data_4DKI
#
_model_server_result.job_id            KbDlLynrouVZKnJMs3FcBw 
_model_server_result.datetime_utc      '2024-12-01 18:14:34' 
_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          4dki 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","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 . . . L 2 -37.133 49.864 67.692 1 110.64 ? OAX RB6 701 B 1 
HETATM 2 C CAW RB6 . . . L 2 -36.994 49.181 66.73 1 110.65 ? CAW RB6 701 B 1 
HETATM 3 C CAY RB6 . . . L 2 -37.763 49.544 65.57 1 113.82 ? CAY RB6 701 B 1 
HETATM 4 C CBB RB6 . . . L 2 -37.066 50.428 64.642 1 114.87 ? CBB RB6 701 B 1 
HETATM 5 N NBF RB6 . . . L 2 -37.649 50.865 63.518 1 115.82 ? NBF RB6 701 B 1 
HETATM 6 S SBE RB6 . . . L 2 -36.555 51.817 62.753 1 113.48 ? SBE RB6 701 B 1 
HETATM 7 C CBD RB6 . . . L 2 -35.373 51.563 63.956 1 113.49 ? CBD RB6 701 B 1 
HETATM 8 N NBG RB6 . . . L 2 -34.129 52.043 64.033 1 112.51 ? NBG RB6 701 B 1 
HETATM 9 N NBC RB6 . . . L 2 -35.81 50.807 64.924 1 114.43 ? NBC RB6 701 B 1 
HETATM 10 N NAZ RB6 . . . L 2 -38.934 49.185 65.285 1 116.85 ? NAZ RB6 701 B 1 
HETATM 11 O OBA RB6 . . . L 2 -39.79 48.36 65.98 1 119.08 ? OBA RB6 701 B 1 
HETATM 12 N N RB6 . . . L 2 -36.193 48.141 66.726 1 108.21 ? N RB6 701 B 1 
HETATM 13 C CA RB6 . . . L 2 -35.175 47.884 67.729 1 105.06 ? CA RB6 701 B 1 
HETATM 14 C C RB6 . . . L 2 -33.746 48.047 67.334 1 100.47 ? C RB6 701 B 1 
HETATM 15 O O RB6 . . . L 2 -33.403 47.911 66.165 1 96.83 ? O RB6 701 B 1 
HETATM 16 C CB RB6 . . . L 2 -35.424 46.647 68.57 1 105.38 ? CB RB6 701 B 1 
HETATM 17 S SAS RB6 . . . L 2 -37.131 46.38 68.638 1 106.31 ? SAS RB6 701 B 1 
HETATM 18 C CAR RB6 . . . L 2 -37.466 45.271 67.375 1 107.98 ? CAR RB6 701 B 1 
HETATM 19 N NAC RB6 . . . L 2 -34.701 45.451 68.19 1 104.44 ? NAC RB6 701 B 1 
HETATM 20 C CAD RB6 . . . L 2 -35.214 44.281 67.81 1 105.93 ? CAD RB6 701 B 1 
HETATM 21 C CBH RB6 . . . L 2 -34.323 43.142 67.849 1 104.02 ? CBH RB6 701 B 1 
HETATM 22 O OBI RB6 . . . L 2 -33.971 42.536 68.889 1 102.31 ? OBI RB6 701 B 1 
HETATM 23 O OBJ RB6 . . . L 2 -33.787 42.794 66.774 1 103.34 ? OBJ RB6 701 B 1 
HETATM 24 C CAE RB6 . . . L 2 -36.501 44.123 67.413 1 108.66 ? CAE RB6 701 B 1 
HETATM 25 C CAF RB6 . . . L 2 -37.019 42.825 66.944 1 111.07 ? CAF RB6 701 B 1 
HETATM 26 C CAG RB6 . . . L 2 -38.088 42.647 66.146 1 112.91 ? CAG RB6 701 B 1 
HETATM 27 C CAH RB6 . . . L 2 -38.537 41.375 65.64 1 114.62 ? CAH RB6 701 B 1 
HETATM 28 O OAI RB6 . . . L 2 -38.024 40.305 65.825 1 113.31 ? OAI RB6 701 B 1 
HETATM 29 C CAQ RB6 . . . L 2 -38.981 43.734 65.641 1 112.91 ? CAQ RB6 701 B 1 
HETATM 30 C CAP RB6 . . . L 2 -40.03 43.025 64.818 1 115.41 ? CAP RB6 701 B 1 
HETATM 31 N NAJ RB6 . . . L 2 -39.571 41.664 64.904 1 117.21 ? NAJ RB6 701 B 1 
HETATM 32 C CAK RB6 . . . L 2 -40.291 40.769 64.015 1 121.69 ? CAK RB6 701 B 1 
HETATM 33 C CAL RB6 . . . L 2 -40.696 39.512 64.724 1 123.3 ? CAL RB6 701 B 1 
HETATM 34 C CAM RB6 . . . L 2 -40.92 38.526 63.601 1 125.05 ? CAM RB6 701 B 1 
HETATM 35 N NAN RB6 . . . L 2 -40.136 39.02 62.47 1 124.22 ? NAN RB6 701 B 1 
HETATM 36 C CAO RB6 . . . L 2 -39.461 40.253 62.863 1 122.02 ? CAO RB6 701 B 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           261 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           36 
#