data_6G88
#
_model_server_result.job_id            1N-16Q3qWHmtLRBZLGGkWw 
_model_server_result.datetime_utc      '2024-11-24 15:49:51' 
_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          6g88 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":700}' 
#
_entry.id    6G88 
#
_exptl.entry_id    6G88 
_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    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.04 
_cell.angle_gamma         90 
_cell.entry_id            6G88 
_cell.length_a            79.194 
_cell.length_b            128.736 
_cell.length_c            238.479 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6G88 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E 1 1 
B,F,G 2 1 
C,H,I 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 D N N 
? 2 F 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 OG SER 391 A SER 422 1_555 D C RB6 . A RB6 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? 
covale ? covale2 B OG SER 391 B SER 422 1_555 F C RB6 . B RB6 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? 
covale ? covale3 C OG SER 391 C SER 422 1_555 H C RB6 . C RB6 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.282 ? 
#
_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 262 n n 
SBE CBD RB6 sing 263 n y 
SBE NBF RB6 sing 264 n y 
CBD NBC RB6 doub 265 n y 
NBF CBB RB6 doub 266 n y 
NBC CBB RB6 sing 267 n y 
O C RB6 doub 268 n n 
CBB CAY RB6 sing 269 n n 
C CA RB6 sing 270 n n 
OBJ CBH RB6 doub 271 n n 
CAY NAZ RB6 doub 272 z n 
CAY CAW RB6 sing 273 n n 
NAZ OBA RB6 sing 274 n n 
CAL CAM RB6 sing 275 n n 
CAL CAK RB6 sing 276 n n 
CAM NAN RB6 sing 277 n n 
N CAW RB6 sing 278 n n 
N CA RB6 sing 279 n n 
CAW OAX RB6 doub 280 n n 
CBH OBI RB6 sing 281 n n 
CBH CAD RB6 sing 282 n n 
CA CB RB6 sing 283 n n 
NAN CAO RB6 sing 284 n n 
CAD NAC RB6 sing 285 n n 
CAD CAE RB6 doub 286 n n 
NAC CB RB6 sing 287 n n 
CAP CAQ RB6 sing 288 n n 
CAP NAJ RB6 sing 289 n n 
CAQ CAG RB6 doub 290 n n 
NAJ CAH RB6 sing 291 n n 
NAJ CAK RB6 sing 292 n n 
CAH CAG RB6 sing 293 n n 
CAH OAI RB6 doub 294 n n 
CAG CAF RB6 sing 295 n n 
CAF CAE RB6 sing 296 n n 
CAO CAK RB6 sing 297 n n 
CAE CAR RB6 sing 298 n n 
CB SAS RB6 sing 299 n n 
CAR SAS RB6 sing 300 n n 
NBG H1 RB6 sing 301 n n 
NBG H2 RB6 sing 302 n n 
OBA H3 RB6 sing 303 n n 
N H4 RB6 sing 304 n n 
CA H5 RB6 sing 305 n n 
C H6 RB6 sing 306 n n 
CB H7 RB6 sing 307 n n 
CAR H8 RB6 sing 308 n n 
CAR H9 RB6 sing 309 n n 
NAC H10 RB6 sing 310 n n 
OBI H11 RB6 sing 311 n n 
CAF H12 RB6 sing 312 n n 
CAF H13 RB6 sing 313 n n 
CAQ H14 RB6 sing 314 n n 
CAP H15 RB6 sing 315 n n 
CAP H16 RB6 sing 316 n n 
CAK H17 RB6 sing 317 n n 
CAL H18 RB6 sing 318 n n 
CAL H19 RB6 sing 319 n n 
CAM H20 RB6 sing 320 n n 
CAM H21 RB6 sing 321 n n 
NAN H22 RB6 sing 322 n n 
CAO H24 RB6 sing 323 n n 
CAO H25 RB6 sing 324 n n 
#
_atom_sites.entry_id                     6G88 
_atom_sites.fract_transf_matrix[1][1]    0.012627 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000892 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007768 
_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]    0.004204 
_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 RB6 A 1 700 700 RB6 RB6 . 
E 3 SO4 A 1 701 701 SO4 SO4 . 
F 2 RB6 B 1 700 700 RB6 RB6 . 
G 3 SO4 B 1 701 701 SO4 SO4 . 
H 2 RB6 C 1 700 700 RB6 RB6 . 
I 3 SO4 C 1 701 701 SO4 SO4 . 
