data_8KDE
#
_model_server_result.job_id            ZOTCjAtzJqxvLmUzqNOkBQ 
_model_server_result.datetime_utc      '2024-12-18 10:59:40' 
_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          8kde 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"IB","auth_seq_id":202}' 
#
_entry.id    8KDE 
#
_exptl.entry_id    8KDE 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              446.706 
_entity.id                          26 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RRR-ALPHA-TOCOPHERYLQUINONE 
_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            8KDE 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8KDE 
_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    octadecameric 
_pdbx_struct_assembly.oligomeric_count      18 
_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,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC 
_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                      26 
_struct_asym.id                             IB 
_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 NE2 HIS 214 D HIS 214 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc2 B NE2 HIS 268 D HIS 268 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc3 C NE2 HIS 23 E HIS 23 1_555 BB FE HEM . E HEM 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? 
metalc ? metalc4 BB FE HEM . E HEM 101 1_555 D NE2 HIS 23 F HIS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc5 P OD1 ASN 27 C ASN 27 1_555 VB MG CLA . C CLA 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc6 Q NE2 HIS 215 A HIS 215 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc7 Q NE2 HIS 272 A HIS 272 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc8 EC O2 BCT . A BCT 401 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc9 EC O3 BCT . A BCT 401 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
#
_chem_comp.formula           'C29 H50 O3' 
_chem_comp.formula_weight    446.706 
_chem_comp.id                VTQ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              RRR-ALPHA-TOCOPHERYLQUINONE 
_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
O3 C9 VTQ sing 1539 n n 
O3 H3 VTQ sing 1540 n n 
C9 C14 VTQ sing 1541 n n 
C9 C11 VTQ sing 1542 n n 
C9 C15 VTQ sing 1543 n n 
C14 H141 VTQ sing 1544 n n 
C14 H142 VTQ sing 1545 n n 
C14 H143 VTQ sing 1546 n n 
C11 C10 VTQ sing 1547 n n 
C11 H111 VTQ sing 1548 n n 
C11 H112 VTQ sing 1549 n n 
C10 C3 VTQ sing 1550 n n 
C10 H101 VTQ sing 1551 n n 
C10 H102 VTQ sing 1552 n n 
C3 C2 VTQ doub 1553 n n 
C3 C4 VTQ sing 1554 n n 
C2 C8 VTQ sing 1555 n n 
C2 C7 VTQ sing 1556 n n 
C8 H8C1 VTQ sing 1557 n n 
C8 H8C2 VTQ sing 1558 n n 
C8 H8C3 VTQ sing 1559 n n 
C4 O1 VTQ doub 1560 n n 
C4 C5 VTQ sing 1561 n n 
C5 C12 VTQ sing 1562 n n 
C5 C6 VTQ doub 1563 n n 
C12 H121 VTQ sing 1564 n n 
C12 H122 VTQ sing 1565 n n 
C12 H123 VTQ sing 1566 n n 
C6 C13 VTQ sing 1567 n n 
C6 C7 VTQ sing 1568 n n 
C13 H131 VTQ sing 1569 n n 
C13 H132 VTQ sing 1570 n n 
C13 H133 VTQ sing 1571 n n 
C7 O2 VTQ doub 1572 n n 
C15 C16 VTQ sing 1573 n n 
C15 H151 VTQ sing 1574 n n 
C15 H152 VTQ sing 1575 n n 
C16 C17 VTQ sing 1576 n n 
C16 H161 VTQ sing 1577 n n 
C16 H162 VTQ sing 1578 n n 
C17 C18 VTQ sing 1579 n n 
C17 H171 VTQ sing 1580 n n 
C17 H172 VTQ sing 1581 n n 
C18 C19 VTQ sing 1582 n n 
C18 C20 VTQ sing 1583 n n 
C18 H18 VTQ sing 1584 n n 
C19 H191 VTQ sing 1585 n n 
C19 H192 VTQ sing 1586 n n 
C19 H193 VTQ sing 1587 n n 
C20 C21 VTQ sing 1588 n n 
C20 H201 VTQ sing 1589 n n 
C20 H202 VTQ sing 1590 n n 
C21 C22 VTQ sing 1591 n n 
C21 H211 VTQ sing 1592 n n 
C21 H212 VTQ sing 1593 n n 
C22 C23 VTQ sing 1594 n n 
C22 H221 VTQ sing 1595 n n 
C22 H222 VTQ sing 1596 n n 
C23 C1 VTQ sing 1597 n n 
C23 C24 VTQ sing 1598 n n 
C23 H23 VTQ sing 1599 n n 
C1 H1C1 VTQ sing 1600 n n 
C1 H1C2 VTQ sing 1601 n n 
C1 H1C3 VTQ sing 1602 n n 
C24 C25 VTQ sing 1603 n n 
C24 H241 VTQ sing 1604 n n 
C24 H242 VTQ sing 1605 n n 
C25 C26 VTQ sing 1606 n n 
C25 H251 VTQ sing 1607 n n 
C25 H252 VTQ sing 1608 n n 
C26 C27 VTQ sing 1609 n n 
C26 H261 VTQ sing 1610 n n 
C26 H262 VTQ sing 1611 n n 
C27 C28 VTQ sing 1612 n n 
C27 C29 VTQ sing 1613 n n 
C27 H27 VTQ sing 1614 n n 
C28 H281 VTQ sing 1615 n n 
C28 H282 VTQ sing 1616 n n 
C28 H283 VTQ sing 1617 n n 
C29 H291 VTQ sing 1618 n n 
C29 H292 VTQ sing 1619 n n 
C29 H293 VTQ sing 1620 n n 
#
_atom_sites.entry_id                     8KDE 
_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
S 19 CLA B 1 601 602 CLA CLA . 
