data_5KDR
#
_model_server_result.job_id            EUsXTDRUxzKvUcl30xVSmg 
_model_server_result.datetime_utc      '2025-03-06 10:17:22' 
_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          5kdr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":301}' 
#
_entry.id    5KDR 
#
_exptl.entry_id    5KDR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              453.531 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'Moiramide B' 
_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          91.94 
_cell.angle_gamma         90 
_cell.entry_id            5KDR 
_cell.length_a            153.807 
_cell.length_b            49.445 
_cell.length_c            100.048 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KDR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 B SG CYS 33 B CYS 33 1_555 H ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc2 B SG CYS 36 B CYS 36 1_555 H ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc3 B SG CYS 52 B CYS 52 1_555 H ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc4 B SG CYS 55 B CYS 55 1_555 H ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
#
_chem_comp.formula           'C25 H31 N3 O5' 
_chem_comp.formula_weight    453.531 
_chem_comp.id                YT5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'Moiramide B' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '(2~{E},4~{E})-~{N}-[(1~{S})-3-[[(2~{S})-3-methyl-1-[(3~{R},4~{S})-4-methyl-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-1-oxi danylidene-butan-2-yl]amino]-3-oxidanylidene-1-phenyl-propyl]hexa-2,4-dienamide' 
#
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
CBE CBF YT5 doub 389 n y 
CBE CBD YT5 sing 390 n y 
CBF CBG YT5 sing 391 n y 
CBD CBC YT5 doub 392 n y 
CBG CBB YT5 doub 393 n y 
CBC CBB YT5 sing 394 n y 
CBB CAT YT5 sing 395 n n 
CAR CAT YT5 sing 396 n n 
CAR CAQ YT5 sing 397 n n 
OAF CAA YT5 doub 398 n n 
CAI CAD YT5 sing 399 n n 
CAT NAU YT5 sing 400 n n 
CAQ OAS YT5 doub 401 n n 
CAQ N YT5 sing 402 n n 
CAE CAA YT5 sing 403 n n 
CAE CAD YT5 sing 404 n n 
CAE C YT5 sing 405 n n 
CAA NAB YT5 sing 406 n n 
NAB CAC YT5 sing 407 n n 
N CA YT5 sing 408 n n 
CAC CAD YT5 sing 409 n n 
CAC OAG YT5 doub 410 n n 
O C YT5 doub 411 n n 
C CA YT5 sing 412 n n 
NAU CAV YT5 sing 413 n n 
CA CB YT5 sing 414 n n 
CAV OBH YT5 doub 415 n n 
CAV CAW YT5 sing 416 n n 
CB CG2 YT5 sing 417 n n 
CB CG1 YT5 sing 418 n n 
CAW CAX YT5 doub 419 e n 
CAX CAY YT5 sing 420 n n 
CAY CAZ YT5 doub 421 e n 
CAZ CBA YT5 sing 422 n n 
CAI H1 YT5 sing 423 n n 
CAI H2 YT5 sing 424 n n 
CAI H3 YT5 sing 425 n n 
CAD H4 YT5 sing 426 n n 
NAB H5 YT5 sing 427 n n 
CAE H6 YT5 sing 428 n n 
CA H7 YT5 sing 429 n n 
CB H8 YT5 sing 430 n n 
CG2 H9 YT5 sing 431 n n 
CG2 H10 YT5 sing 432 n n 
CG2 H11 YT5 sing 433 n n 
CG1 H12 YT5 sing 434 n n 
CG1 H13 YT5 sing 435 n n 
CG1 H14 YT5 sing 436 n n 
N H15 YT5 sing 437 n n 
CAR H16 YT5 sing 438 n n 
CAR H17 YT5 sing 439 n n 
CAT H18 YT5 sing 440 n n 
CBC H19 YT5 sing 441 n n 
CBD H20 YT5 sing 442 n n 
CBE H21 YT5 sing 443 n n 
CBF H22 YT5 sing 444 n n 
CBG H23 YT5 sing 445 n n 
NAU H24 YT5 sing 446 n n 
CAW H25 YT5 sing 447 n n 
CAX H27 YT5 sing 448 n n 
CAY H29 YT5 sing 449 n n 
CAZ H31 YT5 sing 450 n n 
CBA H33 YT5 sing 451 n n 
CBA H34 YT5 sing 452 n n 
CBA H35 YT5 sing 453 n n 
#
_atom_sites.entry_id                     5KDR 
_atom_sites.fract_transf_matrix[1][1]    0.006502 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00022 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020224 
_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]    0.010001 
_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 3 SO4 A 1 401 1 SO4 SO4 . 
D 3 SO4 A 1 402 3 SO4 SO4 . 
E 4 YT5 B 1 301 1 YT5 YT5 . 
F 3 SO4 B 1 302 2 SO4 SO4 . 
G 5 EDO B 1 303 2 EDO EDO . 
H 6 ZN B 1 304 1 ZN ZN . 
I 7 HOH A 1 501 21 HOH HOH . 
I 7 HOH A 2 502 16 HOH HOH . 
I 7 HOH A 3 503 2 HOH HOH . 
I 7 HOH A 4 504 10 HOH HOH . 
I 7 HOH A 5 505 9 HOH HOH . 
I 7 HOH A 6 506 12 HOH HOH . 
I 7 HOH A 7 507 5 HOH HOH . 
I 7 HOH A 8 508 6 HOH HOH . 
