data_8G5D
#
_model_server_result.job_id            m_hSxsjNRoqlQayc9h8Fag 
_model_server_result.datetime_utc      '2025-07-31 02:18:08' 
_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          8g5d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":3303}' 
#
_entry.id    8G5D 
#
_exptl.entry_id    8G5D 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              941.642 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(3S)-citryl-Coenzyme A' 
_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            8G5D 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8G5D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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                      4 
_struct_asym.id                             M 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C27 H42 N7 O22 P3 S' 
_chem_comp.formula_weight    941.642 
_chem_comp.id                Q5B 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(3S)-citryl-Coenzyme A' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '(2~{S})-2-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid' 
#
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
O12 P2 Q5B doub 427 n n 
O10 P2 Q5B sing 428 n n 
P2 O11 Q5B sing 429 n n 
P2 O9 Q5B sing 430 n n 
O5 P1 Q5B doub 431 n n 
O4 P1 Q5B sing 432 n n 
O9 C6 Q5B sing 433 n n 
C6 C7 Q5B sing 434 n n 
C6 C5 Q5B sing 435 n n 
P1 O6 Q5B sing 436 n n 
P1 O3 Q5B sing 437 n n 
O8 C7 Q5B sing 438 n n 
O6 C4 Q5B sing 439 n n 
C4 C5 Q5B sing 440 n n 
C7 C8 Q5B sing 441 n n 
C5 O7 Q5B sing 442 n n 
O2 P Q5B doub 443 n n 
O3 P Q5B sing 444 n n 
C C1 Q5B sing 445 n n 
C8 O7 Q5B sing 446 n n 
C8 N Q5B sing 447 n n 
P O Q5B sing 448 n n 
P O1 Q5B sing 449 n n 
O13 C15 Q5B doub 450 n n 
O C3 Q5B sing 451 n n 
N C9 Q5B sing 452 n y 
N C11 Q5B sing 453 n y 
C9 N1 Q5B doub 454 n y 
C1 C14 Q5B sing 455 n n 
C1 C3 Q5B sing 456 n n 
C1 C2 Q5B sing 457 n n 
C15 C14 Q5B sing 458 n n 
C15 N5 Q5B sing 459 n n 
C14 O21 Q5B sing 460 n n 
C11 N2 Q5B doub 461 n y 
C11 C10 Q5B sing 462 n y 
N1 C10 Q5B sing 463 n y 
N2 C12 Q5B sing 464 n y 
C10 C13 Q5B doub 465 n y 
N5 C16 Q5B sing 466 n n 
C17 C16 Q5B sing 467 n n 
C17 C18 Q5B sing 468 n n 
C12 N3 Q5B doub 469 n y 
C13 N3 Q5B sing 470 n y 
C13 N4 Q5B sing 471 n n 
N6 C18 Q5B sing 472 n n 
N6 C19 Q5B sing 473 n n 
O16 C25 Q5B doub 474 n n 
C18 O14 Q5B doub 475 n n 
C25 C24 Q5B sing 476 n n 
C25 O17 Q5B sing 477 n n 
C24 C23 Q5B sing 478 n n 
S C20 Q5B sing 479 n n 
S C21 Q5B sing 480 n n 
C19 C20 Q5B sing 481 n n 
O18 C26 Q5B doub 482 n n 
C21 O15 Q5B doub 483 n n 
C21 C22 Q5B sing 484 n n 
C22 C23 Q5B sing 485 n n 
C23 C26 Q5B sing 486 n n 
C23 O20 Q5B sing 487 n n 
C26 O19 Q5B sing 488 n n 
