data_4URM # _model_server_result.job_id mD5Q9S6gd86Izu8x6f066A _model_server_result.datetime_utc '2025-07-01 10:56:26' _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 4urm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2000}' # _entry.id 4URM # _exptl.entry_id 4URM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 939.872 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,4aS,5S,6S,8aR)-5-{[(5S)-1-(3-O-acetyl-4-O-carbamoyl-6-deoxy-2-O-methyl-alpha-L-talopyranosyl)-4-hydroxy-2-oxo-5-(propan-2-yl)-2,5-dihydro-1H-pyrrol-3-yl]carbonyl}-6-methyl-4-methylidene-1,2,3,4,4a,5,6,8a-octahydronaphthalen-1-yl 2,6-dideoxy-3-C-[(1S)-1-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}ethyl]-beta-D-ribo-hexopyranoside' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.04 _cell.angle_gamma 90 _cell.entry_id 4URM _cell.length_a 69.28 _cell.length_b 75.55 _cell.length_c 90.45 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4URM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C44 H60 Cl2 N4 O14' _chem_comp.formula_weight 939.872 _chem_comp.id XAM _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,4aS,5S,6S,8aR)-5-{[(5S)-1-(3-O-acetyl-4-O-carbamoyl-6-deoxy-2-O-methyl-alpha-L-talopyranosyl)-4-hydroxy-2-oxo-5-(propan-2-yl)-2,5-dihydro-1H-pyrrol-3-yl]carbonyl}-6-methyl-4-methylidene-1,2,3,4,4a,5,6,8a-octahydronaphthalen-1-yl 2,6-dideoxy-3-C-[(1S)-1-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}ethyl]-beta-D-ribo-hexopyranoside' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Amycolamicin # 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 OCB CBZ XAM doub 363 n n CBZ O4 XAM sing 364 n n CBZ NCA XAM sing 365 n n O4 C4 XAM sing 366 n n C6 C5 XAM sing 367 n n OBY CBW XAM doub 368 n n C4 C5 XAM sing 369 n n C4 C3 XAM sing 370 n n C5 O5 XAM sing 371 n n CBX CBW XAM sing 372 n n CBW O3 XAM sing 373 n n C3 O3 XAM sing 374 n n C3 C2 XAM sing 375 n n CLX CAT XAM sing 376 n n O5 C1 XAM sing 377 n n CAY CAU XAM sing 378 n n C2 C1 XAM sing 379 n n C2 O2 XAM sing 380 n n C1 NBE XAM sing 381 n n CAT CAU XAM doub 382 n y CAT CAS XAM sing 383 n y CAU NAV XAM sing 384 n y CLW CAS XAM sing 385 n n O2 CCL XAM sing 386 n n CAS CAR XAM doub 387 n y OBH CBD XAM doub 388 n n NBE CBD XAM sing 389 n n NBE CBF XAM sing 390 n n CBL CBJ XAM sing 391 n n NAV CAR XAM sing 392 n y CBJ CBF XAM sing 393 n n CBJ CBK XAM sing 394 n n CBD CBA XAM sing 395 n n CAR CAP XAM sing 396 n n CBF CBG XAM sing 397 n n CAP NAO XAM sing 398 n n CAP OAQ XAM doub 399 n n NAO CAM XAM sing 400 n n CBA CBG XAM doub 401 n n CBA CAZ XAM sing 402 n n CAK CAF XAM doub 403 n n CAN CAM XAM sing 404 n n CBG OBI XAM sing 405 n n CAJ CAI XAM sing 406 n n CAJ CAZ XAM sing 407 n