data_6HR9
#
_model_server_result.job_id            OccE5JTq_XW-FL_qY6aLeg 
_model_server_result.datetime_utc      '2024-11-25 14:07:03' 
_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          6hr9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1202}' 
#
_entry.id    6HR9 
#
_exptl.entry_id    6HR9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              534.519 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'Nitrocefin - open form' 
_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            6HR9 
_cell.length_a            68.042 
_cell.length_b            83.261 
_cell.length_c            88.733 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6HR9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 B N N 
? 2 C 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 250 A SER 294 1_555 B C1 NEF . A NEF 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.535 ? 
covale ? covale2 A OG SER 305 A SER 349 1_555 C C1 NEF . A NEF 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.548 ? 
#
_chem_comp.formula           'C21 H18 N4 O9 S2' 
_chem_comp.formula_weight    534.519 
_chem_comp.id                NEF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'Nitrocefin - open form' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '(2R)-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid' 
#
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
O26 N23 NEF sing 224 n n 
N23 O27 NEF doub 225 n n 
N23 C19 NEF sing 226 n n 
C18 C19 NEF doub 227 n y 
C18 C17 NEF sing 228 n y 
C19 C20 NEF sing 229 n y 
C17 C14 NEF doub 230 n y 
S12 C11 NEF sing 231 n y 
S12 C8 NEF sing 232 n y 
C11 C10 NEF doub 233 n y 
C20 C21 NEF doub 234 n y 
C14 C21 NEF sing 235 n y 
C14 C12 NEF sing 236 n n 
C8 C7 NEF sing 237 n n 
C8 C9 NEF doub 238 n y 
C6 C12 NEF doub 239 e n 
C6 C4 NEF sing 240 n n 
C7 C5 NEF sing 241 n n 
O17 C16 NEF doub 242 n n 
C10 C9 NEF sing 243 n y 
C21 N22 NEF sing 244 n n 
O2 C1 NEF doub 245 n n 
C4 C15 NEF doub 246 n n 
C4 C2 NEF sing 247 n n 
C16 C15 NEF sing 248 n n 
C16 O18 NEF sing 249 n n 
N4 C5 NEF sing 250 n n 
N4 C3 NEF sing 251 n n 
C15 N14 NEF sing 252 n n 
C5 O6 NEF doub 253 n n 
C1 C3 NEF sing 254 n n 
C2 S19 NEF sing 255 n n 
N22 O25 NEF doub 256 n n 
N22 O24 NEF sing 257 n n 
C3 C13 NEF sing 258 n n 
N14 C13 NEF sing 259 n n 
C13 S19 NEF sing 260 n n 
C2 H1 NEF sing 261 n n 
C2 H2 NEF sing 262 n n 
C3 H3 NEF sing 263 n n 
C6 H5 NEF sing 264 n n 
C7 H7 NEF sing 265 n n 
C7 H8 NEF sing 266 n n 
C11 H9 NEF sing 267 n n 
C13 H10 NEF sing 268 n n 
C17 H12 NEF sing 269 n n 
N4 H14 NEF sing 270 n n 
C9 H15 NEF sing 271 n n 
C10 H16 NEF sing 272 n n 
O18 H19 NEF sing 273 n n 
C12 H20 NEF sing 274 n n 
C18 H22 NEF sing 275 n n 
C20 H23 NEF sing 276 n n 
C1 OXY NEF sing 277 n n 
OXY HXY NEF sing 278 n n 
N14 H4 NEF sing 279 n n 
#
_atom_sites.entry_id                     6HR9 
_atom_sites.fract_transf_matrix[1][1]    0.014697 
_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]    0.01201 
_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]    0.01127 
_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 NEF A 1 1201 1201 NEF NEF . 
C 2 NEF A 1 1202 1301 NEF NEF . 
D 3 HOH A 1 1301 1098 HOH HOH . 
D 3 HOH A 2 1302 1005 HOH HOH . 
D 3 HOH A 3 1303 1004 HOH HOH . 
D 3 HOH A 4 1304 1006 HOH HOH . 
D 3 HOH A 5 1305 1010 HOH HOH . 
D 3 HOH A 6 1306 1009 HOH HOH . 
D 3 HOH A 7 1307 1007 HOH HOH . 
D 3 HOH A 8 1308 1019 HOH HOH . 
D 3 HOH A 9 1309 1086 HOH HOH . 
D 3 HOH A 10 1310 1008 HOH HOH . 
D 3 HOH A 11 1311 1107 HOH HOH . 
D 3 HOH A 12 1312 1012 HOH HOH . 
D 3 HOH A 13 1313 1014 HOH HOH . 
D 3 HOH A 14 1314 1013 HOH HOH . 
D 3 HOH A 15 1315 1087 HOH HOH . 
D 3 HOH A 16 1316 1079 HOH HOH . 
D 3 HOH A 17 1317 1011 HOH HOH . 
D 3 HOH A 18 1318 1020 HOH HOH . 
D 3 HOH A 19 1319 1017 HOH HOH . 
D 3 HOH A 20 1320 1016 HOH HOH . 
