data_6SEC
#
_model_server_result.job_id            R2DVWpX6PoB7ETwoZknvXw 
_model_server_result.datetime_utc      '2024-11-05 16:28:28' 
_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          6sec 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1104}' 
#
_entry.id    6SEC 
#
_exptl.entry_id    6SEC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              301.249 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '2-nitrophenyl beta-D-galactopyranoside' 
_entity.pdbx_number_of_molecules    1 
_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         120 
_cell.entry_id            6SEC 
_cell.length_a            137.33 
_cell.length_b            137.33 
_cell.length_c            126.784 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6SEC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
metalc ? metalc1 A OD2 ASP 207 A ASP 207 1_555 D NA NA . A NA 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc2 A O PHE 581 A PHE 581 1_555 D NA NA . A NA 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? 
metalc ? metalc3 A OD2 ASP 584 A ASP 584 1_555 D NA NA . A NA 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc4 D NA NA . A NA 1103 1_555 E O6 145 . A 145 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? 
metalc ? metalc5 D NA NA . A NA 1103 1_555 F O HOH . A HOH 1298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 
#
_chem_comp.formula           'C12 H15 N O8' 
_chem_comp.formula_weight    301.249 
_chem_comp.id                145 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              '2-nitrophenyl beta-D-galactopyranoside' 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     '1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE;2-nitrophenyl beta-D-galactoside;2-nitrophenyl D-galactoside;2-nitrophenyl galactoside' 
#
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
C1 C2 145 sing 1 n n 
C1 O5 145 sing 2 n n 
C1 O1 145 sing 3 n n 
C1 H1 145 sing 4 n n 
C2 O2 145 sing 5 n n 
C2 C3 145 sing 6 n n 
C2 H2 145 sing 7 n n 
O2 HO2 145 sing 8 n n 
C3 O3 145 sing 9 n n 
C3 C4 145 sing 10 n n 
C3 H3 145 sing 11 n n 
O3 HO3 145 sing 12 n n 
C4 O4 145 sing 13 n n 
C4 C5 145 sing 14 n n 
C4 H4 145 sing 15 n n 
O4 HO4 145 sing 16 n n 
C5 C6 145 sing 17 n n 
C5 O5 145 sing 18 n n 
C5 H5 145 sing 19 n n 
C6 O6 145 sing 20 n n 
C6 H61 145 sing 21 n n 
C6 H62 145 sing 22 n n 
O6 HO6 145 sing 23 n n 
O1 C1' 145 sing 24 n n 
C1' C2' 145 doub 25 n y 
C1' C6' 145 sing 26 n y 
C2' C3' 145 sing 27 n y 
C2' N1' 145 sing 28 n n 
C3' C4' 145 doub 29 n y 
C3' H3' 145 sing 30 n n 
C4' C5' 145 sing 31 n y 
C4' H4' 145 sing 32 n n 
C5' C6' 145 doub 33 n y 
C5' H5' 145 sing 34 n n 
C6' H6' 145 sing 35 n n 
N1' O2' 145 sing 36 n n 
N1' O3' 145 doub 37 n n 
#
_pdbx_chem_comp_identifier.comp_id            145 
_pdbx_chem_comp_identifier.identifier         1-O-[O-nitrophenyl]-b-D-galactopyranose 
_pdbx_chem_comp_identifier.type               'IUPAC CARBOHYDRATE SYMBOL' 
_pdbx_chem_comp_identifier.program            PDB-CARE 
_pdbx_chem_comp_identifier.program_version    1 
#
_atom_sites.entry_id                     6SEC 
_atom_sites.fract_transf_matrix[1][1]    0.007282 
_atom_sites.fract_transf_matrix[1][2]    0.004204 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008408 
_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]    0.007887 
_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 ACT A 1 1101 1 ACT ACT . 
C 2 ACT A 1 1102 2 ACT ACT . 
D 3 NA A 1 1103 1 NA NA . 
E 4 145 A 1 1104 1 145 145 . 
F 5 HOH A 1 1201 55 HOH HOH . 
F 5 HOH A 2 1202 102 HOH HOH . 
F 5 HOH A 3 1203 48 HOH HOH . 
F 5 HOH A 4 1204 57 HOH HOH . 
F 5 HOH A 5 1205 111 HOH HOH . 
F 5 HOH A 6 1206 63 HOH HOH . 
F 5 HOH A 7 1207 53 HOH HOH . 
F 5 HOH A 8 1208 100 HOH HOH . 
F 5 HOH A 9 1209 105 HOH HOH . 
F 5 HOH A 10 1210 87 HOH HOH . 
F 5 HOH A 11 1211 51 HOH HOH . 
F 5 HOH A 12 1212 128 HOH HOH . 
F 5 HOH A 13 1213 93 HOH HOH . 
F 5 HOH A 14 1214 65 HOH HOH . 
F 5 HOH A 15 1215 61 HOH HOH . 
F 5 HOH A 16 1216 121 HOH HOH . 
F 5 HOH A 17 1217 103 HOH HOH . 
F 5 HOH A 18 1218 18 HOH HOH . 