n CAJ CAE XAM sing 408 n n CAD CAG XAM sing 409 n n CAD CAE XAM sing 410 n n CAD CAC XAM sing 411 n n CAG CAH XAM doub 412 n n CCF CCE XAM sing 413 n n CCF CCG XAM sing 414 n n CAH CAI XAM sing 415 n n CAI CBC XAM sing 416 n n CAZ OBB XAM doub 417 n n CAM CCE XAM sing 418 n n OAL CAC XAM sing 419 n n OAL CCG XAM sing 420 n n CAF CAE XAM sing 421 n n CAF CAA XAM sing 422 n n CAC CAB XAM sing 423 n n CAB CAA XAM sing 424 n n CCE OCK XAM sing 425 n n CCE CCD XAM sing 426 n n CCG OCH XAM sing 427 n n OCH CCC XAM sing 428 n n CCD CCC XAM sing 429 n n CCD OCJ XAM sing 430 n n CCC CCI XAM sing 431 n n C4 H1 XAM sing 432 n n C5 H2 XAM sing 433 n n C6 H3 XAM sing 434 n n C6 H4 XAM sing 435 n n C6 H5 XAM sing 436 n n C3 H6 XAM sing 437 n n CAY H7 XAM sing 438 n n CAY H8 XAM sing 439 n n CAY H9 XAM sing 440 n n NAV H10 XAM sing 441 n n NAO H11 XAM sing 442 n n CAM H12 XAM sing 443 n n CAN H13 XAM sing 444 n n CAN H14 XAM sing 445 n n CAN H15 XAM sing 446 n n CCF H16 XAM sing 447 n n CCF H17 XAM sing 448 n n OCK H18 XAM sing 449 n n CCD H19 XAM sing 450 n n OCJ H20 XAM sing 451 n n CCC H21 XAM sing 452 n n CCI H22 XAM sing 453 n n CCI H23 XAM sing 454 n n CCI H24 XAM sing 455 n n CCG H25 XAM sing 456 n n CAC H26 XAM sing 457 n n CAB H27 XAM sing 458 n n CAB H28 XAM sing 459 n n CAA H29 XAM sing 460 n n CAA H30 XAM sing 461 n n CAK H32 XAM sing 462 n n CAE H35 XAM sing 463 n n CAD H36 XAM sing 464 n n CAG H37 XAM sing 465 n n CAH H38 XAM sing 466 n n CAI H39 XAM sing 467 n n CBC H40 XAM sing 468 n n CBC H41 XAM sing 469 n n CBC H42 XAM sing 470 n n CAJ H43 XAM sing 471 n n OBI H44 XAM sing 472 n n CBF H45 XAM sing 473 n n CBJ H46 XAM sing 474 n n CBL H47 XAM sing 475 n n CBL H48 XAM sing 476 n n CBL H49 XAM sing 477 n n CBK H50 XAM sing 478 n n CBK H51 XAM sing 479 n n CBK H52 XAM sing 480 n n C1 H53 XAM sing 481 n n C2 H54 XAM sing 482 n n CCL H55 XAM sing 483 n n CCL H56 XAM sing 484 n n CCL H57 XAM sing 485 n n NCA H58 XAM sing 486 n n NCA H59 XAM sing 487 n n CBX H60 XAM sing 488 n n CBX H61 XAM sing 489 n n CBX H62 XAM sing 490 n n CAK H31 XAM sing 491 n n # _atom_sites.entry_id 4URM _atom_sites.fract_transf_matrix[1][1] 0.014434 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00001 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013236 _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] 0.011056 _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 E 2 XAM A 1 2000 2000 XAM XAM . F 2 XAM B 1 2000 2000 XAM XAM . G 2 XAM C 1 2000 2000 XAM XAM . H 2 XAM D 1 2000 2000 XAM XAM . I 3 HOH A 1 2001 2001 HOH HOH . I 3 HOH A 2 2002 2002 HOH HOH . I 3 HOH A 3 2003 2003 HOH HOH . I 3 HOH A 4 2004 2004 HOH HOH . I 3 HOH A 5 2005 2005 HOH HOH . J 3 HOH