C H1 Q5B sing 489 n n 
C H2 Q5B sing 490 n n 
C H3 Q5B sing 491 n n 
C12 H4 Q5B sing 492 n n 
C14 H5 Q5B sing 493 n n 
C16 H6 Q5B sing 494 n n 
C16 H7 Q5B sing 495 n n 
C17 H8 Q5B sing 496 n n 
C17 H9 Q5B sing 497 n n 
C19 H10 Q5B sing 498 n n 
C19 H11 Q5B sing 499 n n 
C2 H12 Q5B sing 500 n n 
C2 H13 Q5B sing 501 n n 
C2 H14 Q5B sing 502 n n 
C20 H15 Q5B sing 503 n n 
C20 H16 Q5B sing 504 n n 
C22 H17 Q5B sing 505 n n 
C22 H18 Q5B sing 506 n n 
C24 H19 Q5B sing 507 n n 
C24 H20 Q5B sing 508 n n 
C3 H21 Q5B sing 509 n n 
C3 H22 Q5B sing 510 n n 
C4 H23 Q5B sing 511 n n 
C4 H24 Q5B sing 512 n n 
C5 H25 Q5B sing 513 n n 
C6 H26 Q5B sing 514 n n 
C7 H27 Q5B sing 515 n n 
C8 H28 Q5B sing 516 n n 
C9 H29 Q5B sing 517 n n 
N4 H30 Q5B sing 518 n n 
N4 H31 Q5B sing 519 n n 
N5 H32 Q5B sing 520 n n 
N6 H33 Q5B sing 521 n n 
O1 H34 Q5B sing 522 n n 
O10 H35 Q5B sing 523 n n 
O11 H36 Q5B sing 524 n n 
O17 H37 Q5B sing 525 n n 
O19 H38 Q5B sing 526 n n 
O20 H39 Q5B sing 527 n n 
O21 H40 Q5B sing 528 n n 
O4 H41 Q5B sing 529 n n 
O8 H42 Q5B sing 530 n n 
#
_atom_sites.entry_id                     8G5D 
_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
E 2 ACO A 1 3301 3301 ACO ACO . 
F 3 OAA A 1 3302 3302 OAA OAA . 
G 2 ACO B 1 3301 3301 ACO ACO . 
H 3 OAA B 1 3302 3302 OAA OAA . 
I 2 ACO C 1 3301 3301 ACO ACO . 
J 3 OAA C 1 3302 3302 OAA OAA . 
K 2 ACO D 1 3301 3301 ACO ACO . 
L 3 OAA D 1 3302 3302 OAA OAA . 
M 4 Q5B D 1 3303 3303 Q5B Q5B . 
N 5 ADP D 1 3304 3304 ADP ADP . 
O 6 PO4 D 1 3305 3305 PO4 PO4 . 
P 7 HOH A 1 3401 3402 HOH HOH . 
P 7 HOH A 2 3402 3408 HOH HOH . 
P 7 HOH A 3 3403 3401 HOH HOH . 
P 7 HOH A 4 3404 3403 HOH HOH . 
P 7 HOH A 5 3405 3404 HOH HOH . 
P 7 HOH A 6 3406 3405 HOH HOH . 
P 7 HOH A 7 3407 3409 HOH HOH . 
P 7 HOH A 8 3408 3406 HOH HOH . 
P 7 HOH A 9 3409 3407 HOH HOH . 
Q 7 HOH B 1 3401 3401 HOH HOH . 
Q 7 HOH B 2 3402 3403 HOH HOH . 
Q 7 HOH B 3 3403 3407 HOH HOH . 
Q 7 HOH B 4 3404 3402 HOH HOH . 
Q 7 HOH B 5 3405 3406 HOH HOH . 
Q 7 HOH B 6 3406 3408 HOH HOH . 
Q 7 HOH B 7 3407 3405 HOH HOH . 
Q 7 HOH B 8 3408 3410 HOH HOH . 
Q 7 HOH B 9 3409 3409 HOH HOH . 
Q 7 HOH B 10 3410 3411 HOH HOH . 
Q 7 HOH B 11 3411 3404 HOH HOH . 
R 7 HOH C 1 3401 3401 HOH HOH . 
R 7 HOH C 2 3402 3404 HOH HOH . 
R 7 HOH C 3 3403 3403 HOH HOH . 
R 7 HOH C 4 3404 3406 HOH HOH . 
R 7 HOH C 5 3405 3402 HOH HOH . 
R 7 HOH C 6 3406 3405 HOH HOH . 
R 7 HOH C 7 3407 3407 HOH HOH . 
R 7 HOH C 8 3408 3408 HOH HOH . 
S 7 HOH D 1 3401 3402 HOH HOH . 
S 7 HOH D 2 3402 3401 HOH HOH . 
S 7 HOH D 3 3403 3404 HOH HOH . 
S 7 HOH D 4 3404 3403 HOH HOH . 
S 7 HOH D 5 3405 3405 HOH HOH . 
S 7 HOH D 6 3406 3407 HOH HOH . 
S 7 HOH D 7 3407 3409 HOH HOH . 
S 7 HOH D 8 3408 3406 HOH HOH . 
