data_4URM
#
_model_server_result.job_id            Iat1VVdMEZVcgU21g2wT5w 
_model_server_result.datetime_utc      '2025-07-01 17:12:35' 
_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":"H","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 . . . H 2 14.771 -41.558 95.394 1 86.5 ? C4 XAM 2000 D 1 
HETATM 2 C C5 XAM . . . H 2 13.43 -41.319 96.091 1 86.04 ? C5 XAM 2000 D 1 
HETATM 3 C C6 XAM . . . H 2 13.542 -41.043 97.575 1 85.72 ? C6 XAM 2000 D 1 
HETATM 4 C C3 XAM . . . H 2 15.295 -42.979 95.605 1 87.65 ? C3 XAM 2000 D 1 
HETATM 5 CL CLW XAM . . . H 2 8.145 -44.331 83.554 1 72.08 ? CLW XAM 2000 D 1 
HETATM 6 C CAS XAM . . . H 2 7.583 -44.26 81.935 1 63.67 ? CAS XAM 2000 D 1 
HETATM 7 C CAT XAM . . . H 2 7.085 -43.061 81.301 1 58.07 ? CAT XAM 2000 D 1 
HETATM 8 CL CLX XAM . . . H 2 7.021 -41.513 82.055 1 57.03 ? CLX XAM 2000 D 1 
HETATM 9 C CAU XAM . . . H 2 6.718 -43.439 80.034 1 57.33 ? CAU XAM 2000 D 1 
HETATM 10 C CAY XAM . . . H 2 6.22 -42.616 78.888 1 56.42 ? CAY XAM 2000 D 1 
HETATM 11 N NAV XAM . . . H 2 6.946 -44.775 79.89 1 59.49 ? NAV XAM 2000 D 1 
HETATM 12 C CAR XAM . . . H 2 7.492 -45.288 81.038 1 62.01 ? CAR XAM 2000 D 1 
HETATM 13 C CAP XAM . . . H 2 7.798 -46.726 81.184 1 64.57 ? CAP XAM 2000 D 1 
HETATM 14 O OAQ XAM . . . H 2 7.416 -47.527 80.331 1 65.87 ? OAQ XAM 2000 D 1 
HETATM 15 N NAO XAM . . . H 2 8.41 -47.086 82.324 1 67 ? NAO XAM 2000 D 1 
HETATM 16 C CAM XAM . . . H 2 9.002 -48.442 82.631 1 71.8 ? CAM XAM 2000 D 1 
HETATM 17 C CAN XAM . . . H 2 10.555 -48.375 82.614 1 71.99 ? CAN XAM 2000 D 1 
HETATM 18 C CCE XAM . . . H 2 8.385 -49.042 83.984 1 75.81 ? CCE XAM 2000 D 1 
HETATM 19 C CCF XAM . . . H 2 8.701 -48.073 85.148 1 76.79 ? CCF XAM 2000 D 1 
HETATM 20 O OCK XAM . . . H 2 6.968 -49.002 83.794 1 76.49 ? OCK XAM 2000 D 1 
HETATM 21 C CCD XAM . . . H 2 8.824 -50.583 84.302 1 77.74 ? CCD XAM 2000 D 1 
HETATM 22 O OCJ XAM . . . H 2 7.807 -51.367 83.687 1 79.27 ? OCJ XAM 2000 D 1 
HETATM 23 C CCC XAM . . . H 2 8.937 -50.976 85.771 1 78.66 ? CCC XAM 2000 D 1 
HETATM 24 C CCI XAM . . . H 2 9.809 -52.191 85.985 1 78.6 ? CCI XAM 2000 D 1 
HETATM 25 O OCH XAM . . . H 2 9.517 -49.898 86.532 1 78.95 ? OCH XAM 2000 D 1 
HETATM 26 C CCG XAM . . . H 2 8.716 -48.724 86.51 1 78.12 ? CCG XAM 2000 D 1 
HETATM 27 O OAL XAM . . . H 2 9.099 -47.773 87.479 1 77.77 ? OAL XAM 2000 D 1 
HETATM 28 C CAC XAM . . . H 2 8.615 -48.036 88.817 1 75.57 ? CAC XAM 2000 D 1 
HETATM 29 C CAB XAM . . . H 2 7.289 -47.31 88.965 1 74.23 ? CAB XAM 2000 D 1 
HETATM 30 C CAA XAM . . . H 2 6.817 -47.317 90.418 1 74.91 ? CAA XAM 2000 D 1 
HETATM 31 C CAF XAM . . . H 2 7.874 -46.753 91.329 1 76.83 ? CAF XAM 2000 D 1 
