data_4DKI # _model_server_result.job_id tc5vFevNkC1kHgEHIy8kng _model_server_result.datetime_utc '2024-11-29 12:53:50' _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 4dki # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 4DKI # _exptl.entry_id 4DKI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 536.585 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid' _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 4DKI _cell.length_a 80.847 _cell.length_b 103.471 _cell.length_c 186.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DKI _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 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,C,D,E,F,G,H,I,J,K,T 1 1 B,L,M,N,O,P,Q,R,S,U 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 3 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 ? 2 C N N ? 2 L 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 OG SER 381 A SER 403 1_555 C C RB6 . A RB6 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale2 B OG SER 381 B SER 403 1_555 L C RB6 . B RB6 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? metalc ? metalc1 A O GLY 113 A GLY 135 1_555 I CD CD . A CD 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc2 A ND1 HIS 121 A HIS 143 1_555 G CD CD . A CD 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc3 A OE1 GLU 123 A GLU 145 1_555 G CD CD . A CD 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc4 A OE2 GLU 123 A GLU 145 1_555 N CD CD . B CD 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc5 A OD1 ASP 187 A ASP 209 1_555 O CD CD . B CD 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc6 A OD2 ASP 187 A ASP 209 1_555 O CD CD . B CD 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc7 A NE2 HIS 289 A HIS 311 1_555 I CD CD . A CD 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc8 G CD CD . A CD 705 1_555 B OE2 GLU 123 B GLU 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc9 I CD CD . A CD 707 1_555 B OD2 ASP 187 B ASP 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc10 I CD CD . A CD 707 1_555 B OD1 ASP 187 B ASP 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc11 B O GLY 113 B GLY 135 1_555 O CD CD . B CD 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc12 B ND1 HIS 121 B HIS 143 1_555 N CD CD . B CD 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc13 B OE1 GLU 123 B GLU 145 1_555 N CD CD . B CD 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc14 B NE2 HIS 210 B HIS 232 1_555 P CD CD . B CD 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc15 B NE2 HIS 289 B HIS 311 1_555 O CD CD . B CD 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc16 B OD2 ASP 551 B ASP 573 1_555 Q CD CD . B CD 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc17 B OD1 ASP 551 B ASP 573 1_555 Q CD CD . B CD 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? # _chem_comp.formula 'C20 H24 N8 O6 S2' _chem_comp.formula_weight 536.585 _chem_comp.id RB6 _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'BAL 9141, bound form;ceftobiprole, bound form' # 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 NBG CBD RB6 sing 268 n n SBE CBD RB6 sing 269 n y SBE NBF RB6 sing 270 n y CBD NBC RB6 doub 271 n y NBF CBB RB6 doub 272 n y NBC CBB RB6 sing 273 n y O C RB6 doub 274 n n CBB CAY RB6 sing 275 n n C CA RB6 sing 276 n n OBJ CBH RB6 doub 277 n n CAY NAZ RB6 doub 278 