T 19 CLA B 1 602 603 CLA CLA . 
U 19 CLA B 1 603 604 CLA CLA . 
V 19 CLA B 1 604 605 CLA CLA . 
W 19 CLA B 1 605 606 CLA CLA . 
X 19 CLA B 1 606 607 CLA CLA . 
Y 19 CLA B 1 607 608 CLA CLA . 
Z 19 CLA B 1 608 609 CLA CLA . 
AA 19 CLA B 1 609 610 CLA CLA . 
BA 19 CLA B 1 610 611 CLA CLA . 
CA 19 CLA B 1 611 612 CLA CLA . 
DA 19 CLA B 1 612 613 CLA CLA . 
EA 19 CLA B 1 613 614 CLA CLA . 
FA 19 CLA B 1 614 615 CLA CLA . 
GA 19 CLA B 1 615 616 CLA CLA . 
HA 19 CLA B 1 616 617 CLA CLA . 
IA 20 BCR B 1 617 618 BCR BCR . 
JA 20 BCR B 1 618 619 BCR BCR . 
KA 20 BCR B 1 619 620 BCR BCR . 
LA 21 LMG B 1 620 622 LMG LMG . 
MA 22 LHG B 1 621 412 LHG LHG . 
NA 22 LHG B 1 622 413 LHG LHG . 
OA 21 LMG B 1 623 102 LMG LMG . 
PA 22 LHG B 1 624 201 LHG LHG . 
QA 19 CLA D 1 401 402 CLA CLA . 
RA 19 CLA D 1 402 403 CLA CLA . 
SA 20 BCR D 1 403 404 BCR BCR . 
TA 23 PL9 D 1 404 405 PL9 PL9 . 
UA 22 LHG D 1 405 408 LHG LHG . 
VA 22 LHG D 1 406 409 LHG LHG . 
WA 22 LHG D 1 407 410 LHG LHG . 
XA 21 LMG D 1 408 411 LMG LMG . 
YA 19 CLA D 1 409 406 CLA CLA . 
ZA 24 PHO D 1 410 408 PHO PHO . 
AB 24 PHO D 1 411 409 PHO PHO . 
BB 25 HEM E 1 101 101 HEM HEM . 
CB 20 BCR H 1 101 101 BCR BCR . 
DB 20 BCR K 1 101 516 BCR BCR . 
EB 21 LMG K 1 102 521 LMG LMG . 
FB 22 LHG K 1 103 419 LHG LHG . 
GB 22 LHG L 1 101 101 LHG LHG . 
HB 22 LHG X 1 201 414 LHG LHG . 
IB 26 VTQ X 1 202 102 VTQ VTQ . 
JB 20 BCR Z 1 101 514 BCR BCR . 
KB 21 LMG C 1 601 601 LMG LMG . 
LB 19 CLA C 1 602 501 CLA CLA . 
MB 19 CLA C 1 603 502 CLA CLA . 
NB 19 CLA C 1 604 503 CLA CLA . 
OB 19 CLA C 1 605 504 CLA CLA . 
PB 19 CLA C 1 606 505 CLA CLA . 
QB 19 CLA C 1 607 506 CLA CLA . 
RB 19 CLA C 1 608 507 CLA CLA . 
SB 19 CLA C 1 609 508 CLA CLA . 
TB 19 CLA C 1 610 509 CLA CLA . 
UB 19 CLA C 1 611 510 CLA CLA . 
VB 19 CLA C 1 612 511 CLA CLA . 
WB 19 CLA C 1 613 512 CLA CLA . 
XB 19 CLA C 1 614 513 CLA CLA . 
YB 20 BCR C 1 615 515 BCR BCR . 
ZB 20 BCR C 1 616 517 BCR BCR . 
AC 27 DGD C 1 617 518 DGD DGD . 
BC 27 DGD C 1 618 519 DGD DGD . 
CC 27 DGD C 1 619 520 DGD DGD . 
DC 28 SQD C 1 620 412 SQD SQD . 
EC 29 BCT A 1 401 401 BCT BCT . 
FC 30 FE2 A 1 402 402 FE2 FE2 . 
GC 19 CLA A 1 403 405 CLA CLA . 
