data_8XNP
#
_model_server_result.job_id            NLD0O34Gzop2m3Cu2-QHxQ 
_model_server_result.datetime_utc      '2024-12-22 10:56:23' 
_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          8xnp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"NA","auth_seq_id":201}' 
#
_entry.id    8XNP 
#
_exptl.entry_id    8XNP 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              584.703 
_entity.id                          32 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    23-meric 
_pdbx_struct_assembly.oligomeric_count      23 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA 
_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    ? 
_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                      32 
_struct_asym.id                             NA 
_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
disulf ? disulf1 Q SG CYS 36 X CYS 36 1_555 Q SG CYS 66 X CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
disulf ? disulf2 Q SG CYS 46 X CYS 46 1_555 Q SG CYS 56 X CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf3 Q SG CYS 78 X CYS 78 1_555 Q SG CYS 110 X CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
disulf ? disulf4 Q SG CYS 88 X CYS 88 1_555 Q SG CYS 100 X CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc1 B SG CYS 99 B CYS 99 1_555 X FE1 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc2 B O CYS 194 B CYS 194 1_555 X FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? 
metalc ? metalc3 B SG CYS 194 B CYS 194 1_555 X FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc4 E SG CYS 134 E CYS 134 1_555 AA FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc5 F SG CYS 385 F CYS 385 1_555 CA FE2 SF4 . F SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
metalc ? metalc6 G O PHE 63 G PHE 63 1_555 FA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc7 G SG CYS 75 G CYS 75 1_555 FA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc8 G NE2 HIS 124 G HIS 124 1_555 DA FE1 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? 
metalc ? metalc9 G SG CYS 128 G CYS 128 1_555 DA FE3 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc10 G SG CYS 137 G CYS 137 1_555 DA FE4 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc11 G SG CYS 182 G CYS 182 1_555 EA FE2 SF4 . G SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc12 I SG CYS 116 I CYS 116 1_555 KA FE1 SF4 . I SF4 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc13 I SG CYS 119 I CYS 119 1_555 KA FE2 SF4 . I SF4 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc14 I SG CYS 158 I CYS 158 1_555 JA FE3 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
metalc ? metalc15 L SG CYS 79 R CYS 79 1_555 MA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc16 L NE2 HIS 88 R HIS 88 1_555 MA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
metalc ? metalc17 L SG CYS 104 R CYS 104 1_555 MA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc18 L SG CYS 107 R CYS 107 1_555 MA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
#
_chem_comp.formula           'C25 H49 N2 O9 P S' 