HETATM 32 C CAK XAM . . . H 2 7.649 -45.699 92.093 1 77.32 ? CAK XAM 2000 D 1 
HETATM 33 C CAE XAM . . . H 2 9.206 -47.516 91.252 1 77.32 ? CAE XAM 2000 D 1 
HETATM 34 C CAD XAM . . . H 2 9.712 -47.528 89.782 1 75.79 ? CAD XAM 2000 D 1 
HETATM 35 C CAG XAM . . . H 2 10.987 -48.323 89.665 1 76.1 ? CAG XAM 2000 D 1 
HETATM 36 C CAH XAM . . . H 2 11.887 -48.402 90.637 1 77.71 ? CAH XAM 2000 D 1 
HETATM 37 C CAI XAM . . . H 2 11.777 -47.75 91.989 1 79.55 ? CAI XAM 2000 D 1 
HETATM 38 C CBC XAM . . . H 2 12.237 -48.703 93.094 1 80.12 ? CBC XAM 2000 D 1 
HETATM 39 C CAJ XAM . . . H 2 10.381 -47.084 92.176 1 80.42 ? CAJ XAM 2000 D 1 
HETATM 40 C CAZ XAM . . . H 2 9.928 -47.084 93.67 1 84.27 ? CAZ XAM 2000 D 1 
HETATM 41 O OBB XAM . . . H 2 9.007 -47.983 94.058 1 85.36 ? OBB XAM 2000 D 1 
HETATM 42 C CBA XAM . . . H 2 10.411 -46.236 94.659 1 86.08 ? CBA XAM 2000 D 1 
HETATM 43 C CBD XAM . . . H 2 11.508 -45.255 94.533 1 88.44 ? CBD XAM 2000 D 1 
HETATM 44 O OBH XAM . . . H 2 12.159 -44.935 93.542 1 90.17 ? OBH XAM 2000 D 1 
HETATM 45 C CBG XAM . . . H 2 9.953 -46.234 96.04 1 84.41 ? CBG XAM 2000 D 1 
HETATM 46 O OBI XAM . . . H 2 9.116 -46.947 96.566 1 82.69 ? OBI XAM 2000 D 1 
HETATM 47 C CBF XAM . . . H 2 10.758 -45.154 96.803 1 85.15 ? CBF XAM 2000 D 1 
HETATM 48 C CBJ XAM . . . H 2 9.758 -44.156 97.431 1 82.28 ? CBJ XAM 2000 D 1 
HETATM 49 C CBL XAM . . . H 2 10.342 -43.473 98.664 1 81.77 ? CBL XAM 2000 D 1 
HETATM 50 C CBK XAM . . . H 2 9.255 -43.134 96.419 1 80.6 ? CBK XAM 2000 D 1 
HETATM 51 N NBE XAM . . . H 2 11.738 -44.668 95.824 1 87.45 ? NBE XAM 2000 D 1 
HETATM 52 C C1 XAM . . . H 2 12.947 -43.765 96.173 1 87.19 ? C1 XAM 2000 D 1 
HETATM 53 C C2 XAM . . . H 2 14.236 -44.063 95.416 1 88.49 ? C2 XAM 2000 D 1 
HETATM 54 O O2 XAM . . . H 2 14.748 -45.375 95.677 1 91.34 ? O2 XAM 2000 D 1 
HETATM 55 C CCL XAM . . . H 2 14.501 -45.946 96.972 1 92.5 ? CCL XAM 2000 D 1 
HETATM 56 O O5 XAM . . . H 2 12.528 -42.43 95.905 1 86.52 ? O5 XAM 2000 D 1 
HETATM 57 O O4 XAM . . . H 2 15.748 -40.623 95.905 1 86.32 ? O4 XAM 2000 D 1 
HETATM 58 C CBZ XAM . . . H 2 16.514 -39.788 95.087 1 86.29 ? CBZ XAM 2000 D 1 
HETATM 59 O OCB XAM . . . H 2 16.494 -38.586 95.236 1 85.25 ? OCB XAM 2000 D 1 
HETATM 60 N NCA XAM . . . H 2 17.251 -40.445 94.193 1 87.03 ? NCA XAM 2000 D 1 
HETATM 61 O O3 XAM . . . H 2 15.972 -43.108 96.878 1 87.66 ? O3 XAM 2000 D 1 
HETATM 62 C CBW XAM . . . H 2 17.249 -43.591 96.893 1 85.97 ? CBW XAM 2000 D 1 
HETATM 63 O OBY XAM . . . H 2 17.79 -44.082 95.938 1 85.66 ? OBY XAM 2000 D 1 
HETATM 64 C CBX XAM . . . H 2 17.865 -43.424 98.239 1 84.15 ? CBX XAM 2000 D 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           64 
#