B 1 2001 2001 HOH HOH . J 3 HOH B 2 2002 2002 HOH HOH . J 3 HOH B 3 2003 2003 HOH HOH . J 3 HOH B 4 2004 2004 HOH HOH . J 3 HOH B 5 2005 2005 HOH HOH . K 3 HOH C 1 2001 2001 HOH HOH . K 3 HOH C 2 2002 2002 HOH HOH . K 3 HOH C 3 2003 2003 HOH HOH . L 3 HOH D 1 2001 2001 HOH HOH . L 3 HOH D 2 2002 2002 HOH HOH . L 3 HOH D 3 2003 2003 HOH HOH . L 3 HOH D 4 2004 2004 HOH HOH . L 3 HOH D 5 2005 2005 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 C4 XAM . . . E 2 38.037 -3.151 21.403 1 55.91 ? C4 XAM 2000 A 1 HETATM 2 C C5 XAM . . . E 2 37.637 -1.696 21.158 1 53.52 ? C5 XAM 2000 A 1 HETATM 3 C C6 XAM . . . E 2 37.157 -1.41 19.751 1 55.07 ? C6 XAM 2000 A 1 HETATM 4 C C3 XAM . . . E 2 39.447 -3.441 20.899 1 57.81 ? C3 XAM 2000 A 1 HETATM 5 CL CLW XAM . . . E 2 38.094 1.228 34.138 1 41.62 ? CLW XAM 2000 A 1 HETATM 6 C CAS XAM . . . E 2 37.904 1.572 35.815 1 33.07 ? CAS XAM 2000 A 1 HETATM 7 C CAT XAM . . . E 2 36.65 1.884 36.401 1 31.47 ? CAT XAM 2000 A 1 HETATM 8 CL CLX XAM . . . E 2 35.207 2.029 35.474 1 32.65 ? CLX XAM 2000 A 1 HETATM 9 C CAU XAM . . . E 2 36.898 2.043 37.773 1 25.43 ? CAU XAM 2000 A 1 HETATM 10 C CAY XAM . . . E 2 35.967 2.279 38.918 1 19.15 ? CAY XAM 2000 A 1 HETATM 11 N NAV XAM . . . E 2 38.232 1.873 37.986 1 25.04 ? NAV XAM 2000 A 1 HETATM 12 C CAR XAM . . . E 2 38.866 1.572 36.81 1 27.53 ? CAR XAM 2000 A 1 HETATM 13 C CAP XAM . . . E 2 40.325 1.348 36.821 1 31.48 ? CAP XAM 2000 A 1 HETATM 14 O OAQ XAM . . . E 2 40.961 1.522 37.855 1 34.21 ? OAQ XAM 2000 A 1 HETATM 15 N NAO XAM . . . E 2 40.893 0.998 35.659 1 34.9 ? NAO XAM 2000 A 1 HETATM 16 C CAM XAM . . . E 2 42.254 0.362 35.499 1 34.98 ? CAM XAM 2000 A 1 HETATM 17 C CAN XAM . . . E 2 42.07 -1.157 35.314 1 35.04 ? CAN XAM 2000 A 1 HETATM 18 C CCE XAM . . . E 2 43.057 1.103 34.325 1 34.68 ? CCE XAM 2000 A 1 HETATM 19 C CCF XAM . . . E 2 42.358 0.941 32.941 1 33.88 ? CCF XAM 2000 A 1 HETATM 20 O OCK XAM . . . E 2 43.016 2.491 34.697 1 35.54 ? OCK XAM 2000 A 1 HETATM 21 C CCD XAM . . . E 2 44.587 0.65 34.177 1 32.06 ? CCD XAM 2000 A 1 HETATM 22 O OCJ XAM . . . E 2 45.207 1.13 35.358 1 31.09 ? OCJ XAM 2000 A 1 HETATM 23 C CCC XAM . . . E 2 45.22 1.318 32.962 1 31.5 ? CCC XAM 2000 A 1 HETATM 24 C CCI XAM . . . E 2 46.663 0.919 32.758 1 30.42 ? CCI XAM 2000 A 1 HETATM 25 O OCH XAM . . . E 2 44.502 0.946 31.767 1 32.45 ? OCH XAM 2000 A 1 HETATM 26 C CCG XAM . . . E 2 43.144 1.375 31.72 1 34.63 ? CCG XAM 2000 A 1 HETATM 27 O OAL XAM . . . E 2 42.476 0.939 30.539 1 38.49 ? OAL XAM 2000 A 1 HETATM 28 C CAC XAM . . . E 2 42.937 1.552 29.304 1 43.13 ? CAC XAM 2000 A 1 HETATM 29 C CAB XAM . . . E 2 42.421 2.987 29.29 1 47.48 ? CAB XAM 2000 A 1 HETATM 30 C CAA XAM . . . E 2 42.63 3.658 