data_3L8G
#
_model_server_result.job_id            '_YDf_sg3zy-7YQbbXiu4VA' 
_model_server_result.datetime_utc      '2024-10-12 19:22:56' 
_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          3l8g 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":3523}' 
#
_entry.id    3L8G 
#
_exptl.entry_id    3L8G 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              370.142 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,7-di-O-phosphono-L-glycero-beta-D-manno-heptopyranose 
_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         90 
_cell.entry_id            3L8G 
_cell.length_a            63.669 
_cell.length_b            51.572 
_cell.length_c            52.185 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3L8G 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_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,E,F 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_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
covale ? covale1 A C ALA 38 A ALA 38 1_555 A N MSE 39 A MSE 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? 
covale ? covale2 A C MSE 39 A MSE 39 1_555 A N ARG 40 A ARG 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale3 A C LYS 44 A LYS 44 1_555 A N MSE 45 A MSE 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale4 A C MSE 45 A MSE 45 1_555 A N GLY 46 A GLY 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale5 A C TRP 74 A TRP 74 1_555 A N MSE 75 A MSE 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale6 A C MSE 75 A MSE 75 1_555 A N ASP 76 A ASP 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale7 A C GLY 115 A GLY 115 1_555 A N MSE 116 A MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale8 A C MSE 116 A MSE 116 1_555 A N LEU 117 A LEU 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale9 A C ASP 127 A ASP 127 1_555 A N MSE 128 A MSE 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale10 A C MSE 128 A MSE 128 1_555 A N ALA 129 A ALA 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale11 A C TYR 132 A TYR 132 1_555 A N MSE 133 A MSE 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale12 A C MSE 133 A MSE 133 1_555 A N VAL 134 A VAL 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale13 A C ASP 140 A ASP 140 1_555 A N MSE 141 A MSE 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale14 A C MSE 141 A MSE 141 1_555 A N GLN 142 A GLN 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
metalc ? metalc1 A OD2 ASP 11 A ASP 11 1_555 B MG MG . A MG 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc2 A OD1 ASP 11 A ASP 11 1_555 B MG MG . A MG 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? 
metalc ? metalc3 A O ASP 13 A ASP 13 1_555 B MG MG . A MG 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc4 A OH TYR 22 A TYR 22 1_555 D NA NA . A NA 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? 
metalc ? metalc5 A SG CYS 92 A CYS 92 1_555 C ZN ZN . A ZN 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc6 A ND1 HIS 94 A HIS 94 1_555 C ZN ZN . A ZN 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc7 A SG CYS 107 A CYS 107 1_555 C ZN ZN . A ZN 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc8 A SG CYS 109 A CYS 109 1_555 C ZN ZN . A ZN 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc9 A OD1 ASP 136 A ASP 136 1_555 B MG MG . A MG 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? 
metalc ? metalc10 B MG MG . A MG 188 1_555 F O HOH . A HOH 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? 
metalc ? metalc11 B MG MG . A MG 188 1_555 F O HOH . A HOH 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? 
metalc ? metalc12 B MG MG . A MG 188 1_555 E OP4 GMB . A GMB 3523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
#
_chem_comp.formula           'C7 H16 O13 P2' 
_chem_comp.formula_weight    370.142 
_chem_comp.id                GMB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,7-di-O-phosphono-L-glycero-beta-D-manno-heptopyranose 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     3L8G 
_atom_sites.fract_transf_matrix[1][1]    0.015706 
_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]    0.01939 
_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]    0.019163 
_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 MG A 1 188 187 MG MG . 
C 3 ZN A 1 189 188 ZN ZN . 
D 4 NA A 1 190 189 NA NA . 
E 5 GMB A 1 3523 3523 GMB GMB . 
F 6 HOH A 1 191 1 HOH HOH . 
F 6 HOH A 2 192 2 HOH HOH . 
F 6 HOH A 3 193 3 HOH HOH . 