F 5 HOH A 19 1219 109 HOH HOH . 
F 5 HOH A 20 1220 31 HOH HOH . 
F 5 HOH A 21 1221 126 HOH HOH . 
F 5 HOH A 22 1222 68 HOH HOH . 
F 5 HOH A 23 1223 25 HOH HOH . 
F 5 HOH A 24 1224 13 HOH HOH . 
F 5 HOH A 25 1225 26 HOH HOH . 
F 5 HOH A 26 1226 64 HOH HOH . 
F 5 HOH A 27 1227 62 HOH HOH . 
F 5 HOH A 28 1228 99 HOH HOH . 
F 5 HOH A 29 1229 19 HOH HOH . 
F 5 HOH A 30 1230 20 HOH HOH . 
F 5 HOH A 31 1231 32 HOH HOH . 
F 5 HOH A 32 1232 66 HOH HOH . 
F 5 HOH A 33 1233 79 HOH HOH . 
F 5 HOH A 34 1234 110 HOH HOH . 
F 5 HOH A 35 1235 83 HOH HOH . 
F 5 HOH A 36 1236 84 HOH HOH . 
F 5 HOH A 37 1237 38 HOH HOH . 
F 5 HOH A 38 1238 34 HOH HOH . 
F 5 HOH A 39 1239 21 HOH HOH . 
F 5 HOH A 40 1240 36 HOH HOH . 
F 5 HOH A 41 1241 30 HOH HOH . 
F 5 HOH A 42 1242 35 HOH HOH . 
F 5 HOH A 43 1243 101 HOH HOH . 
F 5 HOH A 44 1244 5 HOH HOH . 
F 5 HOH A 45 1245 69 HOH HOH . 
F 5 HOH A 46 1246 46 HOH HOH . 
F 5 HOH A 47 1247 71 HOH HOH . 
F 5 HOH A 48 1248 9 HOH HOH . 
F 5 HOH A 49 1249 4 HOH HOH . 
F 5 HOH A 50 1250 72 HOH HOH . 
F 5 HOH A 51 1251 3 HOH HOH . 
F 5 HOH A 52 1252 10 HOH HOH . 
F 5 HOH A 53 1253 17 HOH HOH . 
F 5 HOH A 54 1254 56 HOH HOH . 
F 5 HOH A 55 1255 15 HOH HOH . 
F 5 HOH A 56 1256 88 HOH HOH . 
F 5 HOH A 57 1257 78 HOH HOH . 
F 5 HOH A 58 1258 106 HOH HOH . 
F 5 HOH A 59 1259 67 HOH HOH . 
F 5 HOH A 60 1260 8 HOH HOH . 
F 5 HOH A 61 1261 116 HOH HOH . 
F 5 HOH A 62 1262 120 HOH HOH . 
F 5 HOH A 63 1263 94 HOH HOH . 
F 5 HOH A 64 1264 24 HOH HOH . 
F 5 HOH A 65 1265 29 HOH HOH . 
F 5 HOH A 66 1266 47 HOH HOH . 
F 5 HOH A 67 1267 45 HOH HOH . 
F 5 HOH A 68 1268 115 HOH HOH . 
F 5 HOH A 69 1269 77 HOH HOH . 
F 5 HOH A 70 1270 33 HOH HOH . 
F 5 HOH A 71 1271 44 HOH HOH . 
F 5 HOH A 72 1272 124 HOH HOH . 
F 5 HOH A 73 1273 1 HOH HOH . 
F 5 HOH A 74 1274 54 HOH HOH . 
F 5 HOH A 75 1275 133 HOH HOH . 
F 5 HOH A 76 1276 2 HOH HOH . 
F 5 HOH A 77 1277 58 HOH HOH . 
F 5 HOH A 78 1278 37 HOH HOH . 
F 5 HOH A 79 1279 112 HOH HOH . 
F 5 HOH A 80 1280 70 HOH HOH . 
F 5 HOH A 81 1281 86 HOH HOH . 
F 5 HOH A 82 1282 6 HOH HOH . 
F 5 HOH A 83 1283 22 HOH HOH . 
F 5 HOH A 84 1284 23 HOH HOH . 
F 5 HOH A 85 1285 107 HOH HOH . 
F 5 HOH A 86 1286 81 HOH HOH . 
F 5 HOH A 87 1287 50 HOH HOH . 
F 5 HOH A 88 1288 91 HOH HOH . 
F 5 HOH A 89 1289 28 HOH HOH . 
F 5 HOH A 90 1290 76 HOH HOH . 
F 5 HOH A 91 1291 7 HOH HOH . 
F 5 HOH A 92 1292 43 HOH HOH . 
F 5 HOH A 93 1293 41 HOH HOH . 
F 5 HOH A 94 1294 14 HOH HOH . 
F 5 HOH A 95 1295 92 HOH HOH . 
F 5 HOH A 96 1296 80 HOH HOH . 
F 5 HOH A 97 1297 73 HOH HOH . 
F 5 HOH A 98 1298 74 HOH HOH . 
F 5 HOH A 99 1299 90 HOH HOH . 
