data_5NF9 # _model_server_result.job_id 1kt8RV0lnF8ypq3uz76ABw _model_server_result.datetime_utc '2024-11-21 23:42:12' _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 5nf9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5NF9 # _exptl.entry_id 5NF9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 516.496 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-3-yl]-3-methoxy-benzamide _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 5NF9 _cell.length_a 36.87 _cell.length_b 57.95 _cell.length_c 62.98 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NF9 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C22 H32 N2 O12' _chem_comp.formula_weight 516.496 _chem_comp.id 8VW _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-3-yl]-3-methoxy-benzamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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, 8VW sing 1 n n C6, C5, 8VW sing 2 n n O5, C5, 8VW sing 3 n n O5, C1, 8VW sing 4 n n O35 C33 8VW doub 5 n n O2 C2 8VW sing 6 n n C5, C4, 8VW sing 7 n n C34 C33 8VW sing 8 n n C33 N1 8VW sing 9 n n C3 O3 8VW sing 10 n n C3 C2 8VW sing 11 n n C3 C4 8VW sing 12 n n N1 C1, 8VW sing 13 n n C1 C2 8VW sing 14 n n C1 O1 8VW sing 15 n n C1 O5 8VW sing 16 n n C1, C2, 8VW sing 17 n n C4, O1 8VW sing 18 n n C4, C3, 8VW sing 19 n n C5 C4 8VW sing 20 n n C5 O5 8VW sing 21 n n C5 C6 8VW sing 22 n n C4 O4 8VW sing 23 n n O6 C6 8VW sing 24 n n C2, C3, 8VW sing 25 n n C2, N2 8VW sing 26 n n C3, O3, 8VW sing 27 n n O37 C36 8VW doub 28 n n N2 C36 8VW sing 29 n n C36 C38 8VW sing 30 n n C38 C39 8VW doub 31 n y C38 C43 8VW sing 32 n y C39 C40 8VW sing 33 n y C43 C42 8VW doub 34 n y C40 C41 8VW doub 35 n y C42 C41 8VW sing 36 n y C42 O44 8VW sing 37 n n C45 O44 8VW sing 38 n n C34 H1 8VW sing 39 n n C34 H2 8VW sing 40 n n C34 H3 8VW sing 41 n n N1 H4 8VW sing 42 n n C1, H5 8VW sing 43 n n C2, H6 8VW sing 44 n n N2 H7 8VW sing 45 n n C39 H8 8VW sing 46 n n C40 H9 8VW sing 47 n n C41 H10 8VW sing 48 n n C45 H11 8VW sing 49 n n C45 H12 8VW sing 50 n n C45 H13 8VW sing 51 n n C43 H14 8VW sing 52 n n C5, H15 8VW sing 53 n n C6, H16 8VW sing 54 n n C6, H17 8VW sing 55 n n O6, H18 8VW sing 56 n n C4, H19 8VW sing 57 n n C3, H20 8VW sing 58 n n O3, H21 8VW sing 59 n n C1 H22 8VW sing 60 n n C2 H23 8VW sing 61 n n O2 H24 8VW sing 62 n n C3 H25 8VW sing 63 n n O3 H26 8VW sing 64 n n C4 H27 8VW sing 65 n n O4 H28 8VW sing 66 n n C5 H29 8VW sing 67 n n C6 H30 8VW sing 68 n n C6 H31 8VW sing 69 n n O6 H32 8VW sing 70 n n # _atom_sites.entry_id 5NF9 _atom_sites.fract_transf_matrix[1][1] 0.027122 _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] 0.017256 _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] 0.015878 _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 8VW A 1 301 1 8VW Lg3 . C 3 HOH A 1 401 101 HOH HOH . C 3 HOH A 2 402 90 HOH HOH . C 3 HOH A 3 403 31 HOH HOH . C 3 