F 6 HOH A 4 194 4 HOH HOH . 
F 6 HOH A 5 195 5 HOH HOH . 
F 6 HOH A 6 196 6 HOH HOH . 
F 6 HOH A 7 197 7 HOH HOH . 
F 6 HOH A 8 198 8 HOH HOH . 
F 6 HOH A 9 199 9 HOH HOH . 
F 6 HOH A 10 200 10 HOH HOH . 
F 6 HOH A 11 201 11 HOH HOH . 
F 6 HOH A 12 202 12 HOH HOH . 
F 6 HOH A 13 203 13 HOH HOH . 
F 6 HOH A 14 204 14 HOH HOH . 
F 6 HOH A 15 205 15 HOH HOH . 
F 6 HOH A 16 206 16 HOH HOH . 
F 6 HOH A 17 207 17 HOH HOH . 
F 6 HOH A 18 208 18 HOH HOH . 
F 6 HOH A 19 209 19 HOH HOH . 
F 6 HOH A 20 210 20 HOH HOH . 
F 6 HOH A 21 211 21 HOH HOH . 
F 6 HOH A 22 212 22 HOH HOH . 
F 6 HOH A 23 213 23 HOH HOH . 
F 6 HOH A 24 214 24 HOH HOH . 
F 6 HOH A 25 215 25 HOH HOH . 
F 6 HOH A 26 216 26 HOH HOH . 
F 6 HOH A 27 217 27 HOH HOH . 
F 6 HOH A 28 218 28 HOH HOH . 
F 6 HOH A 29 219 29 HOH HOH . 
F 6 HOH A 30 220 30 HOH HOH . 
F 6 HOH A 31 221 31 HOH HOH . 
F 6 HOH A 32 222 32 HOH HOH . 
F 6 HOH A 33 223 33 HOH HOH . 
F 6 HOH A 34 224 34 HOH HOH . 
F 6 HOH A 35 225 35 HOH HOH . 
F 6 HOH A 36 226 36 HOH HOH . 
F 6 HOH A 37 227 37 HOH HOH . 
F 6 HOH A 38 228 38 HOH HOH . 
F 6 HOH A 39 229 39 HOH HOH . 
F 6 HOH A 40 230 40 HOH HOH . 
F 6 HOH A 41 231 41 HOH HOH . 
F 6 HOH A 42 232 42 HOH HOH . 
F 6 HOH A 43 233 43 HOH HOH . 
F 6 HOH A 44 234 44 HOH HOH . 
F 6 HOH A 45 235 45 HOH HOH . 
F 6 HOH A 46 236 46 HOH HOH . 
F 6 HOH A 47 237 47 HOH HOH . 
F 6 HOH A 48 238 48 HOH HOH . 
F 6 HOH A 49 239 49 HOH HOH . 
F 6 HOH A 50 240 50 HOH HOH . 
F 6 HOH A 51 241 51 HOH HOH . 
F 6 HOH A 52 242 52 HOH HOH . 
F 6 HOH A 53 243 53 HOH HOH . 
F 6 HOH A 54 244 54 HOH HOH . 
F 6 HOH A 55 245 55 HOH HOH . 
F 6 HOH A 56 246 56 HOH HOH . 
F 6 HOH A 57 247 57 HOH HOH . 
F 6 HOH A 58 248 58 HOH HOH . 
F 6 HOH A 59 249 59 HOH HOH . 
F 6 HOH A 60 250 60 HOH HOH . 
F 6 HOH A 61 251 61 HOH HOH . 
F 6 HOH A 62 252 62 HOH HOH . 
F 6 HOH A 63 253 63 HOH HOH . 
F 6 HOH A 64 254 64 HOH HOH . 
F 6 HOH A 65 255 65 HOH HOH . 
F 6 HOH A 66 256 66 HOH HOH . 
F 6 HOH A 67 257 67 HOH HOH . 
