data_6PT5
#
_model_server_result.job_id            j8xpYVygxVQ-mPpNahkDaQ 
_model_server_result.datetime_utc      '2024-11-13 05:05:10' 
_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          6pt5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    6PT5 
#
_exptl.entry_id    6PT5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              368.428 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          104.06 
_cell.angle_gamma         90 
_cell.entry_id            6PT5 
_cell.length_a            60.246 
_cell.length_b            107.115 
_cell.length_c            96.105 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PT5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,K 1 1 
B,G,H,L 2 1 
C,I,M 3 1 
D,J,N 4 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
? 3 F N N 
? 3 H N N 
? 3 I N N 
? 3 J 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 68 A SER 70 1_555 F C14 1S7 . A 1S7 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? 
covale ? covale2 B OG SER 68 B SER 70 1_555 H C14 1S7 . B 1S7 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? 
covale ? covale3 B NH1 ARG 248 B ARG 250 1_555 H O6 1S7 . B 1S7 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.304 ? 
covale ? covale4 C OG SER 68 C SER 70 1_555 I C14 1S7 . C 1S7 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? 
covale ? covale5 C NH1 ARG 248 C ARG 250 1_555 I O6 1S7 . C 1S7 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.304 ? 
covale ? covale6 D OG SER 68 D SER 70 1_555 J C14 1S7 . D 1S7 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? 
#
_chem_comp.formula           'C15 H16 N2 O5 S2' 
_chem_comp.formula_weight    368.428 
_chem_comp.id                1S7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Cefoxitin, 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
O C 1S7 sing 1 n n 
C H 1S7 sing 2 n n 
C HA 1S7 sing 3 n n 
C HB 1S7 sing 4 n n 
C1 N 1S7 sing 5 n n 
N C2 1S7 sing 6 n n 
N HN 1S7 sing 7 n n 
C1 O 1S7 sing 8 n n 
C4 S 1S7 sing 9 n y 
C7 S 1S7 sing 10 n y 
C8 C1 1S7 sing 11 n n 
C14 C1 1S7 sing 12 n n 
O1 C2 1S7 doub 13 n n 
C9 S1 1S7 sing 14 n n 
S1 C8 1S7 sing 15 n n 
C2 C3 1S7 sing 16 n n 
C8 N2 1S7 sing 17 n n 
C13 N2 1S7 doub 18 n n 
C3 C4 1S7 sing 19 n n 
C3 H3 1S7 sing 20 n n 
C3 H3A 1S7 sing 21 n n 
C5 C4 1S7 doub 22 n y 
O4 C14 1S7 doub 23 n n 
C5 C6 1S7 sing 24 n y 
C5 H5 1S7 sing 25 n n 
C15 O5 1S7 doub 26 n n 
C6 C7 1S7 doub 27 n y 
C6 H6 1S7 sing 28 n n 
C15 O6 1S7 sing 29 n n 
O6 HO6 1S7 sing 30 n n 
C7 H7 1S7 sing 31 n n 
C8 H8 1S7 sing 32 n n 
C9 C10 1S7 sing 33 n n 
C9 H9 1S7 sing 34 n n 
C9 H9A 1S7 sing 35 n n 
C11 C10 1S7 doub 36 n n 
C10 C13 1S7 sing 37 n n 
C11 H11 1S7 sing 38 n n 
C11 H11A 1S7 sing 39 n n 
C13 C15 1S7 sing 40 n n 
C14 H14 1S7 sing 41 n n 
#
_atom_sites.entry_id                     6PT5 
_atom_sites.fract_transf_matrix[1][1]    0.016599 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004158 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009336 
_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]    0.010727 
_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
E 2 CL A 1 301 2 CL CL . 
F 3 1S7 A 1 302 4 1S7 1S7 . 
G 2 CL B 1 301 1 CL CL . 
H 3 1S7 B 1 302 8 1S7 1S7 . 
I 3 1S7 C 1 301 9 1S7 1S7 . 
J 3 1S7 D 1 301 7 1S7 1S7 . 
K 4 HOH A 1 401 183 HOH HOH . 
K 4 HOH A 2 402 94 HOH HOH . 
K 4 HOH A 3 403 64 HOH HOH . 
K 4 HOH A 4 404 133 HOH HOH . 
K 4 HOH A 5 405 54 HOH HOH . 
K 4 HOH A 6 406 68 HOH HOH . 
K 4 HOH A 7 407 63 HOH HOH . 
K 4 HOH A 8 408 187 HOH HOH . 
K 4 HOH A 9 409 13 HOH HOH . 
K 4 HOH A 10 410 10 HOH HOH . 
K 4 HOH A 11 411 15 HOH HOH . 
K 4 HOH A 12 412 3 HOH HOH . 
K 4 HOH A 13 413 188 HOH HOH . 
K 4 HOH A 14 414 207 HOH HOH . 
K 4 HOH A 15 415 100 HOH HOH . 
K 4 HOH A 16 416 69 HOH HOH . 
K 4 HOH A 17 417 72 HOH HOH . 
K 4 HOH A 18 418 39 HOH HOH . 