D 3 HOH A 21 1321 1015 HOH HOH . 
D 3 HOH A 22 1322 1024 HOH HOH . 
D 3 HOH A 23 1323 1018 HOH HOH . 
D 3 HOH A 24 1324 1021 HOH HOH . 
D 3 HOH A 25 1325 1027 HOH HOH . 
D 3 HOH A 26 1326 1075 HOH HOH . 
D 3 HOH A 27 1327 1035 HOH HOH . 
D 3 HOH A 28 1328 1023 HOH HOH . 
D 3 HOH A 29 1329 1025 HOH HOH . 
D 3 HOH A 30 1330 1028 HOH HOH . 
D 3 HOH A 31 1331 1026 HOH HOH . 
D 3 HOH A 32 1332 1022 HOH HOH . 
D 3 HOH A 33 1333 1096 HOH HOH . 
D 3 HOH A 34 1334 1033 HOH HOH . 
D 3 HOH A 35 1335 1034 HOH HOH . 
D 3 HOH A 36 1336 1031 HOH HOH . 
D 3 HOH A 37 1337 1036 HOH HOH . 
D 3 HOH A 38 1338 1045 HOH HOH . 
D 3 HOH A 39 1339 1032 HOH HOH . 
D 3 HOH A 40 1340 1093 HOH HOH . 
D 3 HOH A 41 1341 1080 HOH HOH . 
D 3 HOH A 42 1342 1043 HOH HOH . 
D 3 HOH A 43 1343 1105 HOH HOH . 
D 3 HOH A 44 1344 1038 HOH HOH . 
D 3 HOH A 45 1345 1042 HOH HOH . 
D 3 HOH A 46 1346 1037 HOH HOH . 
D 3 HOH A 47 1347 1106 HOH HOH . 
D 3 HOH A 48 1348 1056 HOH HOH . 
D 3 HOH A 49 1349 1047 HOH HOH . 
D 3 HOH A 50 1350 1039 HOH HOH . 
D 3 HOH A 51 1351 1044 HOH HOH . 
D 3 HOH A 52 1352 1050 HOH HOH . 
D 3 HOH A 53 1353 1048 HOH HOH . 
D 3 HOH A 54 1354 1054 HOH HOH . 
D 3 HOH A 55 1355 1078 HOH HOH . 
D 3 HOH A 56 1356 1040 HOH HOH . 
D 3 HOH A 57 1357 1084 HOH HOH . 
D 3 HOH A 58 1358 1046 HOH HOH . 
D 3 HOH A 59 1359 1097 HOH HOH . 
D 3 HOH A 60 1360 1049 HOH HOH . 
D 3 HOH A 61 1361 1052 HOH HOH . 
D 3 HOH A 62 1362 1029 HOH HOH . 
D 3 HOH A 63 1363 1051 HOH HOH . 
D 3 HOH A 64 1364 1085 HOH HOH . 
D 3 HOH A 65 1365 1092 HOH HOH . 
D 3 HOH A 66 1366 1100 HOH HOH . 
D 3 HOH A 67 1367 1095 HOH HOH . 
D 3 HOH A 68 1368 1059 HOH HOH . 
D 3 HOH A 69 1369 1041 HOH HOH . 
D 3 HOH A 70 1370 1083 HOH HOH . 
D 3 HOH A 71 1371 1081 HOH HOH . 
D 3 HOH A 72 1372 1055 HOH HOH . 
D 3 HOH A 73 1373 1053 HOH HOH . 
D 3 HOH A 74 1374 1058 HOH HOH . 
D 3 HOH A 75 1375 1088 HOH HOH . 
D 3 HOH A 76 1376 1060 HOH HOH . 
D 3 HOH A 77 1377 1089 HOH HOH . 
D 3 HOH A 78 1378 1063 HOH HOH . 
D 3 HOH A 79 1379 1099 HOH HOH . 
D 3 HOH A 80 1380 1057 HOH HOH . 
D 3 HOH A 81 1381 1062 HOH HOH . 
D 3 HOH A 82 1382 1077 HOH HOH . 
D 3 HOH A 83 1383 1076 HOH HOH . 
D 3 HOH A 84 1384 1091 HOH HOH . 
D 3 HOH A 85 1385 1064 HOH HOH . 
D 3 HOH A 86 1386 1102 HOH HOH . 
D 3 HOH A 87 1387 1061 HOH HOH . 
D 3 HOH A 88 1388 1065 HOH HOH . 
D 3 HOH A 89 1389 1066 HOH HOH . 
D 3 HOH A 90 1390 1067 HOH HOH . 
D 3 HOH A 91 1391 1073 HOH HOH . 
D 3 HOH A 92 1392 1094 HOH HOH . 
D 3 HOH A 93 1393 1068 HOH HOH . 
D 3 HOH A 94 1394 1090 HOH HOH . 
D 3 HOH A 95 1395 1103 HOH HOH . 
D 3 HOH A 96 1396 1069 HOH HOH . 
D 3 HOH A 97 1397 1074 HOH HOH . 
D 3 HOH A 98 1398 1071 HOH HOH . 
D 3 HOH A 99 1399 1072 HOH HOH . 