F 6 HOH A 68 258 68 HOH HOH . 
F 6 HOH A 69 259 69 HOH HOH . 
F 6 HOH A 70 260 70 HOH HOH . 
F 6 HOH A 71 261 71 HOH HOH . 
F 6 HOH A 72 262 72 HOH HOH . 
F 6 HOH A 73 263 73 HOH HOH . 
F 6 HOH A 74 264 74 HOH HOH . 
F 6 HOH A 75 265 75 HOH HOH . 
F 6 HOH A 76 266 76 HOH HOH . 
F 6 HOH A 77 267 77 HOH HOH . 
F 6 HOH A 78 268 78 HOH HOH . 
F 6 HOH A 79 269 79 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 GMB . . . E 5 -12.965 1.041 -24.34 1 46.19 ? C1 GMB 3523 A 1 
HETATM 2 O O1 GMB . . . E 5 -11.877 0.234 -24.654 1 53.34 ? O1 GMB 3523 A 1 
HETATM 3 P P1 GMB . . . E 5 -10.451 0.565 -24.317 1 57.31 ? P1 GMB 3523 A 1 
HETATM 4 C C2 GMB . . . E 5 -14.334 0.363 -24.508 1 46.72 ? C2 GMB 3523 A 1 
HETATM 5 O O2 GMB . . . E 5 -14.573 -0.844 -23.78 1 44.66 ? O2 GMB 3523 A 1 
HETATM 6 P P2 GMB . . . E 5 -13.022 5.872 -19.5 1 35.57 ? P2 GMB 3523 A 1 
HETATM 7 C C3 GMB . . . E 5 -15.476 1.374 -24.479 1 45.04 ? C3 GMB 3523 A 1 
HETATM 8 O O3 GMB . . . E 5 -16.776 0.856 -24.737 1 46.52 ? O3 GMB 3523 A 1 
HETATM 9 C C4 GMB . . . E 5 -15.335 1.884 -23.061 1 42.47 ? C4 GMB 3523 A 1 
HETATM 10 O O4 GMB . . . E 5 -16.422 2.639 -22.564 1 43.46 ? O4 GMB 3523 A 1 
HETATM 11 C C5 GMB . . . E 5 -13.994 2.593 -23.016 1 42.77 ? C5 GMB 3523 A 1 
HETATM 12 O O5 GMB . . . E 5 -12.957 1.613 -23.03 1 41.92 ? O5 GMB 3523 A 1 
HETATM 13 C C6 GMB . . . E 5 -14.014 3.438 -21.761 1 38.77 ? C6 GMB 3523 A 1 
HETATM 14 O O6 GMB . . . E 5 -14.237 2.651 -20.585 1 38.85 ? O6 GMB 3523 A 1 
HETATM 15 C C7 GMB . . . E 5 -12.95 4.512 -21.638 1 35.59 ? C7 GMB 3523 A 1 
HETATM 16 O O7 GMB . . . E 5 -13.32 5.715 -20.958 1 34.93 ? O7 GMB 3523 A 1 
HETATM 17 O OP1 GMB . . . E 5 -10.131 2.011 -24.518 1 42.08 ? OP1 GMB 3523 A 1 
HETATM 18 O OP2 GMB . . . E 5 -10.254 0.19 -22.883 1 51.26 ? OP2 GMB 3523 A 1 
HETATM 19 O OP3 GMB . . . E 5 -9.553 -0.256 -25.174 1 47.76 ? OP3 GMB 3523 A 1 
HETATM 20 O OP4 GMB . . . E 5 -13.48 4.639 -18.814 1 30.93 ? OP4 GMB 3523 A 1 
HETATM 21 O OP5 GMB . . . E 5 -11.561 6.059 -19.272 1 26.5 ? OP5 GMB 3523 A 1 
HETATM 22 O OP6 GMB . . . E 5 -13.805 7.04 -18.972 1 27.08 ? OP6 GMB 3523 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           22 
#