I 7 HOH A 9 509 15 HOH HOH . 
I 7 HOH A 10 510 14 HOH HOH . 
I 7 HOH A 11 511 13 HOH HOH . 
I 7 HOH A 12 512 4 HOH HOH . 
J 7 HOH B 1 401 1 HOH HOH . 
J 7 HOH B 2 402 20 HOH HOH . 
J 7 HOH B 3 403 3 HOH HOH . 
J 7 HOH B 4 404 17 HOH HOH . 
J 7 HOH B 5 405 11 HOH HOH . 
J 7 HOH B 6 406 7 HOH HOH . 
J 7 HOH B 7 407 19 HOH HOH . 
J 7 HOH B 8 408 8 HOH HOH . 
J 7 HOH B 9 409 18 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 CAI YT5 . . . E 4 8.919 -8.913 19.879 1 58.57 ? CAI YT5 301 B 1 
HETATM 2 C CAD YT5 . . . E 4 8.897 -7.602 20.653 1 58.35 ? CAD YT5 301 B 1 
HETATM 3 C CAC YT5 . . . E 4 7.652 -7.005 20.559 1 62.39 ? CAC YT5 301 B 1 
HETATM 4 O OAG YT5 . . . E 4 6.606 -7.587 20.861 1 70.16 ? OAG YT5 301 B 1 
HETATM 5 N NAB YT5 . . . E 4 7.74 -5.708 20.258 1 59.55 ? NAB YT5 301 B 1 
HETATM 6 C CAA YT5 . . . E 4 9.019 -5.386 20.084 1 59.67 ? CAA YT5 301 B 1 
HETATM 7 O OAF YT5 . . . E 4 9.363 -4.251 19.745 1 60.05 ? OAF YT5 301 B 1 
HETATM 8 C CAE YT5 . . . E 4 9.845 -6.539 20.076 1 58.37 ? CAE YT5 301 B 1 
HETATM 9 C C YT5 . . . E 4 11.132 -6.403 20.673 1 55.06 ? C YT5 301 B 1 
HETATM 10 O O YT5 . . . E 4 11.77 -5.359 20.577 1 52.48 ? O YT5 301 B 1 
HETATM 11 C CA YT5 . . . E 4 11.788 -7.643 21.312 1 54.36 ? CA YT5 301 B 1 
HETATM 12 C CB YT5 . . . E 4 12.471 -7.262 22.627 1 52.2 ? CB YT5 301 B 1 
HETATM 13 C CG2 YT5 . . . E 4 12.742 -8.547 23.418 1 51.57 ? CG2 YT5 301 B 1 
HETATM 14 C CG1 YT5 . . . E 4 11.6 -6.327 23.473 1 51.41 ? CG1 YT5 301 B 1 
HETATM 15 N N YT5 . . . E 4 12.832 -8.222 20.443 1 54.67 ? N YT5 301 B 1 
HETATM 16 C CAQ YT5 . . . E 4 12.771 -9.482 19.971 1 57.7 ? CAQ YT5 301 B 1 
HETATM 17 O OAS YT5 . . . E 4 11.836 -10.251 20.178 1 58.38 ? OAS YT5 301 B 1 
HETATM 18 C CAR YT5 . . . E 4 13.972 -9.953 19.13 1 61.27 ? CAR YT5 301 B 1 
HETATM 19 C CAT YT5 . . . E 4 14.808 -10.968 19.941 1 63.97 ? CAT YT5 301 B 1 
HETATM 20 C CBB YT5 . . . E 4 15.738 -11.644 19.13 1 66 ? CBB YT5 301 B 1 
HETATM 21 C CBC YT5 . . . E 4 15.644 -13.024 18.926 1 65.53 ? CBC YT5 301 B 1 
HETATM 22 C CBD YT5 . . . E 4 16.578 -13.677 18.125 1 66.04 ? CBD YT5 301 B 1 
HETATM 23 C CBE YT5 . . . E 4 17.618 -12.963 17.532 1 66.83 ? CBE YT5 301 B 1 
HETATM 24 C CBF YT5 . . . E 4 17.726 -11.589 17.739 1 66.51 ? CBF YT5 301 B 1 
HETATM 25 C CBG YT5 . . . E 4 16.791 -10.937 18.539 1 66.88 ? CBG YT5 301 B 1 
HETATM 26 N NAU YT5 . . . E 4 15.577 -10.312 21.014 1 64.1 ? NAU YT5 301 B 1 
HETATM 27 C CAV YT5 . . . E 4 15.882 -11 22.127 1 66.75 ? CAV YT5 301 B 1 
HETATM 28 O OBH YT5 . . . E 4 15.54 -12.17 22.322 1 68.17 ? OBH YT5 301 B 1 
HETATM 29 C CAW YT5 . . . E 4 16.738 -10.257 23.118 1 67.35 ? CAW YT5 301 B 1 
HETATM 30 C CAX YT5 . . . E 4 16.507 -10.927 24.465 1 67.03 ? CAX YT5 301 B 1 
HETATM 31 C CAY YT5 . . . E 4 17.793 -10.639 25.22 1 67.85 ? CAY YT5 301 B 1 
HETATM 32 C CAZ YT5 . . . E 4 17.554 -11.228 26.595 1 69.2 ? CAZ YT5 301 B 1 
HETATM 33 C CBA YT5 . . . E 4 18.822 -10.924 27.402 1 70.5 ? CBA YT5 301 B 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           33 
#