HOH A 4 404 20 HOH HOH . C 3 HOH A 5 405 21 HOH HOH . C 3 HOH A 6 406 39 HOH HOH . C 3 HOH A 7 407 34 HOH HOH . C 3 HOH A 8 408 81 HOH HOH . C 3 HOH A 9 409 64 HOH HOH . C 3 HOH A 10 410 25 HOH HOH . C 3 HOH A 11 411 89 HOH HOH . C 3 HOH A 12 412 4 HOH HOH . C 3 HOH A 13 413 41 HOH HOH . C 3 HOH A 14 414 10 HOH HOH . C 3 HOH A 15 415 99 HOH HOH . C 3 HOH A 16 416 40 HOH HOH . C 3 HOH A 17 417 95 HOH HOH . C 3 HOH A 18 418 63 HOH HOH . C 3 HOH A 19 419 77 HOH HOH . C 3 HOH A 20 420 69 HOH HOH . C 3 HOH A 21 421 30 HOH HOH . C 3 HOH A 22 422 36 HOH HOH . C 3 HOH A 23 423 100 HOH HOH . C 3 HOH A 24 424 50 HOH HOH . C 3 HOH A 25 425 55 HOH HOH . C 3 HOH A 26 426 8 HOH HOH . C 3 HOH A 27 427 46 HOH HOH . C 3 HOH A 28 428 102 HOH HOH . C 3 HOH A 29 429 85 HOH HOH . C 3 HOH A 30 430 37 HOH HOH . C 3 HOH A 31 431 67 HOH HOH . C 3 HOH A 32 432 15 HOH HOH . C 3 HOH A 33 433 94 HOH HOH . C 3 HOH A 34 434 14 HOH HOH . C 3 HOH A 35 435 18 HOH HOH . C 3 HOH A 36 436 1 HOH HOH . C 3 HOH A 37 437 42 HOH HOH . C 3 HOH A 38 438 3 HOH HOH . C 3 HOH A 39 439 23 HOH HOH . C 3 HOH A 40 440 66 HOH HOH . C 3 HOH A 41 441 38 HOH HOH . C 3 HOH A 42 442 16 HOH HOH . C 3 HOH A 43 443 7 HOH HOH . C 3 HOH A 44 444 29 HOH HOH . C 3 HOH A 45 445 49 HOH HOH . C 3 HOH A 46 446 92 HOH HOH . C 3 HOH A 47 447 76 HOH HOH . C 3 HOH A 48 448 28 HOH HOH . C 3 HOH A 49 449 52 HOH HOH . C 3 HOH A 50 450 75 HOH HOH . C 3 HOH A 51 451 22 HOH HOH . C 3 HOH A 52 452 48 HOH HOH . C 3 HOH A 53 453 91 HOH HOH . C 3 HOH A 54 454 70 HOH HOH . C 3 HOH A 55 455 93 HOH HOH . C 3 HOH A 56 456 56 HOH HOH . C 3 HOH A 57 457 51 HOH HOH . C 3 HOH A 58 458 17 HOH HOH . C 3 HOH A 59 459 98 HOH HOH . C 3 HOH A 60 460 12 HOH HOH . C 3 HOH A 61 461 35 HOH HOH . C 3 HOH A 62 462 19 HOH HOH . C 3 HOH A 63 463 33 HOH HOH . C 3 HOH A 64 464 58 HOH HOH . C 3 HOH A 65 465 11 HOH HOH . C 3 HOH A 66 466 74 HOH HOH . C 3 HOH A 67 467 9 HOH HOH . C 3 HOH A 68 468 87 HOH HOH . C 3 HOH A 69 469 13 HOH HOH . C 3 HOH A 70 470 97 HOH HOH . C 3 HOH A 71 471 45 HOH HOH . C 3 HOH A 72 472 57 HOH HOH . C 3 HOH A 73 473 27 HOH HOH . C 3 HOH A 74 474 53 HOH HOH . C 3 HOH A 75 475 62 HOH HOH . C 3 HOH A 76 476 72 HOH HOH . C 3 HOH A 77 477 54 HOH HOH . C 3 HOH A 78 478 59 HOH HOH . C 3 HOH A 79 479 24 HOH HOH . C 3 HOH A 80 480 43 HOH HOH . C 3 HOH A 81 481 47 HOH HOH . C 3 HOH A 82 482 68 HOH HOH . C 3 HOH A 83 483 6 HOH HOH . C 3 HOH A 84 484 5 HOH HOH . C 3 HOH A 85 485 84 HOH HOH . C 3 HOH A 86 486 2 HOH HOH . C 3 HOH A 87 487 96 HOH HOH . C 3 HOH A 88 488 61 HOH HOH . C 3 HOH A 89 489 86 HOH HOH . C 3 HOH A 90 490 32 HOH HOH . C 3 HOH A 91 491 83 HOH HOH . C 3 HOH A 92 492 80 HOH HOH . C 3 HOH A 93 493 82 HOH HOH . C 3 HOH A 94 494 79 HOH HOH . C 3 HOH A 95 495 71 HOH HOH . C 3 HOH A 96 496 78 HOH HOH . C 3 HOH A 97 497 26 HOH HOH . C 3 HOH A 98 498 60 HOH HOH . C 3 HOH A 99 499 73 HOH HOH . C 3 HOH A 100 