27.926 1 49.35 ? CAA XAM 2000 A 1 HETATM 31 C CAF XAM . . . E 2 42.143 2.753 26.827 1 50.2 ? CAF XAM 2000 A 1 HETATM 32 C CAK XAM . . . E 2 41.092 3.04 26.079 1 51.76 ? CAK XAM 2000 A 1 HETATM 33 C CAE XAM . . . E 2 42.946 1.463 26.774 1 46.15 ? CAE XAM 2000 A 1 HETATM 34 C CAD XAM . . . E 2 42.565 0.646 28.044 1 42.2 ? CAD XAM 2000 A 1 HETATM 35 C CAG XAM . . . E 2 43.339 -0.643 28.056 1 41.57 ? CAG XAM 2000 A 1 HETATM 36 C CAH XAM . . . E 2 43.83 -1.256 26.981 1 42.72 ? CAH XAM 2000 A 1 HETATM 37 C CAI XAM . . . E 2 43.716 -0.764 25.563 1 42.3 ? CAI XAM 2000 A 1 HETATM 38 C CBC XAM . . . E 2 45.089 -0.686 24.893 1 39.23 ? CBC XAM 2000 A 1 HETATM 39 C CAJ XAM . . . E 2 42.886 0.539 25.524 1 44.69 ? CAJ XAM 2000 A 1 HETATM 40 C CAZ XAM . . . E 2 43.16 1.3 24.179 1 45.62 ? CAZ XAM 2000 A 1 HETATM 41 O OBB XAM . . . E 2 44.153 2.222 24.092 1 45.98 ? OBB XAM 2000 A 1 HETATM 42 C CBA XAM . . . E 2 42.436 1.058 23.036 1 46.62 ? CBA XAM 2000 A 1 HETATM 43 C CBD XAM . . . E 2 41.411 0.044 22.945 1 48.4 ? CBD XAM 2000 A 1 HETATM 44 O OBH XAM . . . E 2 41.004 -0.732 23.8 1 48.1 ? OBH XAM 2000 A 1 HETATM 45 C CBG XAM . . . E 2 42.539 1.706 21.729 1 46.08 ? CBG XAM 2000 A 1 HETATM 46 O OBI XAM . . . E 2 43.413 2.448 21.31 1 44.65 ? OBI XAM 2000 A 1 HETATM 47 C CBF XAM . . . E 2 41.37 1.181 20.83 1 48.13 ? CBF XAM 2000 A 1 HETATM 48 C CBJ XAM . . . E 2 40.23 2.225 20.673 1 50.56 ? CBJ XAM 2000 A 1 HETATM 49 C CBL XAM . . . E 2 40.753 3.649 20.496 1 51.85 ? CBL XAM 2000 A 1 HETATM 50 C CBK XAM . . . E 2 39.264 1.862 19.539 1 49.29 ? CBK XAM 2000 A 1 HETATM 51 N NBE XAM . . . E 2 40.892 0.057 21.639 1 49.36 ? NBE XAM 2000 A 1 HETATM 52 C C1 XAM . . . E 2 40.069 -1.075 21.098 1 50.29 ? C1 XAM 2000 A 1 HETATM 53 C C2 XAM . . . E 2 40.435 -2.485 21.546 1 52.87 ? C2 XAM 2000 A 1 HETATM 54 O O2 XAM . . . E 2 41.796 -2.901 21.369 1 48.65 ? O2 XAM 2000 A 1 HETATM 55 C CCL XAM . . . E 2 42.526 -2.326 20.277 1 45.79 ? CCL XAM 2000 A 1 HETATM 56 O O5 XAM . . . E 2 38.723 -0.791 21.459 1 48.9 ? O5 XAM 2000 A 1 HETATM 57 O O4 XAM . . . E 2 37.099 -4.031 20.748 1 58.26 ? O4 XAM 2000 A 1 HETATM 58 C CBZ XAM . . . E 2 36.747 -5.298 21.262 1 62.32 ? CBZ XAM 2000 A 1 HETATM 59 O OCB XAM . . . E 2 35.631 -5.735 21.091 1 64.68 ? OCB XAM 2000 A 1 HETATM 60 N NCA XAM . . . E 2 37.732 -5.933 21.892 1 62.67 ? NCA XAM 2000 A 1 HETATM 61 O O3 XAM . . . E 2 39.502 -3.256 19.465 1 64.16 ? O3 XAM 2000 A 1 HETATM 62 C CBW XAM . . . E 2 39.83 -4.314 18.689 1 70.22 ? CBW XAM 2000 A 1 HETATM 63 O OBY XAM . . . E 2 39.793 -5.456 19.067 1 73.65 ? OBY XAM 2000 A 1 HETATM 64 C CBX XAM . . . E 2 40.24 -3.861 17.33 1 70.95 ? CBX XAM 2000 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 64 #