1 VDW 301 AAA 1 HETATM 7 C CG1 VDW . . . B 2 17.772 6.413 -12.875 0.7 69.63 0 CG1 VDW 301 AAA 1 HETATM 8 C CD1 VDW . . . B 2 17.344 7.736 -13.467 0.7 69.71 0 CD1 VDW 301 AAA 1 HETATM 9 O OE1 VDW . . . B 2 17.927 8.277 -14.397 0.7 64.77 0 OE1 VDW 301 AAA 1 HETATM 10 N N2 VDW . . . B 2 16.302 8.306 -12.881 0.7 74.73 0 N2 VDW 301 AAA 1 HETATM 11 C CA2 VDW . . . B 2 15.435 9.244 -13.558 0.7 72.1 0 CA2 VDW 301 AAA 1 HETATM 12 C C2 VDW . . . B 2 14.348 9.782 -12.635 0.7 64.55 0 C2 VDW 301 AAA 1 HETATM 13 O O2 VDW . . . B 2 13.372 9.078 -12.398 0.7 57.19 0 O2 VDW 301 AAA 1 HETATM 14 C CB2 VDW . . . B 2 14.828 8.611 -14.8 0.7 80.17 0 CB2 VDW 301 AAA 1 HETATM 15 S SG2 VDW . . . B 2 14.16 9.788 -16.004 0.7 95.98 0 SG2 VDW 301 AAA 1 HETATM 16 N N3 VDW . . . B 2 14.579 10.957 -12.039 0.7 69.06 0 N3 VDW 301 AAA 1 HETATM 17 C CA3 VDW . . . B 2 13.608 11.595 -11.176 0.7 66.67 0 CA3 VDW 301 AAA 1 HETATM 18 C C3 VDW . . . B 2 14.165 11.967 -9.805 0.7 70.32 0 C3 VDW 301 AAA 1 HETATM 19 O O31 VDW . . . B 2 13.814 13.072 -9.356 0.7 82.59 0 O31 VDW 301 AAA 1 HETATM 20 O O32 VDW . . . B 2 14.911 11.146 -9.218 0.7 61.2 0 O32 VDW 301 AAA 1 HETATM 21 H HN13 VDW . . . B 2 21.403 3.977 -12.236 0.7 69.78 0 HN13 VDW 301 AAA 1 HETATM 22 H HN11 VDW . . . B 2 21.175 5.388 -11.844 0.7 69.86 0 HN11 VDW 301 AAA 1 HETATM 23 H HN12 VDW . . . B 2 21.501 5.052 -13.251 0.7 69.86 0 HN12 VDW 301 AAA 1 HETATM 24 H HA1 VDW . . . B 2 19.127 4.479 -11.956 0.7 68.97 0 HA1 VDW 301 AAA 1 HETATM 25 H HB13 VDW . . . B 2 19.778 6.624 -13.284 0.7 70.85 0 HB13 VDW 301 AAA 1 HETATM 26 H HB12 VDW . . . B 2 19.014 5.799 -14.398 0.7 70.84 0 HB12 VDW 301 AAA 1 HETATM 27 H HG13 VDW . . . B 2 17.082 5.742 -13.061 0.7 70.23 0 HG13 VDW 301 AAA 1 HETATM 28 H HG12 VDW . . . B 2 17.845 6.508 -11.902 0.7 70.23 0 HG12 VDW 301 AAA 1 HETATM 29 H HN2 VDW . . . B 2 16.134 8.128 -12.048 0.7 72.34 0 HN2 VDW 301 AAA 1 HETATM 30 H HA2 VDW . . . B 2 15.987 10.004 -13.847 0.7 72.5 0 HA2 VDW 301 AAA 1 HETATM 31 H HB23 VDW . . . B 2 15.515 8.075 -15.24 0.7 81.42 0 HB23 VDW 301 AAA 1 HETATM 32 H HB22 VDW . . . B 2 14.112 8.009 -14.521 0.7 81.23 0 HB22 VDW 301 AAA 1 HETATM 33 H HSG VDW . . . B 2 13.789 8.987 -16.819 0 36.63 0 HSG VDW 301 AAA 1 HETATM 34 H HN3 VDW . . . B 2 15.346 11.353 -12.175 0.7 67.44 0 HN3 VDW 301 AAA 1 HETATM 35 H HA31 VDW . . . B 2 12.846 10.998 -11.049 0.7 68.05 0 HA31 VDW 301 AAA 1 HETATM 36 H HA32 VDW . . . B 2 13.284 12.408 -11.61 0.7 68.1 0 HA32 VDW 301 AAA 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 36 #