data_5B2F # _model_server_result.job_id YEmKcr1358YfGizXBdPQbQ _model_server_result.datetime_utc '2025-01-03 05:21:57' _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 5b2f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":302}' # _entry.id 5B2F # _exptl.entry_id 5B2F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 257.178 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucopyranose _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 90 _cell.angle_gamma 120 _cell.entry_id 5B2F _cell.length_a 77.821 _cell.length_b 77.821 _cell.length_c 229.23 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B2F _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,G,H,I,J,K,L _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 ? 3 E N N ? 3 G N N ? 3 I 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 metalc ? metalc1 A ND1 HIS 44 A HIS 44 1_555 D ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc2 A OD2 ASP 47 A ASP 47 1_555 D ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc3 A NE2 HIS 155 A HIS 155 1_555 D ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc4 D ZN ZN . A ZN 301 1_555 E O72 MQG . A MQG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc5 B ND1 HIS 44 B HIS 44 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B OD1 ASP 47 B ASP 47 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc7 B OD2 ASP 47 B ASP 47 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc8 B NE2 HIS 155 B HIS 155 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc9 F ZN ZN . B ZN 301 1_555 G O72 MQG . B MQG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc10 C ND1 HIS 44 C HIS 44 1_555 H ZN ZN . C ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc11 C OD2 ASP 47 C ASP 47 1_555 H ZN ZN . C ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc12 C NE2 HIS 155 C HIS 155 1_555 H ZN ZN . C ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc13 H ZN ZN . C ZN 301 1_555 I O72 MQG . C MQG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? # _chem_comp.formula 'C7 H16 N O7 P' _chem_comp.formula_weight 257.178 _chem_comp.id MQG _chem_comp.mon_nstd_flag n _chem_comp.name 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms '~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]-methyl-phosphonamidic acid;2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucose;2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-D-glucose;2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-glucose' # 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 O6 C6 MQG sing 237 n n C6 C5 MQG sing 238 n n O4 C4 MQG sing 239 n n C4 C5 MQG sing 240 n n C4 C3 MQG sing 241 n n C5 O5 MQG sing 242 n n O3 C3 MQG sing 243 n n O5 C1 MQG sing 244 n n C3 C2 MQG sing 245 n n C2 C1 MQG sing 246 n n C2 N2 MQG sing 247 n n C1 O1 MQG sing 248 n n O71 P7 MQG doub 249 n n O72 P7 MQG sing 250 n n N2 P7 MQG sing 251 n n P7 C8 MQG sing 252 n n C2 H2 MQG sing 253 n n C3 H3 MQG sing 254 n n C4 H4 MQG sing 255 n n C5 H5 MQG sing 256 n n C6 H61 MQG sing 257 n n C6 H62 MQG sing 258 n n C8 H7 MQG sing 259 n n C8 H8 MQG sing 260 n n C8 H9 MQG sing 261 n n O1 HO1 MQG sing 262 n n C1 H1 MQG sing 263 n n O3 HO3 MQG sing 264 n n O72 H13 MQG sing 265 n n N2 HN21 MQG sing 266 n n O4 HO4 MQG sing 267 n n O6 HO6 MQG sing 268 n n # _atom_sites.entry_id 5B2F _atom_sites.fract_transf_matrix[1][1] 0.01285 _atom_sites.fract_transf_matrix[1][2] 0.007419 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014838 _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] 0.004362 _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 ZN A 1 301 1 ZN ZN . E 3 MQG A 1 302 1 MQG MPG . F 2 ZN B 1 301 2 ZN ZN . G 3 MQG B 1 302 2 MQG MPG . H 2 ZN C 1 301 3 ZN ZN . I 3 MQG C 1 302 3 MQG MPG . J 4 HOH A 1 401 142 HOH HOH . J 4 HOH A 2 402 116 HOH HOH . J 4 HOH A 3 403 163 HOH HOH . J 4 HOH A 4 404 179 HOH HOH . J 4 HOH A 5 405 70 HOH HOH . J 4 HOH A 6 406 153 HOH HOH . J 4 HOH A 7 407 125 HOH HOH . J 4 HOH A 8 408 93 HOH HOH . J 4 HOH A 9 409 184 HOH HOH . J 4 HOH A 10 410 12 HOH HOH . J 4 HOH A 11 411 108 HOH HOH . J 4 HOH A 12 412 51 HOH HOH . J 4 HOH A 13 413 71 HOH HOH . J 4 HOH A 14 414 138 HOH HOH . J 4 HOH A 15 415 156 HOH HOH . J 4 HOH A 16 416 6 HOH HOH . J 4 HOH A 17 417 136 HOH HOH . J 4 HOH A 18 418 59 HOH HOH . J 4 HOH A 19 419 39 HOH HOH . J 4 HOH A 20 420 78 HOH HOH . J 4 HOH A 21 421 94 HOH HOH . J 4 HOH A 22 422 34 HOH HOH . J 4 HOH A 23 423 57 HOH HOH . J 4 HOH A 24 424 92 HOH HOH . J 4 HOH A 25 425 74 HOH HOH . J 4 HOH A 26 426 72 HOH HOH . J 4 HOH A 27 427 134 HOH HOH . J 4 HOH A 28 428 33 HOH HOH . J 4 HOH A 29 429 130 HOH HOH . J 4 HOH A 30 430 68 HOH HOH . J 4 HOH A 31 431 118 HOH HOH . J 4 HOH A 32 432 171 HOH HOH . J 4 HOH A 33 433 75 HOH HOH . J 4 HOH A 34 434 4 HOH HOH . J 4 HOH A 35 435 30 HOH HOH . J 4 HOH A 36 436 7 HOH HOH . J 4 HOH A 37 437 154 HOH HOH . J 4 HOH A 38 438 98 HOH HOH . J 4 HOH A 39 439 96 HOH HOH . J 4 HOH A 40 440 107 HOH HOH . J 4 HOH A 41 441 85 HOH HOH . J 4 HOH A 42 442 127 HOH HOH . J 4 HOH A 43 443 48 HOH HOH . J 4 HOH A 44 444 103 HOH HOH . J 4 HOH A 45 445 150 HOH HOH . J 4 HOH A 46 446 63 HOH HOH . J 4 HOH A 47 447 35 HOH HOH . J 4 HOH A 48 448 144 HOH HOH . J 4 HOH A 49 449 159 HOH HOH . J 4 HOH A 50 450 52 HOH HOH . J 4 HOH A 51 451 119 HOH HOH . J 4 HOH A 52 452 100 HOH HOH . J 4 HOH A 53 453 128 HOH HOH . J 4 HOH A 54 454 3 HOH HOH . J 4 HOH A 55 455 46 HOH HOH . J 4 HOH A 56 456 164 HOH HOH . J 4 HOH A 57 457 121 HOH HOH . J 4 HOH A 58 458 53 HOH HOH . J 4 HOH A 59 459 132 HOH HOH . J 4 HOH A 60 460 147 HOH HOH . J 4 HOH A 61 461 87 HOH HOH . J 4 HOH A 62 462 180 HOH HOH . J 4 HOH A 63 463 28 HOH HOH . J 4 HOH A 64 464 26 HOH HOH . J 4 HOH A 65 465 1 HOH HOH . J 4 HOH A 66 466 172 HOH HOH . J 4 HOH A 67 467 151 HOH HOH . J 4 HOH A 68 468 40 HOH HOH . J 4 HOH A 69 469 5 HOH HOH . J 4 HOH A 70 470 112 HOH HOH . J 4 HOH A 71 471 16 HOH HOH . J 4 HOH A 72 472 20 HOH HOH . J 4 HOH A 73 473 32 HOH HOH . J 4 HOH A 74 474 80 HOH HOH . J 4 HOH A 75 475 82 HOH HOH . J 4 HOH A 76 476 36 HOH HOH . J 4 HOH A 77 477 178 HOH HOH . J 4 HOH A 78 478 167 HOH HOH . J 4 HOH A 79 479 175 HOH HOH . J 4 HOH A 80 480 186 HOH HOH . J 4 HOH A 81 481 170 HOH HOH . J 4 HOH A 82 482 168 HOH HOH . J 4 HOH A 83 483 185 HOH HOH . J 4 HOH A 84 484 158 HOH HOH . K 4 HOH B 1 401 50 HOH HOH . K 4 HOH B 2 402 131 HOH HOH . K 4 HOH B 3 403 58 HOH HOH . K 4 HOH B 4 404 133 HOH HOH . K 4 HOH B 5 405 149 HOH HOH . K 4 HOH B 6 406 42 HOH HOH . K 4 HOH B 7 407 89 HOH HOH . K 4 HOH B 8 408 77 HOH HOH . K 4 HOH B 9 409 83 HOH HOH . K 4 HOH B 10 410 67 HOH HOH . K 4 HOH B 11 411 106 HOH HOH . K 4 HOH B 12 412 14 HOH HOH . K 4 HOH B 13 413 64 HOH HOH . K 4 HOH B 14 414 56 HOH HOH . K 4 HOH B 15 415 13 HOH HOH . K 4 HOH B 16 416 19 HOH HOH . K 4 HOH B 17 417 84 HOH HOH . K 4 HOH B 18 418 45 HOH HOH . K 4 HOH B 19 419 38 HOH HOH . K 4 HOH B 20 420 10 HOH HOH . K 4 HOH B 21 421 17 HOH HOH . K 4 HOH B 22 422 41 HOH HOH . K 4 HOH B 23 423 95 HOH HOH . K 4 HOH B 24 424 54 HOH HOH . K 4 HOH B 25 425 91 HOH HOH . K 4 HOH B 26 426 99 HOH HOH . K 4 HOH B 27 427 173 HOH HOH . K 4 HOH B 28 428 152 HOH HOH . K 4 HOH B 29 429 105 HOH HOH . K 4 HOH B 30 430 90 HOH HOH . K 4 HOH B 31 431 18 HOH HOH . K 4 HOH B 32 432 60 HOH HOH . K 4 HOH B 33 433 122 HOH HOH . K 4 HOH B 34 434 160 HOH HOH . K 4 HOH B 35 435 44 HOH HOH . K 4 HOH B 36 436 22 HOH HOH . K 4 HOH B 37 437 43 HOH HOH . K 4 HOH B 38 438 169 HOH HOH . K 4 HOH B 39 439 176 HOH HOH . K 4 HOH B 40 440 177 HOH HOH . L 4 HOH C 1 401 110 HOH HOH . L 4 HOH C 2 402 86 HOH HOH . L 4 HOH C 3 403 165 HOH HOH . L 4 HOH C 4 404 143 HOH HOH . L 4 HOH C 5 405 65 HOH HOH . L 4 HOH C 6 406 135 HOH HOH . L 4 HOH C 7 407 109 HOH HOH . L 4 HOH C 8 408 62 HOH HOH . L 4 HOH C 9 409 61 HOH HOH . L 4 HOH C 10 410 126 HOH HOH . L 4 HOH C 11 411 157 HOH HOH . L 4 HOH C 12 412 140 HOH HOH . L 4 HOH C 13 413 11 HOH HOH . L 4 HOH C 14 414 162 HOH HOH . L 4 HOH C 15 415 27 HOH HOH . L 4 HOH C 16 416 76 HOH HOH . L 4 HOH C 17 417 8 HOH HOH . L 4 HOH C 18 418 73 HOH HOH . L 4 HOH C 19 419 114 HOH HOH . L 4 HOH C 20 420 31 HOH HOH . L 4 HOH C 21 421 148 HOH HOH . L 4 HOH C 22 422 88 HOH HOH . L 4 HOH C 23 423 166 HOH HOH . L 4 HOH C 24 424 21 HOH HOH . L 4 HOH C 25 425 101 HOH HOH . L 4 HOH C 26 426 139 HOH HOH . L 4 HOH C 27 427 55 HOH HOH . L 4 HOH C 28 428 104 HOH HOH . L 4 HOH C 29 429 113 HOH HOH . L 4 HOH C 30 430 15 HOH HOH . L 4 HOH C 31 431 123 HOH HOH . L 4 HOH C 32 432 120 HOH HOH . L 4 HOH C 33 433 66 HOH HOH . L 4 HOH C 34 434 97 HOH HOH . L 4 HOH C 35 435 137 HOH HOH . L 4 HOH C 36 436 81 HOH HOH . L 4 HOH C 37 437 49 HOH HOH . L 4 HOH C 38 438 155 HOH HOH . L 4 HOH C 39 439 124 HOH HOH . L 4 HOH C 40 440 29 HOH HOH . L 4 HOH C 41 441 174 HOH HOH . L 4 HOH C 42 442 47 HOH HOH . L 4 HOH C 43 443 23 HOH HOH . L 4 HOH C 44 444 117 HOH HOH . L 4 HOH C 45 445 111 HOH HOH . L 4 HOH C 46 446 182 HOH HOH . L 4 HOH C 47 447 145 HOH HOH . L 4 HOH C 48 448 102 HOH HOH . L 4 HOH C 49 449 146 HOH HOH . L 4 HOH C 50 450 69 HOH HOH . L 4 HOH C 51 451 37 HOH HOH . L 4 HOH C 52 452 161 HOH HOH . L 4 HOH C 53 453 25 HOH HOH . L 4 HOH C 54 454 9 HOH HOH . L 4 HOH C 55 455 2 HOH HOH . L 4 HOH C 56 456 79 HOH HOH . L 4 HOH C 57 457 129 HOH HOH . L 4 HOH C 58 458 24 HOH HOH . L 4 HOH C 59 459 141 HOH HOH . L 4 HOH C 60 460 183 HOH HOH . L 4 HOH C 61 461 181 HOH HOH . L 4 HOH C 62 462 115 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 MQG . . . E 3 19.72 52.18 22.202 1 28.58 ? C2 MQG 302 A 1 HETATM 2 C C3 MQG . . . E 3 19.086 53.308 21.382 1 27.06 ? C3 MQG 302 A 1 HETATM 3 C C4 MQG . . . E 3 18.467 52.693 20.143 1 28.3 ? C4 MQG 302 A 1 HETATM 4 C C5 MQG . . . E 3 17.555 51.486 20.566 1 29.04 ? C5 MQG 302 A 1 HETATM 5 C C6 MQG . . . E 3 16.998 50.769 19.343 1 29.3 ? C6 MQG 302 A 1 HETATM 6 C C8 MQG . . . E 3 22.162 53.424 25.301 1 26.98 ? C8 MQG 302 A 1 HETATM 7 O O1 MQG . . . E 3 19.391 49.976 23.11 1 34.97 ? O1 MQG 302 A 1 HETATM 8 C C1 MQG . . . E 3 18.704 51.046 22.525 1 31.33 ? C1 MQG 302 A 1 HETATM 9 O O3 MQG . . . E 3 20.025 54.398 21.075 1 26.14 ? O3 MQG 302 A 1 HETATM 10 O O71 MQG . . . E 3 22.147 54.44 22.805 1 24.6 ? O71 MQG 302 A 1 HETATM 11 P P7 MQG . . . E 3 21.886 53.132 23.547 1 29.64 ? P7 MQG 302 A 1 HETATM 12 O O72 MQG . . . E 3 22.918 52.122 22.956 1 25.75 ? O72 MQG 302 A 1 HETATM 13 N N2 MQG . . . E 3 20.201 52.625 23.499 1 25.06 ? N2 MQG 302 A 1 HETATM 14 O O4 MQG . . . E 3 17.707 53.748 19.475 1 27.28 ? O4 MQG 302 A 1 HETATM 15 O O5 MQG . . . E 3 18.264 50.477 21.352 1 25.98 ? O5 MQG 302 A 1 HETATM 16 O O6 MQG . . . E 3 18.129 50.305 18.581 1 36.28 ? O6 MQG 302 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 461 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 16 #