HC 19 CLA A 1 404 407 CLA CLA . 
IC 19 CLA A 1 405 410 CLA CLA . 
JC 20 BCR A 1 406 411 BCR BCR . 
KC 21 LMG A 1 407 413 LMG LMG . 
LC 22 LHG A 1 408 415 LHG LHG . 
#
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 O3 VTQ . . . IB 26 159.883 188.981 199.045 1 80.32 0 O3 VTQ 202 X 1 
HETATM 2 C C9 VTQ . . . IB 26 159.765 190.163 199.775 1 80.32 0 C9 VTQ 202 X 1 
HETATM 3 C C14 VTQ . . . IB 26 158.362 190.271 200.334 1 80.32 0 C14 VTQ 202 X 1 
HETATM 4 C C11 VTQ . . . IB 26 160.791 190.176 200.933 1 80.32 0 C11 VTQ 202 X 1 
HETATM 5 C C10 VTQ . . . IB 26 160.597 188.925 201.852 1 80.32 0 C10 VTQ 202 X 1 
HETATM 6 C C3 VTQ . . . IB 26 161.88 188.678 202.73 1 80.32 0 C3 VTQ 202 X 1 
HETATM 7 C C2 VTQ . . . IB 26 162.087 189.326 203.868 1 80.32 0 C2 VTQ 202 X 1 
HETATM 8 C C8 VTQ . . . IB 26 161.086 190.362 204.398 1 80.32 0 C8 VTQ 202 X 1 
HETATM 9 C C4 VTQ . . . IB 26 162.905 187.651 202.244 1 80.32 0 C4 VTQ 202 X 1 
HETATM 10 O O1 VTQ . . . IB 26 162.718 187.073 201.229 1 80.32 0 O1 VTQ 202 X 1 
HETATM 11 C C5 VTQ . . . IB 26 164.182 187.362 203.057 1 80.32 0 C5 VTQ 202 X 1 
HETATM 12 C C12 VTQ . . . IB 26 165.168 186.317 202.507 1 80.32 0 C12 VTQ 202 X 1 
HETATM 13 C C6 VTQ . . . IB 26 164.381 188.011 204.192 1 80.32 0 C6 VTQ 202 X 1 
HETATM 14 C C13 VTQ . . . IB 26 165.624 187.777 205.052 1 80.32 0 C13 VTQ 202 X 1 
HETATM 15 C C7 VTQ . . . IB 26 163.353 189.041 204.682 1 80.32 0 C7 VTQ 202 X 1 
HETATM 16 O O2 VTQ . . . IB 26 163.541 189.621 205.7 1 80.32 0 O2 VTQ 202 X 1 
HETATM 17 C C15 VTQ . . . IB 26 160.044 191.357 198.845 1 80.32 0 C15 VTQ 202 X 1 
HETATM 18 C C16 VTQ . . . IB 26 159.74 190.983 197.37 1 80.32 0 C16 VTQ 202 X 1 
HETATM 19 C C17 VTQ . . . IB 26 159.568 192.301 196.538 1 80.32 0 C17 VTQ 202 X 1 
HETATM 20 C C18 VTQ . . . IB 26 160.439 192.284 195.262 1 80.32 0 C18 VTQ 202 X 1 
HETATM 21 C C19 VTQ . . . IB 26 161.597 193.213 195.448 1 80.32 0 C19 VTQ 202 X 1 
HETATM 22 C C20 VTQ . . . IB 26 159.578 192.748 194.053 1 80.32 0 C20 VTQ 202 X 1 
HETATM 23 C C21 VTQ . . . IB 26 160.371 192.678 192.672 1 80.32 0 C21 VTQ 202 X 1 
HETATM 24 C C22 VTQ . . . IB 26 161.043 191.28 192.385 1 80.32 0 C22 VTQ 202 X 1 
HETATM 25 C C23 VTQ . . . IB 26 160.048 190.094 192.18 1 80.32 0 C23 VTQ 202 X 1 
HETATM 26 C C1 VTQ . . . IB 26 158.76 190.542 191.529 1 80.32 0 C1 VTQ 202 X 1 
HETATM 27 C C24 VTQ . . . IB 26 159.758 189.414 193.535 1 80.32 0 C24 VTQ 202 X 1 
HETATM 28 C C25 VTQ . . . IB 26 159.064 188.032 193.336 1 80.32 0 C25 VTQ 202 X 1 
HETATM 29 C C26 VTQ . . . IB 26 160.089 186.984 192.796 1 80.32 0 C26 VTQ 202 X 1 
HETATM 30 C C27 VTQ . . . IB 26 159.485 185.57 192.93 1 80.32 0 C27 VTQ 202 X 1 
HETATM 31 C C28 VTQ . . . IB 26 158.276 185.433 192.012 1 80.32 0 C28 VTQ 202 X 1 
HETATM 32 C C29 VTQ . . . IB 26 160.553 184.52 192.538 1 80.32 0 C29 VTQ 202 X 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           32 
#