#
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 . . . D 2 -25.217 -19.711 101.125 1 60.46 ? OAX RB6 700 A 1 
HETATM 2 C CAW RB6 . . . D 2 -25.179 -20.086 99.966 1 59.84 ? CAW RB6 700 A 1 
HETATM 3 C CAY RB6 . . . D 2 -26.268 -20.549 99.368 1 62.95 ? CAY RB6 700 A 1 
HETATM 4 C CBB RB6 . . . D 2 -27.402 -19.599 99.117 1 64.25 ? CBB RB6 700 A 1 
HETATM 5 N NBF RB6 . . . D 2 -27.398 -18.221 99.4 1 65.38 ? NBF RB6 700 A 1 
HETATM 6 S SBE RB6 . . . D 2 -28.774 -17.689 99.098 1 67.37 ? SBE RB6 700 A 1 
HETATM 7 C CBD RB6 . . . D 2 -29.669 -18.859 98.71 1 66.36 ? CBD RB6 700 A 1 
HETATM 8 N NBG RB6 . . . D 2 -30.92 -18.879 98.26 1 65.99 ? NBG RB6 700 A 1 
HETATM 9 N NBC RB6 . . . D 2 -28.892 -19.974 98.917 1 65.14 ? NBC RB6 700 A 1 
HETATM 10 N NAZ RB6 . . . D 2 -26.544 -21.779 99.439 1 64.03 ? NAZ RB6 700 A 1 
HETATM 11 O OBA RB6 . . . D 2 -25.556 -22.734 99.672 1 63.99 ? OBA RB6 700 A 1 
HETATM 12 N N RB6 . . . D 2 -24.077 -20.03 99.232 1 56.62 ? N RB6 700 A 1 
HETATM 13 C CA RB6 . . . D 2 -23.044 -19.053 99.559 1 53.42 ? CA RB6 700 A 1 
HETATM 14 C C RB6 . . . D 2 -22.671 -18.158 98.408 1 49.23 ? C RB6 700 A 1 
HETATM 15 O O RB6 . . . D 2 -23.21 -18.291 97.327 1 48.73 ? O RB6 700 A 1 
HETATM 16 C CB RB6 . . . D 2 -21.807 -19.803 100.048 1 53.17 ? CB RB6 700 A 1 
HETATM 17 S SAS RB6 . . . D 2 -22.224 -20.888 101.361 1 51.72 ? SAS RB6 700 A 1 
HETATM 18 C CAR RB6 . . . D 2 -22.883 -22.273 100.518 1 52.48 ? CAR RB6 700 A 1 
HETATM 19 N NAC RB6 . . . D 2 -21.296 -20.523 98.88 1 54.93 ? NAC RB6 700 A 1 
HETATM 20 C CAD RB6 . . . D 2 -21.212 -21.855 98.7 1 56.77 ? CAD RB6 700 A 1 
HETATM 21 C CBH RB6 . . . D 2 -20.386 -22.24 97.715 1 56.87 ? CBH RB6 700 A 1 
HETATM 22 O OBI RB6 . . . D 2 -19.792 -21.348 97.076 1 57.3 ? OBI RB6 700 A 1 
HETATM 23 O OBJ RB6 . . . D 2 -20.202 -23.444 97.427 1 57.64 ? OBJ RB6 700 A 1 
HETATM 24 C CAE RB6 . . . D 2 -21.901 -22.716 99.471 1 52.18 ? CAE RB6 700 A 1 
HETATM 25 C CAF RB6 . . . D 2 -21.738 -24.174 99.41 1 56.82 ? CAF RB6 700 A 1 
HETATM 26 C CAG RB6 . . . D 2 -20.734 -24.68 100.13 1 50.94 ? CAG RB6 700 A 1 
HETATM 27 C CAH RB6 . . . D 2 -20.467 -25.965 100.203 1 58 ? CAH RB6 700 A 1 
HETATM 28 O OAI RB6 . . . D 2 -21.141 -26.819 99.651 1 61.88 ? OAI RB6 700 A 1 
HETATM 29 C CAQ RB6 . . . D 2 -19.774 -23.837 100.936 1 59.79 ? CAQ RB6 700 A 1 
HETATM 30 C CAP RB6 . . . D 2 -18.802 -24.867 101.522 1 51.89 ? CAP RB6 700 A 1 
HETATM 31 N NAJ RB6 . . . D 2 -19.415 -26.083 101.006 1 71.17 ? NAJ RB6 700 A 1 
HETATM 32 C CAK RB6 . . . D 2 -18.821 -27.318 101.512 1 56.07 ? CAK RB6 700 A 1 
HETATM 33 C CAL RB6 . . . D 2 -19.398 -28.502 100.752 1 64.76 ? CAL RB6 700 A 1 
HETATM 34 C CAM RB6 . . . D 2 -19.607 -29.59 101.794 1 62.85 ? CAM RB6 700 A 1 
HETATM 35 N NAN RB6 . . . D 2 -19.715 -28.906 103.098 1 63.5 ? NAN RB6 700 A 1 
HETATM 36 C CAO RB6 . . . D 2 -19.369 -27.479 102.923 1 64.69 ? CAO RB6 700 A 1 
#
_model_server_stats.io_time_ms              43 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    37 
_model_server_stats.query_time_ms           468 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#