_chem_comp.formula_weight    584.703 
_chem_comp.id                EHZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate' 
_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
O7 P1 EHZ sing 470 n n 
O9 P1 EHZ doub 471 n n 
P1 O6 EHZ sing 472 n n 
O6 C20 EHZ sing 473 n n 
C20 C17 EHZ sing 474 n n 
O5 C16 EHZ sing 475 n n 
C19 C17 EHZ sing 476 n n 
C17 C16 EHZ sing 477 n n 
C17 C18 EHZ sing 478 n n 
C16 C15 EHZ sing 479 n n 
C15 O4 EHZ doub 480 n n 
C15 N2 EHZ sing 481 n n 
N2 C14 EHZ sing 482 n n 
C13 C14 EHZ sing 483 n n 
C13 C12 EHZ sing 484 n n 
N1 C12 EHZ sing 485 n n 
N1 C11 EHZ sing 486 n n 
C12 O3 EHZ doub 487 n n 
C11 C10 EHZ sing 488 n n 
O2 C9 EHZ doub 489 n n 
C10 S1 EHZ sing 490 n n 
C7 C6 EHZ sing 491 n n 
C7 C8 EHZ sing 492 n n 
C7 O1 EHZ sing 493 n n 
C9 S1 EHZ sing 494 n n 
C9 C8 EHZ sing 495 n n 
C6 C5 EHZ sing 496 n n 
C22 C21 EHZ sing 497 n n 
C1 C21 EHZ sing 498 n n 
C1 C2 EHZ sing 499 n n 
C3 C2 EHZ sing 500 n n 
C3 C4 EHZ sing 501 n n 
C5 C4 EHZ sing 502 n n 
O1 H1 EHZ sing 503 n n 
C1 H2 EHZ sing 504 n n 
C1 H3 EHZ sing 505 n n 
C2 H4 EHZ sing 506 n n 
C2 H5 EHZ sing 507 n n 
C3 H6 EHZ sing 508 n n 
C3 H7 EHZ sing 509 n n 
C4 H8 EHZ sing 510 n n 
C4 H9 EHZ sing 511 n n 
C5 H10 EHZ sing 512 n n 
C5 H11 EHZ sing 513 n n 
C6 H12 EHZ sing 514 n n 
C6 H13 EHZ sing 515 n n 
C7 H14 EHZ sing 516 n n 
C8 H15 EHZ sing 517 n n 
C8 H16 EHZ sing 518 n n 
C10 H17 EHZ sing 519 n n 
C10 H18 EHZ sing 520 n n 
C11 H19 EHZ sing 521 n n 
C11 H20 EHZ sing 522 n n 
C13 H21 EHZ sing 523 n n 
C13 H22 EHZ sing 524 n n 
C14 H23 EHZ sing 525 n n 
C14 H24 EHZ sing 526 n n 
C16 H25 EHZ sing 527 n n 
C18 H26 EHZ sing 528 n n 
C18 H27 EHZ sing 529 n n 
C18 H28 EHZ sing 530 n n 
C19 H29 EHZ sing 531 n n 
C19 H30 EHZ sing 532 n n 
C19 H31 EHZ sing 533 n n 
C20 H32 EHZ sing 534 n n 
C20 H33 EHZ sing 535 n n 
C21 H34 EHZ sing 536 n n 
C21 H35 EHZ sing 537 n n 
C22 H36 EHZ sing 538 n n 
C22 H37 EHZ sing 539 n n 
N1 H39 EHZ sing 540 n n 
N2 H40 EHZ sing 541 n n 
O5 H41 EHZ sing 542 n n 
O7 H42 EHZ sing 543 n n 
P1 OP3 EHZ sing 544 n n 
C22 C23 EHZ sing 545 n n 
C23 C24 EHZ sing 546 n n 
C24 C25 EHZ sing 547 n n 
OP3 H44 EHZ sing 548 n n 
C23 H45 EHZ sing 549 n n 
C23 H46 EHZ sing 550 n n 
C24 H47 EHZ sing 551 n n 
C24 H48 EHZ sing 552 n n 
C25 H49 EHZ sing 553 n n 
C25 H50 EHZ sing 554 n n 
C25 H51 EHZ sing 555 n n 
#
_atom_sites.entry_id                     8XNP 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
X 24 SF4 B 1 301 236 SF4 SF4 . 
Y 25 UQ9 B 1 302 399 UQ9 UQ9 . 
Z 26 PC1 B 1 303 406 PC1 PC1 . 
AA 27 FES E 1 301 332 FES FES . 
BA 28 FMN F 1 501 521 FMN FMN . 
CA 24 SF4 F 1 502 522 SF4 SF4 . 
DA 24 SF4 G 1 801 824 SF4 SF4 . 
EA 24 SF4 G 1 802 825 SF4 SF4 . 
FA 27 FES G 1 803 826 FES FES . 
GA 26 PC1 H 1 401 402 PC1 PC1 . 
HA 29 3PE I 1 301 403 3PE 3PE . 
IA 26 PC1 I 1 302 404 PC1 PC1 . 
JA 24 SF4 I 1 303 235 SF4 SF4 . 
KA 24 SF4 I 1 304 236 SF4 SF4 . 
LA 30 NDP P 1 401 536 NDP NDP . 
MA 31 ZN R 1 201 221 ZN ZN . 
NA 32 EHZ W 1 201 201 EHZ EHZ . 
OA 29 3PE Z 1 401 401 3PE 3PE . 
PA 33 CDL a 1 101 405 CDL CDL . 