500 44 HOH HOH . C 3 HOH A 101 501 88 HOH HOH . C 3 HOH A 102 502 65 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 O O35 8VW . . . B 2 27.004 -12.612 -2.355 1 36.75 ? O35 8VW 301 A 1 HETATM 2 C C33 8VW . . . B 2 27.421 -11.511 -2.01 1 46.05 ? C33 8VW 301 A 1 HETATM 3 C C34 8VW . . . B 2 28.871 -11.137 -2.124 1 43.7 ? C34 8VW 301 A 1 HETATM 4 N N1 8VW . . . B 2 26.613 -10.566 -1.504 1 35.54 ? N1 8VW 301 A 1 HETATM 5 C C1, 8VW . . . B 2 25.204 -10.743 -1.303 1 31.05 ? C1, 8VW 301 A 1 HETATM 6 C C2, 8VW . . . B 2 24.84 -9.842 -0.096 1 27.14 ? C2, 8VW 301 A 1 HETATM 7 N N2 8VW . . . B 2 25.505 -10.36 1.085 1 27.92 ? N2 8VW 301 A 1 HETATM 8 C C36 8VW . . . B 2 26.658 -9.895 1.597 1 32.95 ? C36 8VW 301 A 1 HETATM 9 C C38 8VW . . . B 2 27.127 -10.427 2.939 1 38.97 ? C38 8VW 301 A 1 HETATM 10 C C39 8VW . . . B 2 26.704 -11.653 3.528 1 41.38 ? C39 8VW 301 A 1 HETATM 11 C C40 8VW . . . B 2 27.156 -11.981 4.829 1 42.86 ? C40 8VW 301 A 1 HETATM 12 C C41 8VW . . . B 2 28.018 -11.078 5.506 1 45.52 ? C41 8VW 301 A 1 HETATM 13 C C42 8VW . . . B 2 28.438 -9.87 4.898 1 44.67 ? C42 8VW 301 A 1 HETATM 14 O O44 8VW . . . B 2 29.289 -8.985 5.515 1 50.79 ? O44 8VW 301 A 1 HETATM 15 C C45 8VW . . . B 2 29.43 -7.601 5.172 1 50.48 ? C45 8VW 301 A 1 HETATM 16 C C43 8VW . . . B 2 27.982 -9.555 3.629 1 40.26 ? C43 8VW 301 A 1 HETATM 17 O O37 8VW . . . B 2 27.259 -8.97 1.075 1 34.99 ? O37 8VW 301 A 1 HETATM 18 O O5, 8VW . . . B 2 24.471 -10.287 -2.452 1 28.85 ? O5, 8VW 301 A 1 HETATM 19 C C5, 8VW . . . B 2 23.063 -10.48 -2.305 1 27.65 ? C5, 8VW 301 A 1 HETATM 20 C C6, 8VW . . . B 2 22.442 -10.114 -3.66 1 29.19 ? C6, 8VW 301 A 1 HETATM 21 O O6, 8VW . . . B 2 22.622 -8.71 -4.018 1 36.5 ? O6, 8VW 301 A 1 HETATM 22 C C4, 8VW . . . B 2 22.612 -9.545 -1.157 1 24.68 ? C4, 8VW 301 A 1 HETATM 23 C C3, 8VW . . . B 2 23.353 -9.885 0.127 1 26.33 ? C3, 8VW 301 A 1 HETATM 24 O O3, 8VW . . . B 2 23.027 -9.038 1.249 1 19.99 ? O3, 8VW 301 A 1 HETATM 25 O O1 8VW . . . B 2 21.245 -9.723 -0.934 1 26.68 ? O1 8VW 301 A 1 HETATM 26 C C1 8VW . . . B 2 20.503 -8.566 -1.35 1 25.24 ? C1 8VW 301 A 1 HETATM 27 C C2 8VW . . . B 2 19.072 -9 -1.325 1 27.59 ? C2 8VW 301 A 1 HETATM 28 O O2 8VW . . . B 2 18.803 -10.003 -2.328 1 29.32 ? O2 8VW 301 A 1 HETATM 29 C C3 8VW . . . B 2 18.197 -7.786 -1.63 1 23.9 ? C3 8VW 301 A 1 HETATM 30 O O3 8VW . . . B 2 16.829 -8.151 -1.505 1 24.27 ? O3 8VW 301 A 1 HETATM 31 C C4 8VW . . . B 2 18.529 -6.63 -0.708 1 22.4 ? C4 8VW 301 A 1 HETATM 32 O O4 8VW . . . B 2 18.123 -6.966 0.641 1 20.24 ? O4 8VW 301 A 1 HETATM 33 C C5 8VW . . . B 2 19.999 -6.275 -0.831 1 20.48 ? C5 8VW 301 A 1 HETATM 34 O O5 8VW . . . B 2 20.809 -7.424 -0.497 1 21.92 ? O5 8VW 301 A 1 HETATM 35 C C6 8VW . . . B 2 20.465 -5.113 0.056 1 18.62 ? C6 8VW 301 A 1 HETATM 36 O O6 8VW . . . B 2 21.838 -4.988 -0.24 1 19.67 ? O6 8VW 301 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #