data_6VR3 # _model_server_result.job_id oJHDoSJL109yBb-7vRCe3Q _model_server_result.datetime_utc '2025-08-31 21:52:00' _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 6vr3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 6VR3 # _exptl.entry_id 6VR3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 517.616 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-[(2S,3R)-2-{[(1R,2S,3S,4R,6S)-6-amino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-lyxopyranosyl]oxy}-4-(ethylamino) -2-hydroxycyclohexyl]oxy}-6-(aminomethyl)-3,4-dihydro-2H-pyran-3-yl]acetamide' _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 120 _cell.entry_id 6VR3 _cell.length_a 73.038 _cell.length_b 73.038 _cell.length_c 145.55 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VR3 _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 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,G,H _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 C N N ? 2 E N N # _chem_comp.formula 'C23 H43 N5 O8' _chem_comp.formula_weight 517.616 _chem_comp.id NTL _chem_comp.mon_nstd_flag . _chem_comp.name 'N-[(2S,3R)-2-{[(1R,2S,3S,4R,6S)-6-amino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-lyxopyranosyl]oxy}-4-(ethylamino) -2-hydroxycyclohexyl]oxy}-6-(aminomethyl)-3,4-dihydro-2H-pyran-3-yl]acetamide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms acetylated-netilmicin # 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 N33 C34 NTL sing 323 n n N33 C32 NTL sing 324 n n C01 C02 NTL sing 325 n n O36 C35 NTL sing 326 n n C32 C35 NTL sing 327 n n C32 C29 NTL sing 328 n n C35 C26 NTL sing 329 n n C02 N03 NTL sing 330 n n N03 C04 NTL sing 331 n n C30 C29 NTL sing 332 n n O31 C29 NTL sing 333 n n C29 C28 NTL sing 334 n n C26 O25 NTL sing 335 n n C26 O27 NTL sing 336 n n C04 C24 NTL sing 337 n n C04 C05 NTL sing 338 n n O25 C24 NTL sing 339 n n C28 O27 NTL sing 340 n n C24 C22 NTL sing 341 n n C05 C06 NTL sing 342 n n C22 O23 NTL sing 343 n n C22 C08 NTL sing 344 n n C06 N07 NTL sing 345 n n C06 C08 NTL sing 346 n n C08 O09 NTL sing 347 n n N14 C13 NTL sing 348 n n O09 C10 NTL sing 349 n n O11 C10 NTL sing 350 n n O11 C12 NTL sing 351 n n C10 C17 NTL sing 352 n n C13 C12 NTL sing 353 n n C12 C15 NTL doub 354 n n C15 C16 NTL sing 355 n n C17 N18 NTL sing 356 n n C17 C16 NTL sing 357 n n N18 C19 NTL sing 358 n n C19 C20 NTL sing 359 n n C19 O21 NTL doub 360 n n C01 H1 NTL sing 361 n n C01 H2 NTL sing 362 n n C01 H3 NTL sing 363 n n C02 H4 NTL sing 364 n n C02 H5 NTL sing 365 n n C04 H6 NTL sing 366 n n C05 H7 NTL sing 367 n n C05 H8 NTL sing 368 n n C06 H9 NTL sing 369 n n C08 H10 NTL sing 370 n n C10 H11 NTL sing 371 n n C13 H13 NTL sing 372 n n C13 H14 NTL sing 373 n n C15 H15 NTL sing 374 n n C16 H17 NTL sing 375 n n C16 H18 NTL sing 376 n n C17 H19 NTL sing 377 n n C20 H20 NTL sing 378 n n C20 H21 NTL sing 379 n n C20 H22 NTL sing 380 n n C22 H23 NTL sing 381 n n C24 H24 NTL sing 382 n n C26 H25 NTL sing 383 n n C28 H26 NTL sing 384 n n C28 