#
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 O1 EHZ . . . NA 32 241.204 203.746 221.41 1 60.02 0 O1 EHZ 201 W 1 
HETATM 2 C C2 EHZ . . . NA 32 238.244 198.745 218.877 1 60.02 0 C2 EHZ 201 W 1 
HETATM 3 C C3 EHZ . . . NA 32 238.657 200.209 218.889 1 60.02 0 C3 EHZ 201 W 1 
HETATM 4 C C4 EHZ . . . NA 32 239.887 200.366 219.773 1 60.02 0 C4 EHZ 201 W 1 
HETATM 5 O O2 EHZ . . . NA 32 239.778 203.405 224.888 1 60.02 0 O2 EHZ 201 W 1 
HETATM 6 C C5 EHZ . . . NA 32 239.815 201.707 220.495 1 60.02 0 C5 EHZ 201 W 1 
HETATM 7 C C6 EHZ . . . NA 32 240.388 201.569 221.9 1 60.02 0 C6 EHZ 201 W 1 
HETATM 8 C C7 EHZ . . . NA 32 240.66 202.969 222.435 1 60.02 0 C7 EHZ 201 W 1 
HETATM 9 C C8 EHZ . . . NA 32 241.647 202.902 223.591 1 60.02 0 C8 EHZ 201 W 1 
HETATM 10 C C10 EHZ . . . NA 32 240.897 204.281 227.656 1 60.02 0 C10 EHZ 201 W 1 
HETATM 11 C C11 EHZ . . . NA 32 241.417 205.325 228.641 1 60.02 0 C11 EHZ 201 W 1 
HETATM 12 C C12 EHZ . . . NA 32 240.388 206.82 230.351 1 60.02 0 C12 EHZ 201 W 1 
HETATM 13 C C13 EHZ . . . NA 32 239.252 207.685 230.875 1 60.02 0 C13 EHZ 201 W 1 
HETATM 14 C C14 EHZ . . . NA 32 239.312 207.638 232.396 1 60.02 0 C14 EHZ 201 W 1 
HETATM 15 C C15 EHZ . . . NA 32 238.15 208.608 234.398 1 60.02 0 C15 EHZ 201 W 1 
HETATM 16 C C16 EHZ . . . NA 32 237.041 209.474 234.984 1 60.02 0 C16 EHZ 201 W 1 
HETATM 17 C C17 EHZ . . . NA 32 236.236 208.756 236.068 1 60.02 0 C17 EHZ 201 W 1 
HETATM 18 C C18 EHZ . . . NA 32 236.954 208.858 237.408 1 60.02 0 C18 EHZ 201 W 1 
HETATM 19 C C19 EHZ . . . NA 32 234.882 209.44 236.201 1 60.02 0 C19 EHZ 201 W 1 
HETATM 20 C C20 EHZ . . . NA 32 236.007 207.286 235.724 1 60.02 0 C20 EHZ 201 W 1 
HETATM 21 C C9 EHZ . . . NA 32 240.952 203.485 224.813 1 60.02 0 C9 EHZ 201 W 1 
HETATM 22 N N1 EHZ . . . NA 32 240.297 206.14 229.078 1 60.02 0 N1 EHZ 201 W 1 
HETATM 23 N N2 EHZ . . . NA 32 238.261 208.46 232.961 1 60.02 0 N2 EHZ 201 W 1 
HETATM 24 O O3 EHZ . . . NA 32 241.36 206.686 231.006 1 60.02 0 O3 EHZ 201 W 1 
HETATM 25 O O4 EHZ . . . NA 32 238.928 208.075 235.108 1 60.02 0 O4 EHZ 201 W 1 
HETATM 26 O O5 EHZ . . . NA 32 237.616 210.634 235.506 1 60.02 0 O5 EHZ 201 W 1 
HETATM 27 O O6 EHZ . . . NA 32 234.932 206.804 236.478 1 60.02 0 O6 EHZ 201 W 1 
HETATM 28 O O7 EHZ . . . NA 32 234.362 205.473 234.229 1 60.02 0 O7 EHZ 201 W 1 
HETATM 29 O O9 EHZ . . . NA 32 232.508 206.139 235.89 1 60.02 -1 O9 EHZ 201 W 1 
HETATM 30 P P1 EHZ . . . NA 32 233.901 205.722 235.785 1 60.02 0 P1 EHZ 201 W 1 
HETATM 31 S S1 EHZ . . . NA 32 241.891 204.296 226.137 1 60.02 0 S1 EHZ 201 W 1 
HETATM 32 O OP3 EHZ . . . NA 32 233.834 204.481 236.548 1 60.02 0 OP3 EHZ 201 W 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    108 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           32 
#