S 7 HOH D 9 3409 3408 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 N N Q5B . . . M 4 70.713 103.863 65.446 1 80.37 ? N Q5B 3303 D 1 
HETATM 2 C C Q5B . . . M 4 59.693 102.251 62.199 1 80.37 ? C Q5B 3303 D 1 
HETATM 3 O O Q5B . . . M 4 61.983 102.98 63.775 1 80.37 ? O Q5B 3303 D 1 
HETATM 4 C C1 Q5B . . . M 4 59.724 102.081 63.7 1 80.37 ? C1 Q5B 3303 D 1 
HETATM 5 C C10 Q5B . . . M 4 72.359 104.171 66.78 1 80.37 ? C10 Q5B 3303 D 1 
HETATM 6 C C11 Q5B . . . M 4 71.974 104.306 65.528 1 80.37 ? C11 Q5B 3303 D 1 
HETATM 7 C C12 Q5B . . . M 4 74.05 105.185 64.928 1 80.37 ? C12 Q5B 3303 D 1 
HETATM 8 C C13 Q5B . . . M 4 73.646 104.551 67.082 1 80.37 ? C13 Q5B 3303 D 1 
HETATM 9 C C14 Q5B . . . M 4 59.159 103.384 64.395 1 80.37 ? C14 Q5B 3303 D 1 
HETATM 10 C C15 Q5B . . . M 4 57.695 103.332 64.906 1 80.37 ? C15 Q5B 3303 D 1 
HETATM 11 C C16 Q5B . . . M 4 56.407 104.508 62.897 1 80.37 ? C16 Q5B 3303 D 1 
HETATM 12 C C17 Q5B . . . M 4 55.438 103.599 62.081 1 80.37 ? C17 Q5B 3303 D 1 
HETATM 13 C C18 Q5B . . . M 4 54.123 104.384 61.787 1 80.37 ? C18 Q5B 3303 D 1 
HETATM 14 C C19 Q5B . . . M 4 51.845 104.518 60.811 1 80.37 ? C19 Q5B 3303 D 1 
HETATM 15 C C2 Q5B . . . M 4 58.961 100.814 64.024 1 80.37 ? C2 Q5B 3303 D 1 
HETATM 16 C C20 Q5B . . . M 4 50.566 103.693 61.076 1 80.37 ? C20 Q5B 3303 D 1 
HETATM 17 C C21 Q5B . . . M 4 50.036 104.544 63.806 1 80.37 ? C21 Q5B 3303 D 1 
HETATM 18 C C22 Q5B . . . M 4 48.804 104.375 64.696 1 80.37 ? C22 Q5B 3303 D 1 
HETATM 19 C C23 Q5B . . . M 4 48.84 105.183 65.969 1 80.37 ? C23 Q5B 3303 D 1 
HETATM 20 C C24 Q5B . . . M 4 47.873 106.373 65.793 1 80.37 ? C24 Q5B 3303 D 1 
HETATM 21 C C25 Q5B . . . M 4 47.432 106.98 67.163 1 80.37 ? C25 Q5B 3303 D 1 
HETATM 22 C C26 Q5B . . . M 4 48.352 104.229 67.031 1 80.37 ? C26 Q5B 3303 D 1 
HETATM 23 C C3 Q5B . . . M 4 61.174 101.873 64.131 1 80.37 ? C3 Q5B 3303 D 1 
HETATM 24 C C4 Q5B . . . M 4 66.692 104.502 63.861 1 80.37 ? C4 Q5B 3303 D 1 
HETATM 25 C C5 Q5B . . . M 4 68.006 104.6 63.092 1 80.37 ? C5 Q5B 3303 D 1 
HETATM 26 C C6 Q5B . . . M 4 68.403 103.448 62.591 1 80.37 ? C6 Q5B 3303 D 1 
HETATM 27 C C7 Q5B . . . M 4 69.432 102.777 63.633 1 80.37 ? C7 Q5B 3303 D 1 
HETATM 28 C C8 Q5B . . . M 4 70.189 103.992 64.106 1 80.37 ? C8 Q5B 3303 D 1 
HETATM 29 C C9 Q5B . . . M 4 70.302 103.455 66.647 1 80.37 ? C9 Q5B 3303 D 1 
HETATM 30 N N1 Q5B . . . M 4 71.333 103.63 67.487 1 80.37 ? N1 Q5B 3303 D 1 