z n CAY CAW RB6 sing 279 n n NAZ OBA RB6 sing 280 n n CAL CAM RB6 sing 281 n n CAL CAK RB6 sing 282 n n CAM NAN RB6 sing 283 n n N CAW RB6 sing 284 n n N CA RB6 sing 285 n n CAW OAX RB6 doub 286 n n CBH OBI RB6 sing 287 n n CBH CAD RB6 sing 288 n n CA CB RB6 sing 289 n n NAN CAO RB6 sing 290 n n CAD NAC RB6 sing 291 n n CAD CAE RB6 doub 292 n n NAC CB RB6 sing 293 n n CAP CAQ RB6 sing 294 n n CAP NAJ RB6 sing 295 n n CAQ CAG RB6 doub 296 n n NAJ CAH RB6 sing 297 n n NAJ CAK RB6 sing 298 n n CAH CAG RB6 sing 299 n n CAH OAI RB6 doub 300 n n CAG CAF RB6 sing 301 n n CAF CAE RB6 sing 302 n n CAO CAK RB6 sing 303 n n CAE CAR RB6 sing 304 n n CB SAS RB6 sing 305 n n CAR SAS RB6 sing 306 n n NBG H1 RB6 sing 307 n n NBG H2 RB6 sing 308 n n OBA H3 RB6 sing 309 n n N H4 RB6 sing 310 n n CA H5 RB6 sing 311 n n C H6 RB6 sing 312 n n CB H7 RB6 sing 313 n n CAR H8 RB6 sing 314 n n CAR H9 RB6 sing 315 n n NAC H10 RB6 sing 316 n n OBI H11 RB6 sing 317 n n CAF H12 RB6 sing 318 n n CAF H13 RB6 sing 319 n n CAQ H14 RB6 sing 320 n n CAP H15 RB6 sing 321 n n CAP H16 RB6 sing 322 n n CAK H17 RB6 sing 323 n n CAL H18 RB6 sing 324 n n CAL H19 RB6 sing 325 n n CAM H20 RB6 sing 326 n n CAM H21 RB6 sing 327 n n NAN H22 RB6 sing 328 n n CAO H24 RB6 sing 329 n n CAO H25 RB6 sing 330 n n # _atom_sites.entry_id 4DKI _atom_sites.fract_transf_matrix[1][1] 0.012369 _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] 0.009665 _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] 0.005362 _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 RB6 A 1 701 669 RB6 RB6 . D 3 BCT A 1 702 1 BCT BCT . E 3 BCT A 1 703 1 BCT BCT . F 3 BCT A 1 704 1 BCT BCT . G 4 CD A 1 705 1001 CD CD . H 4 CD A 1 706 1004 CD CD . I 4 CD A 1 707 1005 CD CD . J 5 CL A 1 708 1009 CL CL . K 5 CL A 1 709 1011 CL CL . L 2 RB6 B 1 701 669 RB6 RB6 . M 3 BCT B 1 702 1 BCT BCT . N 4 CD B 1 703 1002 CD CD . O 4 CD B 1 704 1003 CD CD . P 4 CD B 1 705 1006 CD CD . Q 4 CD B 1 706 1007 CD CD . R 5 CL B 1 707 1008 CL CL . S 5 CL B 1 708 1010 CL CL . T 6 HOH A 1 801 5 HOH HOH . T 6 HOH A 2 802 6 HOH HOH . T 6 HOH A 3 803 7 HOH HOH . T 6 HOH A 4 804 1 HOH HOH . T 6 HOH A 5 805 2 HOH HOH . T 6 HOH A 6 806 11 HOH HOH . T 6 HOH A 7 807 15 HOH HOH . T 6 HOH A 8 808 18 HOH HOH . T 6 HOH A 9 809 20 HOH HOH . T 6 HOH A 10 810 21 HOH HOH . T 6 HOH A 11 811 22 HOH HOH . T 6 HOH A 12 812 23 HOH HOH . T 6 HOH A 13 813 24 HOH HOH . T 6 HOH A 14 814 25 HOH HOH . T 6 HOH A 15 815 1 HOH HOH . T 6 HOH A 16 816 4 HOH HOH . T 6 HOH A 17 817 8 HOH HOH . T 6 HOH A 18 818 11 HOH HOH . U 6 HOH B 1 801 1 HOH HOH . U 6 HOH B 2 802 3 HOH HOH . U 6 HOH B 3 803 8 HOH HOH . U 6 HOH B 4 804 9 HOH HOH . U 6 HOH B 5 805 3 HOH HOH . U 6 HOH B 6 806 4 HOH HOH . U 6 HOH B 7 807 6 HOH HOH . U 6 HOH B 8 808 9 HOH HOH . U 6 HOH B 9 809 12 HOH HOH . U 6 HOH B 10 810 16 HOH HOH . U 6 HOH B 11 811 17 HOH HOH . U 6 HOH B 12 812 19 HOH HOH . U 6 HOH B 13 813 26 HOH HOH . U 6 HOH B 14 814 2 HOH HOH . U 6 HOH B 15 815 3 HOH HOH . U 6 HOH B 16 816 5 HOH HOH . U 6 HOH B 17 817 6 HOH HOH . U 6 HOH B 18 818 7 HOH HOH . U 6 HOH B 19 819 9 HOH HOH . U 6 HOH B 20 820 10 HOH HOH . U 6 HOH B 21 821 12 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 O OAX RB6 . . . C 2 28.322 24.886 87.585 1 78.88 ? OAX RB6 701 A 1 HETATM 2 C CAW RB6 . . . C 2 28.626 25.789 86.862 1 76.3 ? CAW RB6 701 A 1 HETATM 3 C CAY