F 5 HOH A 100 1300 129 HOH HOH . 
F 5 HOH A 101 1301 39 HOH HOH . 
F 5 HOH A 102 1302 60 HOH HOH . 
F 5 HOH A 103 1303 97 HOH HOH . 
F 5 HOH A 104 1304 75 HOH HOH . 
F 5 HOH A 105 1305 127 HOH HOH . 
F 5 HOH A 106 1306 11 HOH HOH . 
F 5 HOH A 107 1307 12 HOH HOH . 
F 5 HOH A 108 1308 52 HOH HOH . 
F 5 HOH A 109 1309 85 HOH HOH . 
F 5 HOH A 110 1310 113 HOH HOH . 
F 5 HOH A 111 1311 49 HOH HOH . 
F 5 HOH A 112 1312 40 HOH HOH . 
F 5 HOH A 113 1313 89 HOH HOH . 
F 5 HOH A 114 1314 96 HOH HOH . 
F 5 HOH A 115 1315 95 HOH HOH . 
F 5 HOH A 116 1316 114 HOH HOH . 
F 5 HOH A 117 1317 122 HOH HOH . 
F 5 HOH A 118 1318 98 HOH HOH . 
F 5 HOH A 119 1319 59 HOH HOH . 
F 5 HOH A 120 1320 119 HOH HOH . 
F 5 HOH A 121 1321 108 HOH HOH . 
F 5 HOH A 122 1322 131 HOH HOH . 
F 5 HOH A 123 1323 42 HOH HOH . 
F 5 HOH A 124 1324 104 HOH HOH . 
F 5 HOH A 125 1325 132 HOH HOH . 
F 5 HOH A 126 1326 16 HOH HOH . 
F 5 HOH A 127 1327 123 HOH HOH . 
F 5 HOH A 128 1328 130 HOH HOH . 
F 5 HOH A 129 1329 27 HOH HOH . 
F 5 HOH A 130 1330 118 HOH HOH . 
F 5 HOH A 131 1331 117 HOH HOH . 
F 5 HOH A 132 1332 82 HOH HOH . 
F 5 HOH A 133 1333 125 HOH HOH . 
F 5 HOH A 134 1334 134 HOH HOH . 
F 5 HOH A 135 1335 135 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 C1 145 . . . E 4 36.759 38.596 17.863 1 85.71 ? C1 145 1104 A 1 
HETATM 2 C C2 145 . . . E 4 36.48 38.208 19.345 1 92.74 ? C2 145 1104 A 1 
HETATM 3 O O2 145 . . . E 4 37.257 39.007 20.234 1 102.01 ? O2 145 1104 A 1 
HETATM 4 C C3 145 . . . E 4 36.744 36.79 19.711 1 80.35 ? C3 145 1104 A 1 
HETATM 5 O O3 145 . . . E 4 36.203 36.529 20.993 1 75.55 ? O3 145 1104 A 1 
HETATM 6 C C4 145 . . . E 4 36.148 35.81 18.725 1 77.26 ? C4 145 1104 A 1 
HETATM 7 O O4 145 . . . E 4 34.758 35.915 18.749 1 63.56 ? O4 145 1104 A 1 
HETATM 8 C C5 145 . . . E 4 36.709 36.179 17.336 1 80.05 ? C5 145 1104 A 1 
HETATM 9 C C6 145 . . . E 4 36.5 35.055 16.299 1 77.29 ? C6 145 1104 A 1 
HETATM 10 O O6 145 . . . E 4 35.298 35.014 15.683 1 73.19 ? O6 145 1104 A 1 
HETATM 11 O O5 145 . . . E 4 36.239 37.509 16.915 1 79.33 ? O5 145 1104 A 1 
HETATM 12 O O1 145 . . . E 4 36.279 39.856 17.617 1 89.71 ? O1 145 1104 A 1 
HETATM 13 C C1' 145 . . . E 4 35.744 40.271 16.313 1 102.35 ? C1' 145 1104 A 1 
HETATM 14 C C2' 145 . . . E 4 36.195 41.472 15.701 1 105.44 ? C2' 145 1104 A 1 
HETATM 15 C C3' 145 . . . E 4 35.674 41.871 14.483 1 95.17 ? C3' 145 1104 A 1 
HETATM 16 C C4' 145 . . . E 4 34.7 41.13 13.83 1 93.54 ? C4' 145 1104 A 1 
HETATM 17 C C5' 145 . . . E 4 34.229 39.957 14.419 1 98.07 ? C5' 145 1104 A 1 
HETATM 18 C C6' 145 . . . E 4 34.743 39.555 15.649 1 102.68 ? C6' 145 1104 A 1 
HETATM 19 N N1' 145 . . . E 4 37.238 42.328 16.305 1 111.12 ? N1' 145 1104 A 1 
HETATM 20 O O2' 145 . . . E 4 37.477 43.568 15.749 1 108.71 ? O2' 145 1104 A 1 
HETATM 21 O O3' 145 . . . E 4 37.891 41.959 17.26 1 110.17 ? O3' 145 1104 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           21 
#