D 3 HOH A 100 1400 1070 HOH HOH . 
D 3 HOH A 101 1401 1082 HOH HOH . 
D 3 HOH A 102 1402 1104 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 C2 NEF . . . C 2 4.273 5.865 21.488 1 79.79 ? C2 NEF 1202 A 1 
HETATM 2 C C3 NEF . . . C 2 2.432 2.907 19.967 1 75.98 ? C3 NEF 1202 A 1 
HETATM 3 C C4 NEF . . . C 2 3.915 6.235 20.099 1 80.23 ? C4 NEF 1202 A 1 
HETATM 4 C C6 NEF . . . C 2 5.053 6.159 19.324 1 86.82 ? C6 NEF 1202 A 1 
HETATM 5 C C7 NEF . . . C 2 3.19 1.844 16.598 1 98.99 ? C7 NEF 1202 A 1 
HETATM 6 C C8 NEF . . . C 2 3.819 2.966 15.831 1 109.6 ? C8 NEF 1202 A 1 
HETATM 7 C C11 NEF . . . C 2 5.414 4.369 14.645 1 108.96 ? C11 NEF 1202 A 1 
HETATM 8 C C13 NEF . . . C 2 2.415 4.074 20.862 1 72.06 ? C13 NEF 1202 A 1 
HETATM 9 C C14 NEF . . . C 2 7.452 6.58 18.941 1 89.62 ? C14 NEF 1202 A 1 
HETATM 10 C C15 NEF . . . C 2 2.58 6.262 19.747 1 70.36 ? C15 NEF 1202 A 1 
HETATM 11 C C16 NEF . . . C 2 1.909 7.333 18.902 1 66.35 ? C16 NEF 1202 A 1 
HETATM 12 C C17 NEF . . . C 2 8.759 6.37 19.381 1 87.6 ? C17 NEF 1202 A 1 
HETATM 13 S S19 NEF . . . C 2 4.2 4.134 21.075 1 76.53 ? S19 NEF 1202 A 1 
HETATM 14 C C1 NEF . . . C 2 0.909 2.418 19.863 1 68.89 ? C1 NEF 1202 A 1 
HETATM 15 O O2 NEF . . . C 2 0.832 1.432 19.048 1 71.7 ? O2 NEF 1202 A 1 
HETATM 16 N N4 NEF . . . C 2 2.963 3.098 18.631 1 79.61 ? N4 NEF 1202 A 1 
HETATM 17 C C5 NEF . . . C 2 3.586 2.1 18.03 1 84.97 ? C5 NEF 1202 A 1 
HETATM 18 O O6 NEF . . . C 2 4.468 1.461 18.587 1 80.16 ? O6 NEF 1202 A 1 
HETATM 19 C C9 NEF . . . C 2 3.191 3.855 14.989 1 113.74 ? C9 NEF 1202 A 1 
HETATM 20 C C10 NEF . . . C 2 4.159 4.602 14.249 1 111.62 ? C10 NEF 1202 A 1 
HETATM 21 S S12 NEF . . . C 2 5.465 3.338 15.991 1 110.1 ? S12 NEF 1202 A 1 
HETATM 22 N N14 NEF . . . C 2 1.847 5.23 20.17 1 74.58 ? N14 NEF 1202 A 1 
HETATM 23 O O17 NEF . . . C 2 2.28 7.421 17.814 1 51.23 ? O17 NEF 1202 A 1 
HETATM 24 O O18 NEF . . . C 2 1.045 7.978 19.423 1 70.42 ? O18 NEF 1202 A 1 
HETATM 25 C C12 NEF . . . C 2 6.297 6.275 19.768 1 88.77 ? C12 NEF 1202 A 1 
HETATM 26 C C18 NEF . . . C 2 9.858 6.646 18.594 1 92.12 ? C18 NEF 1202 A 1 
HETATM 27 C C19 NEF . . . C 2 9.643 7.167 17.322 1 94.66 ? C19 NEF 1202 A 1 
HETATM 28 C C20 NEF . . . C 2 8.374 7.401 16.824 1 90.45 ? C20 NEF 1202 A 1 
HETATM 29 C C21 NEF . . . C 2 7.311 7.092 17.648 1 88.11 ? C21 NEF 1202 A 1 
HETATM 30 N N22 NEF . . . C 2 6.021 7.321 17.07 1 84.75 ? N22 NEF 1202 A 1 
HETATM 31 N N23 NEF . . . C 2 10.748 7.443 16.439 1 100.38 ? N23 NEF 1202 A 1 
HETATM 32 O O24 NEF . . . C 2 5.696 6.629 16.14 1 75.05 ? O24 NEF 1202 A 1 
HETATM 33 O O25 NEF . . . C 2 5.311 8.16 17.558 1 85 ? O25 NEF 1202 A 1 
HETATM 34 O O26 NEF . . . C 2 11.533 8.328 16.728 1 101.54 ? O26 NEF 1202 A 1 
HETATM 35 O O27 NEF . . . C 2 10.795 6.811 15.4 1 96.2 ? O27 NEF 1202 A 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           259 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           35 
#