H27 NTL sing 385 n n C30 H28 NTL sing 386 n n C30 H29 NTL sing 387 n n C30 H30 NTL sing 388 n n C32 H31 NTL sing 389 n n C34 H32 NTL sing 390 n n C34 H33 NTL sing 391 n n C34 H34 NTL sing 392 n n C35 H35 NTL sing 393 n n N03 H36 NTL sing 394 n n N07 H38 NTL sing 395 n n N07 H39 NTL sing 396 n n N14 H41 NTL sing 397 n n N14 H42 NTL sing 398 n n N18 H44 NTL sing 399 n n N33 H45 NTL sing 400 n n O23 H47 NTL sing 401 n n O31 H48 NTL sing 402 n n O36 H49 NTL sing 403 n n # _atom_sites.entry_id 6VR3 _atom_sites.fract_transf_matrix[1][1] 0.013692 _atom_sites.fract_transf_matrix[1][2] 0.007905 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01581 _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] 0.00687 _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 C 2 NTL A 1 201 1 NTL NTL . D 3 COA A 1 202 1 COA COA . E 2 NTL B 1 201 2 NTL NTL . F 3 COA B 1 202 2 COA COA . G 4 HOH A 1 301 17 HOH HOH . G 4 HOH A 2 302 62 HOH HOH . G 4 HOH A 3 303 75 HOH HOH . G 4 HOH A 4 304 57 HOH HOH . G 4 HOH A 5 305 46 HOH HOH . G 4 HOH A 6 306 67 HOH HOH . G 4 HOH A 7 307 65 HOH HOH . G 4 HOH A 8 308 42 HOH HOH . G 4 HOH A 9 309 48 HOH HOH . G 4 HOH A 10 310 171 HOH HOH . G 4 HOH A 11 311 53 HOH HOH . G 4 HOH A 12 312 1 HOH HOH . G 4 HOH A 13 313 49 HOH HOH . G 4 HOH A 14 314 167 HOH HOH . G 4 HOH A 15 315 130 HOH HOH . G 4 HOH A 16 316 54 HOH HOH . G 4 HOH A 17 317 136 HOH HOH . G 4 HOH A 18 318 66 HOH HOH . G 4 HOH A 19 319 43 HOH HOH . G 4 HOH A 20 320 11 HOH HOH . G 4 HOH A 21 321 47 HOH HOH . G 4 HOH A 22 322 71 HOH HOH . G 4 HOH A 23 323 2 HOH HOH . G 4 HOH A 24 324 21 HOH HOH . G 4 HOH A 25 325 166 HOH HOH . G 4 HOH A 26 326 131 HOH HOH . G 4 HOH A 27 327 39 HOH HOH . G 4 HOH A 28 328 72 HOH HOH . G 4 HOH A 29 329 112 HOH HOH . G 4 HOH A 30 330 127 HOH HOH . G 4 HOH A 31 331 3 HOH HOH . G 4 HOH A 32 332 44 HOH HOH . G 4 HOH A 33 333 58 HOH HOH . G 4 HOH A 34 334 59 HOH HOH . G 4 HOH A 35 335 125 HOH HOH . G 4 HOH A 36 336 74 HOH HOH . G 4 HOH A 37 337 56 HOH HOH . G 4 HOH A 38 338 73 HOH HOH . G 4 HOH A 39 339 170 HOH HOH . G 4 HOH A 40 340 6 HOH HOH . G 4 HOH A 41 341 126 HOH HOH . G 4 HOH A 42 342 55 HOH HOH . G 4 HOH A 43 343 108 HOH HOH . G 4 HOH A 44 344 114 HOH HOH . G 4 HOH A 45 345 168 HOH HOH . G 4 HOH A 46 346 38 HOH HOH . G 4 HOH A 47 347 51 HOH HOH . G 4 HOH A 48 348 137 HOH HOH . G 4 HOH A 49 349 79 HOH HOH . G 4 HOH A 50 350 68 HOH HOH . G 4 HOH A 51 351 50 HOH HOH . G 4 HOH A 52 352 109 HOH HOH . G 4 HOH A 53 353 52 HOH HOH . G 4 HOH A 54 354 61 HOH HOH . G 4 HOH A 55 355 45 HOH HOH . G 4 HOH A 56 356 77 HOH HOH . G 4 HOH A 57 357 12 HOH HOH . G 4 HOH A 58 358 78 HOH HOH . G 4 HOH A 59 359 113 HOH HOH . G 4 HOH A 60 360 124 HOH HOH . G 4 HOH A 61 361 111 HOH HOH . G 4 HOH A 62 362 115 HOH HOH . G 4 HOH A 63 363 76 HOH HOH . G 4 HOH A 64 364 41 HOH HOH . G 4 HOH A 65 365 8 HOH HOH . G 4 HOH A 66 366 37 HOH HOH . G 4 HOH A 67 367 63 HOH HOH . G 4 HOH A 68 368 138 HOH HOH . G 4 HOH A 69 369 36 HOH HOH . G 4 HOH A 70 370 