K 4 HOH A 19 419 114 HOH HOH . 
K 4 HOH A 20 420 79 HOH HOH . 
K 4 HOH A 21 421 103 HOH HOH . 
K 4 HOH A 22 422 211 HOH HOH . 
K 4 HOH A 23 423 109 HOH HOH . 
K 4 HOH A 24 424 59 HOH HOH . 
K 4 HOH A 25 425 131 HOH HOH . 
K 4 HOH A 26 426 162 HOH HOH . 
K 4 HOH A 27 427 108 HOH HOH . 
K 4 HOH A 28 428 16 HOH HOH . 
K 4 HOH A 29 429 186 HOH HOH . 
K 4 HOH A 30 430 174 HOH HOH . 
K 4 HOH A 31 431 159 HOH HOH . 
K 4 HOH A 32 432 185 HOH HOH . 
K 4 HOH A 33 433 168 HOH HOH . 
K 4 HOH A 34 434 77 HOH HOH . 
K 4 HOH A 35 435 113 HOH HOH . 
K 4 HOH A 36 436 153 HOH HOH . 
K 4 HOH A 37 437 92 HOH HOH . 
L 4 HOH B 1 401 172 HOH HOH . 
L 4 HOH B 2 402 191 HOH HOH . 
L 4 HOH B 3 403 11 HOH HOH . 
L 4 HOH B 4 404 53 HOH HOH . 
L 4 HOH B 5 405 195 HOH HOH . 
L 4 HOH B 6 406 194 HOH HOH . 
L 4 HOH B 7 407 150 HOH HOH . 
L 4 HOH B 8 408 209 HOH HOH . 
L 4 HOH B 9 409 198 HOH HOH . 
L 4 HOH B 10 410 167 HOH HOH . 
L 4 HOH B 11 411 124 HOH HOH . 
L 4 HOH B 12 412 118 HOH HOH . 
L 4 HOH B 13 413 71 HOH HOH . 
L 4 HOH B 14 414 5 HOH HOH . 
L 4 HOH B 15 415 110 HOH HOH . 
L 4 HOH B 16 416 144 HOH HOH . 
L 4 HOH B 17 417 116 HOH HOH . 
L 4 HOH B 18 418 102 HOH HOH . 
L 4 HOH B 19 419 142 HOH HOH . 
L 4 HOH B 20 420 200 HOH HOH . 
L 4 HOH B 21 421 98 HOH HOH . 
L 4 HOH B 22 422 151 HOH HOH . 
L 4 HOH B 23 423 212 HOH HOH . 
L 4 HOH B 24 424 30 HOH HOH . 
L 4 HOH B 25 425 201 HOH HOH . 
L 4 HOH B 26 426 175 HOH HOH . 
L 4 HOH B 27 427 138 HOH HOH . 
L 4 HOH B 28 428 161 HOH HOH . 
L 4 HOH B 29 429 104 HOH HOH . 
L 4 HOH B 30 430 87 HOH HOH . 
L 4 HOH B 31 431 106 HOH HOH . 
L 4 HOH B 32 432 117 HOH HOH . 
L 4 HOH B 33 433 210 HOH HOH . 
L 4 HOH B 34 434 193 HOH HOH . 
M 4 HOH C 1 401 55 HOH HOH . 
M 4 HOH C 2 402 154 HOH HOH . 
M 4 HOH C 3 403 34 HOH HOH . 
M 4 HOH C 4 404 180 HOH HOH . 
M 4 HOH C 5 405 99 HOH HOH . 
M 4 HOH C 6 406 115 HOH HOH . 
M 4 HOH C 7 407 126 HOH HOH . 
M 4 HOH C 8 408 52 HOH HOH . 
M 4 HOH C 9 409 45 HOH HOH . 
M 4 HOH C 10 410 76 HOH HOH . 
M 4 HOH C 11 411 83 HOH HOH . 
M 4 HOH C 12 412 19 HOH HOH . 
M 4 HOH C 13 413 166 HOH HOH . 
M 4 HOH C 14 414 196 HOH HOH . 
M 4 HOH C 15 415 28 HOH HOH . 
M 4 HOH C 16 416 163 HOH HOH . 
M 4 HOH C 17 417 74 HOH HOH . 
M 4 HOH C 18 418 160 HOH HOH . 
M 4 HOH C 19 419 56 HOH HOH . 
M 4 HOH C 20 420 14 HOH HOH . 
M 4 HOH C 21 421 86 HOH HOH . 
M 4 HOH C 22 422 120 HOH HOH . 
M 4 HOH C 23 423 176 HOH HOH . 
M 4 HOH C 24 424 38 HOH HOH . 
M 4 HOH C 25 425 123 HOH HOH . 
M 4 HOH C 26 426 189 HOH HOH . 
M 4 HOH C 27 427 112 HOH HOH . 
M 4 HOH C 28 428 81 HOH HOH . 
M 4 HOH C 29 429 31 HOH HOH . 
M 4 HOH C 30 430 135 HOH HOH . 
M 4 HOH C 31 431 164 HOH HOH . 