HETATM 31 N N2 Q5B . . . M 4 72.793 104.811 64.597 1 80.37 ? N2 Q5B 3303 D 1 
HETATM 32 N N3 Q5B . . . M 4 74.47 105.04 66.201 1 80.37 ? N3 Q5B 3303 D 1 
HETATM 33 N N4 Q5B . . . M 4 74.295 104.489 68.358 1 80.37 ? N4 Q5B 3303 D 1 
HETATM 34 N N5 Q5B . . . M 4 56.515 103.852 64.231 1 80.37 ? N5 Q5B 3303 D 1 
HETATM 35 N N6 Q5B . . . M 4 53.007 103.732 61.043 1 80.37 ? N6 Q5B 3303 D 1 
HETATM 36 O O1 Q5B . . . M 4 63.156 105.151 64.362 1 80.37 ? O1 Q5B 3303 D 1 
HETATM 37 O O10 Q5B . . . M 4 68.034 102.145 59.731 1 80.37 ? O10 Q5B 3303 D 1 
HETATM 38 O O11 Q5B . . . M 4 69.139 104.19 58.798 1 80.37 ? O11 Q5B 3303 D 1 
HETATM 39 O O12 Q5B . . . M 4 67.121 104.343 60.017 1 80.37 ? O12 Q5B 3303 D 1 
HETATM 40 O O13 Q5B . . . M 4 57.495 102.871 65.98 1 80.37 ? O13 Q5B 3303 D 1 
HETATM 41 O O14 Q5B . . . M 4 54.012 105.52 62.161 1 80.37 ? O14 Q5B 3303 D 1 
HETATM 42 O O15 Q5B . . . M 4 50.635 105.576 63.741 1 80.37 ? O15 Q5B 3303 D 1 
HETATM 43 O O16 Q5B . . . M 4 48.286 107.501 67.906 1 80.37 ? O16 Q5B 3303 D 1 
HETATM 44 O O17 Q5B . . . M 4 46.204 106.947 67.511 1 80.37 ? O17 Q5B 3303 D 1 
HETATM 45 O O18 Q5B . . . M 4 49.105 103.878 67.929 1 80.37 ? O18 Q5B 3303 D 1 
HETATM 46 O O19 Q5B . . . M 4 47.161 103.785 66.95 1 80.37 ? O19 Q5B 3303 D 1 
HETATM 47 O O2 Q5B . . . M 4 62.025 103.981 66.164 1 80.37 ? O2 Q5B 3303 D 1 
HETATM 48 O O20 Q5B . . . M 4 50.14 105.623 66.333 1 80.37 ? O20 Q5B 3303 D 1 
HETATM 49 O O21 Q5B . . . M 4 59.403 104.463 63.592 1 80.37 ? O21 Q5B 3303 D 1 
HETATM 50 O O3 Q5B . . . M 4 64.206 103.003 65.435 1 80.37 ? O3 Q5B 3303 D 1 
HETATM 51 O O4 Q5B . . . M 4 66.502 101.874 65.377 1 80.37 ? O4 Q5B 3303 D 1 
HETATM 52 O O5 Q5B . . . M 4 64.82 101.156 63.712 1 80.37 ? O5 Q5B 3303 D 1 
HETATM 53 O O6 Q5B . . . M 4 65.905 103.434 63.388 1 80.37 ? O6 Q5B 3303 D 1 
HETATM 54 O O7 Q5B . . . M 4 69.135 105.074 64.086 1 80.37 ? O7 Q5B 3303 D 1 
HETATM 55 O O8 Q5B . . . M 4 70.312 101.94 62.953 1 80.37 ? O8 Q5B 3303 D 1 
HETATM 56 O O9 Q5B . . . M 4 69.144 103.735 61.378 1 80.37 ? O9 Q5B 3303 D 1 
HETATM 57 P P Q5B . . . M 4 62.831 103.809 64.924 1 80.37 ? P Q5B 3303 D 1 
HETATM 58 P P1 Q5B . . . M 4 65.379 102.327 64.463 1 80.37 ? P1 Q5B 3303 D 1 
HETATM 59 P P2 Q5B . . . M 4 68.358 103.596 59.938 1 80.37 ? P2 Q5B 3303 D 1 
HETATM 60 S S Q5B . . . M 4 50.569 103.094 62.765 1 80.37 ? S Q5B 3303 D 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           60 
#