141 HOH HOH . G 4 HOH A 71 371 133 HOH HOH . G 4 HOH A 72 372 120 HOH HOH . G 4 HOH A 73 373 139 HOH HOH . G 4 HOH A 74 374 69 HOH HOH . G 4 HOH A 75 375 116 HOH HOH . G 4 HOH A 76 376 123 HOH HOH . G 4 HOH A 77 377 10 HOH HOH . G 4 HOH A 78 378 134 HOH HOH . G 4 HOH A 79 379 132 HOH HOH . G 4 HOH A 80 380 110 HOH HOH . G 4 HOH A 81 381 70 HOH HOH . G 4 HOH A 82 382 14 HOH HOH . G 4 HOH A 83 383 135 HOH HOH . G 4 HOH A 84 384 5 HOH HOH . G 4 HOH A 85 385 140 HOH HOH . G 4 HOH A 86 386 35 HOH HOH . H 4 HOH B 1 301 16 HOH HOH . H 4 HOH B 2 302 105 HOH HOH . H 4 HOH B 3 303 98 HOH HOH . H 4 HOH B 4 304 24 HOH HOH . H 4 HOH B 5 305 144 HOH HOH . H 4 HOH B 6 306 102 HOH HOH . H 4 HOH B 7 307 25 HOH HOH . H 4 HOH B 8 308 121 HOH HOH . H 4 HOH B 9 309 165 HOH HOH . H 4 HOH B 10 310 29 HOH HOH . H 4 HOH B 11 311 118 HOH HOH . H 4 HOH B 12 312 97 HOH HOH . H 4 HOH B 13 313 161 HOH HOH . H 4 HOH B 14 314 100 HOH HOH . H 4 HOH B 15 315 60 HOH HOH . H 4 HOH B 16 316 86 HOH HOH . H 4 HOH B 17 317 9 HOH HOH . H 4 HOH B 18 318 31 HOH HOH . H 4 HOH B 19 319 4 HOH HOH . H 4 HOH B 20 320 96 HOH HOH . H 4 HOH B 21 321 26 HOH HOH . H 4 HOH B 22 322 64 HOH HOH . H 4 HOH B 23 323 157 HOH HOH . H 4 HOH B 24 324 85 HOH HOH . H 4 HOH B 25 325 87 HOH HOH . H 4 HOH B 26 326 160 HOH HOH . H 4 HOH B 27 327 33 HOH HOH . H 4 HOH B 28 328 13 HOH HOH . H 4 HOH B 29 329 30 HOH HOH . H 4 HOH B 30 330 15 HOH HOH . H 4 HOH B 31 331 149 HOH HOH . H 4 HOH B 32 332 103 HOH HOH . H 4 HOH B 33 333 27 HOH HOH . H 4 HOH B 34 334 88 HOH HOH . H 4 HOH B 35 335 154 HOH HOH . H 4 HOH B 36 336 82 HOH HOH . H 4 HOH B 37 337 122 HOH HOH . H 4 HOH B 38 338 148 HOH HOH . H 4 HOH B 39 339 107 HOH HOH . H 4 HOH B 40 340 101 HOH HOH . H 4 HOH B 41 341 152 HOH HOH . H 4 HOH B 42 342 18 HOH HOH . H 4 HOH B 43 343 174 HOH HOH . H 4 HOH B 44 344 92 HOH HOH . H 4 HOH B 45 345 153 HOH HOH . H 4 HOH B 46 346 176 HOH HOH . H 4 HOH B 47 347 119 HOH HOH . H 4 HOH B 48 348 93 HOH HOH . H 4 HOH B 49 349 104 HOH HOH . H 4 HOH B 50 350 23 HOH HOH . H 4 HOH B 51 351 90 HOH HOH . H 4 HOH B 52 352 146 HOH HOH . H 4 HOH B 53 353 32 HOH HOH . H 4 HOH B 54 354 163 HOH HOH . H 4 HOH B 55 355 169 HOH HOH . H 4 HOH B 56 356 28 HOH HOH . H 4 HOH B 57 357 147 HOH HOH . H 4 HOH B 58 358 173 HOH HOH . H 4 HOH B 59 359 143 HOH HOH . H 4 HOH B 60 360 20 HOH HOH . H 4 HOH B 61 361 94 HOH HOH . H 4 HOH B 62 362 145 HOH HOH . H 4 HOH B 63 363 156 HOH HOH . H 4 HOH B 64 364 164 HOH HOH . H 4 HOH B 65 365 129 HOH HOH . H 4 HOH B 66 366 22 HOH HOH . H 4 HOH B 67 367 128 HOH HOH . H 4 HOH B 68 368 151 HOH HOH . H 4 HOH B 69 369 117 HOH HOH . H 4 HOH B 70 370 159 HOH HOH . H 4 HOH B 71 371 175 HOH HOH . H 4 HOH B 72 372 80 HOH HOH . H 4 HOH B 73 373 7 HOH HOH . H 4 HOH B 74 374 106 HOH HOH . H 4 HOH B 75 375 155 HOH HOH . H 4 HOH B 76 376 142 HOH HOH . H 4 HOH B 77 377 162 HOH HOH . H 4 HOH B 78 378 19 HOH HOH . H 4 HOH B 79 379 172 HOH HOH . H 4 HOH B 80 380 81 HOH HOH . H 4 HOH B 81 381 34 HOH HOH . H 4 HOH B 82 382 