RB6 . A . C 2 29.882 25.572 86.181 0.5 74.47 ? CAY RB6 701 A 1 HETATM 4 C CAY RB6 . B . C 2 29.881 25.776 86.125 0.5 79.41 ? CAY RB6 701 A 1 HETATM 5 C CBB RB6 . A . C 2 29.86 24.627 85.051 0.5 68.98 ? CBB RB6 701 A 1 HETATM 6 C CBB RB6 . B . C 2 30.914 26.699 86.633 0.5 80.34 ? CBB RB6 701 A 1 HETATM 7 N NBF RB6 . A . C 2 30.996 24.331 84.413 0.5 65.81 ? NBF RB6 701 A 1 HETATM 8 N NBF RB6 . B . C 2 32.097 26.808 86.011 0.5 81.11 ? NBF RB6 701 A 1 HETATM 9 S SBE RB6 . A . C 2 30.639 23.233 83.266 0.5 63.71 ? SBE RB6 701 A 1 HETATM 10 S SBE RB6 . B . C 2 32.965 27.947 86.806 0.5 81.06 ? SBE RB6 701 A 1 HETATM 11 C CBD RB6 . A . C 2 28.978 23.268 83.642 0.5 64.89 ? CBD RB6 701 A 1 HETATM 12 C CBD RB6 . B . C 2 31.745 28.175 87.965 0.5 80.89 ? CBD RB6 701 A 1 HETATM 13 N NBG RB6 . A . C 2 27.974 22.603 83.066 0.5 65.45 ? NBG RB6 701 A 1 HETATM 14 N NBG RB6 . B . C 2 31.762 28.979 89.027 0.5 81.69 ? NBG RB6 701 A 1 HETATM 15 N NBC RB6 . A . C 2 28.717 24.049 84.652 0.5 65.75 ? NBC RB6 701 A 1 HETATM 16 N NBC RB6 . B . C 2 30.688 27.44 87.728 0.5 80.14 ? NBC RB6 701 A 1 HETATM 17 N NAZ RB6 . A . C 2 30.995 26.092 86.481 0.5 77.14 ? NAZ RB6 701 A 1 HETATM 18 N NAZ RB6 . B . C 2 30.183 25.11 85.082 0.5 80.62 ? NAZ RB6 701 A 1 HETATM 19 O OBA RB6 . A . C 2 31.295 26.993 87.476 0.5 77.8 ? OBA RB6 701 A 1 HETATM 20 O OBA RB6 . B . C 2 29.478 24.187 84.338 0.5 80.27 ? OBA RB6 701 A 1 HETATM 21 N N RB6 . . . C 2 27.879 26.865 86.761 1 72.55 ? N RB6 701 A 1 HETATM 22 C CA RB6 . . . C 2 26.485 26.976 87.172 1 68.54 ? CA RB6 701 A 1 HETATM 23 C C RB6 . . . C 2 25.518 27.158 86.054 1 62.93 ? C RB6 701 A 1 HETATM 24 O O RB6 . . . C 2 25.901 27.602 84.982 1 60.13 ? O RB6 701 A 1 HETATM 25 C CB RB6 . . . C 2 26.259 28.141 88.11 1 67.21 ? CB RB6 701 A 1 HETATM 26 S SAS RB6 . . . C 2 27.665 28.335 89.099 1 66.95 ? SAS RB6 701 A 1 HETATM 27 C CAR RB6 . . . C 2 28.582 29.603 88.35 1 66.58 ? CAR RB6 701 A 1 HETATM 28 N NAC RB6 . . . C 2 25.882 29.347 87.381 1 64.58 ? NAC RB6 701 A 1 HETATM 29 C CAD RB6 . . . C 2 26.461 30.539 87.374 1 62.41 ? CAD RB6 701 A 1 HETATM 30 C CBH RB6 . . . C 2 25.666 31.657 86.881 1 58.08 ? CBH RB6 701 A 1 HETATM 31 O OBI RB6 . . . C 2 24.469 31.883 87.154 1 55.12 ? OBI RB6 701 A 1 HETATM 32 O OBJ RB6 . . . C 2 26.161 32.464 86.07 1 58.58 ? OBJ RB6 701 A 1 HETATM 33 C CAE RB6 . . . C 2 27.722 30.718 87.814 1 65.98 ? CAE RB6 701 A 1 HETATM 34 C CAF RB6 . . . C 2 28.299 32.058 87.795 1 70.61 ? CAF RB6 701 A 1 HETATM 35 C CAG RB6 . . . C 2 29.571 32.424 87.722 1 76.61 ? CAG RB6 701 A 1 HETATM 36 C CAH RB6 . . . C 2 29.987 33.799 87.72 1 79.37 ? CAH RB6 701 A 1 HETATM 37 O OAI RB6 . . . C 2 29.3 34.781 87.787 1 76.64 ? OAI RB6 701 A 1 HETATM 38 C CAQ RB6 . . . C 2 30.743 31.511 87.648 1 79.4 ? CAQ RB6 701 A 1 HETATM 39 C CAP RB6 . . . C 2 31.925 32.456 87.592 1 82.94 ? CAP RB6 701 A 1 HETATM 40 N NAJ RB6 . . . C 2 31.274 33.743 87.672 1 84.44 ? NAJ RB6 701 A 1 HETATM 41 C CAK RB6 . . . C 2 32.117 34.916 87.814 1 89.3 ? CAK RB6 701 A 1 HETATM 42 C CAL RB6 . . . C 2 31.908 35.803 86.621 1 89.7 ? CAL RB6 701 A 1 HETATM 43 C CAM RB6 . . . C 2 33.1 36.717 86.721 1 91.56 ? CAM RB6 701 A 1 HETATM 44 N NAN RB6 . . . C 2 34.181 35.854 87.19 1 93.29 ? NAN RB6 701 A 1 HETATM 45 C CAO RB6 . . . C 2 33.609 34.665 87.813 1 92.49 ? CAO RB6 701 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 45 #