N 4 HOH D 1 401 181 HOH HOH . 
N 4 HOH D 2 402 205 HOH HOH . 
N 4 HOH D 3 403 140 HOH HOH . 
N 4 HOH D 4 404 192 HOH HOH . 
N 4 HOH D 5 405 146 HOH HOH . 
N 4 HOH D 6 406 62 HOH HOH . 
N 4 HOH D 7 407 6 HOH HOH . 
N 4 HOH D 8 408 158 HOH HOH . 
N 4 HOH D 9 409 137 HOH HOH . 
N 4 HOH D 10 410 57 HOH HOH . 
N 4 HOH D 11 411 73 HOH HOH . 
N 4 HOH D 12 412 139 HOH HOH . 
N 4 HOH D 13 413 90 HOH HOH . 
N 4 HOH D 14 414 199 HOH HOH . 
N 4 HOH D 15 415 41 HOH HOH . 
N 4 HOH D 16 416 202 HOH HOH . 
N 4 HOH D 17 417 197 HOH HOH . 
N 4 HOH D 18 418 203 HOH HOH . 
N 4 HOH D 19 419 129 HOH HOH . 
N 4 HOH D 20 420 177 HOH HOH . 
N 4 HOH D 21 421 173 HOH HOH . 
N 4 HOH D 22 422 24 HOH HOH . 
N 4 HOH D 23 423 37 HOH HOH . 
N 4 HOH D 24 424 66 HOH HOH . 
N 4 HOH D 25 425 27 HOH HOH . 
N 4 HOH D 26 426 97 HOH HOH . 
N 4 HOH D 27 427 204 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 C C 1S7 . . . F 3 14.368 17.077 45.769 0.84 48.6 ? C 1S7 302 A 1 
HETATM 2 N N 1S7 . . . F 3 12.268 16.61 43.681 0.84 49.12 ? N 1S7 302 A 1 
HETATM 3 O O 1S7 . . . F 3 12.962 16.899 45.915 0.84 51.84 ? O 1S7 302 A 1 
HETATM 4 S S 1S7 . . . F 3 15.228 18.669 41.537 0.84 62.24 ? S 1S7 302 A 1 
HETATM 5 C C1 1S7 . . . F 3 12.315 16.016 45.013 0.84 49.91 ? C1 1S7 302 A 1 
HETATM 6 O O1 1S7 . . . F 3 11.829 18.778 44.195 0.84 55.92 ? O1 1S7 302 A 1 
HETATM 7 S S1 1S7 . . . F 3 9.75 17.03 45.387 0.84 53.84 ? S1 1S7 302 A 1 
HETATM 8 C C2 1S7 . . . F 3 12.167 17.912 43.392 0.84 51.6 ? C2 1S7 302 A 1 
HETATM 9 N N2 1S7 . . . F 3 10.559 14.562 44.584 0.84 51.16 ? N2 1S7 302 A 1 
HETATM 10 C C3 1S7 . . . F 3 12.538 18.307 41.991 0.84 52.9 ? C3 1S7 302 A 1 
HETATM 11 C C4 1S7 . . . F 3 13.697 19.261 42.084 0.84 58.68 ? C4 1S7 302 A 1 
HETATM 12 O O4 1S7 . . . F 3 13.34 14.156 43.949 0.84 43.49 ? O4 1S7 302 A 1 
HETATM 13 C C5 1S7 . . . F 3 13.823 20.562 42.568 0.84 52.72 ? C5 1S7 302 A 1 
HETATM 14 O O5 1S7 . . . F 3 8.67 12.419 42.82 0.84 58.11 ? O5 1S7 302 A 1 
HETATM 15 C C6 1S7 . . . F 3 15.129 21.052 42.468 0.84 61.82 ? C6 1S7 302 A 1 
HETATM 16 O O6 1S7 . . . F 3 10.013 11.841 44.453 0.84 56.39 -1 O6 1S7 302 A 1 
HETATM 17 C C7 1S7 . . . F 3 16.04 20.147 41.926 0.84 60.91 ? C7 1S7 302 A 1 
HETATM 18 C C8 1S7 . . . F 3 10.919 15.635 45.487 0.84 50.21 ? C8 1S7 302 A 1 
HETATM 19 C C9 1S7 . . . F 3 8.244 16.037 45.595 0.84 56.12 ? C9 1S7 302 A 1 
HETATM 20 C C10 1S7 . . . F 3 8.208 14.955 44.548 0.84 58.18 ? C10 1S7 302 A 1 
HETATM 21 C C11 1S7 . . . F 3 7.12 14.777 43.821 0.84 61.38 ? C11 1S7 302 A 1 
HETATM 22 C C13 1S7 . . . F 3 9.387 14.12 44.347 0.84 53.12 ? C13 1S7 302 A 1 
HETATM 23 C C14 1S7 . . . F 3 13.122 14.743 44.987 0.84 49.31 ? C14 1S7 302 A 1 
HETATM 24 C C15 1S7 . . . F 3 9.343 12.696 43.835 0.84 54.26 ? C15 1S7 302 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          18 
_model_server_stats.element_count           24 
#