95 HOH HOH . H 4 HOH B 83 383 91 HOH HOH . H 4 HOH B 84 384 89 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 C01 NTL . . . E 2 64.681 10.384 156.215 1 30.87 ? C01 NTL 201 B 1 HETATM 2 C C02 NTL . . . E 2 64.334 10.809 157.663 1 20.36 ? C02 NTL 201 B 1 HETATM 3 C C04 NTL . . . E 2 62.402 11.37 159.238 1 19.17 ? C04 NTL 201 B 1 HETATM 4 C C05 NTL . . . E 2 63.073 12.744 159.564 1 16.58 ? C05 NTL 201 B 1 HETATM 5 C C06 NTL . . . E 2 62.672 13.366 160.933 1 21.39 ? C06 NTL 201 B 1 HETATM 6 C C08 NTL . . . E 2 62.962 12.381 162.112 1 23.4 ? C08 NTL 201 B 1 HETATM 7 C C10 NTL . . . E 2 63.047 12.409 164.508 1 19.46 ? C10 NTL 201 B 1 HETATM 8 C C12 NTL . . . E 2 65.351 12.989 164.711 1 19.47 ? C12 NTL 201 B 1 HETATM 9 C C13 NTL . . . E 2 66.803 12.51 164.39 1 20.41 ? C13 NTL 201 B 1 HETATM 10 C C15 NTL . . . E 2 64.971 14.236 164.691 1 23.47 ? C15 NTL 201 B 1 HETATM 11 C C16 NTL . . . E 2 63.658 14.692 165.253 1 15.1 ? C16 NTL 201 B 1 HETATM 12 C C17 NTL . . . E 2 62.767 13.459 165.609 1 19.4 ? C17 NTL 201 B 1 HETATM 13 C C19 NTL . . . E 2 60.761 14.152 166.921 1 21.06 ? C19 NTL 201 B 1 HETATM 14 C C20 NTL . . . E 2 59.266 14.426 167.114 1 24.2 ? C20 NTL 201 B 1 HETATM 15 C C22 NTL . . . E 2 62.205 10.989 161.814 1 27.3 ? C22 NTL 201 B 1 HETATM 16 C C24 NTL . . . E 2 62.663 10.339 160.415 1 25.5 ? C24 NTL 201 B 1 HETATM 17 C C26 NTL . . . E 2 62.724 7.952 160.208 1 33.04 ? C26 NTL 201 B 1 HETATM 18 C C28 NTL . . . E 2 61.238 6.794 161.685 1 42.33 ? C28 NTL 201 B 1 HETATM 19 C C29 NTL . . . E 2 60.852 5.662 160.725 1 48.55 ? C29 NTL 201 B 1 HETATM 20 C C30 NTL . . . E 2 59.393 5.323 160.831 1 50.8 ? C30 NTL 201 B 1 HETATM 21 C C32 NTL . . . E 2 61.116 6.074 159.182 1 50.26 ? C32 NTL 201 B 1 HETATM 22 C C34 NTL . . . E 2 59.721 6.229 157.106 1 50.74 ? C34 NTL 201 B 1 HETATM 23 C C35 NTL . . . E 2 62.417 6.972 158.975 1 43.3 ? C35 NTL 201 B 1 HETATM 24 N N03 NTL . . . E 2 62.866 10.827 157.926 1 18.32 ? N03 NTL 201 B 1 HETATM 25 N N07 NTL . . . E 2 63.37 14.647 161.184 1 15.18 ? N07 NTL 201 B 1 HETATM 26 N N14 NTL . . . E 2 67.078 11.853 163.096 1 22.38 ? N14 NTL 201 B 1 HETATM 27 N N18 NTL . . . E 2 61.34 13.692 165.756 1 20.75 ? N18 NTL 201 B 1 HETATM 28 N N33 NTL . . . E 2 59.953 6.712 158.487 1 52.83 ? N33 NTL 201 B 1 HETATM 29 O O09 NTL . . . E 2 62.528 13 163.316 1 21.75 ? O09 NTL 201 B 1 HETATM 30 O O11 NTL . . . E 2 64.385 11.952 164.556 1 21.62 ? O11 NTL 201 B 1 HETATM 31 O O21 NTL . . . E 2 61.507 14.341 167.878 1 20.1 ? O21 NTL 201 B 1 HETATM 32 O O23 NTL . . . E 2 62.556 10.032 162.78 1 26.57 ? O23 NTL 201 B 1 HETATM 33 O O25 NTL . . . E 2 61.977 9.144 160.191 1 30.8 ? O25 NTL 201 B 1 HETATM 34 O O27 NTL . . . E 2 62.5 7.325 161.412 1 35.05 ? O27 NTL 201 B 1 HETATM 35 O O31 NTL . . . E 2 61.572 4.491 160.922 1 47.64 ? O31 NTL 201 B 1 HETATM 36 O O36 NTL . . . E 2 62.261 7.817 157.869 1 43.29 ? O36 NTL 201 B 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 430 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #