data_8XX8
#
_model_server_result.job_id            XN83cwuqO3kn67ngXs-s-A 
_model_server_result.datetime_utc      '2024-11-23 04:03:43' 
_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          8xx8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"BB","auth_seq_id":310}' 
#
_entry.id    8XX8 
#
_exptl.entry_id    8XX8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.436 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RETINAL 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          104.77 
_cell.angle_gamma         90 
_cell.entry_id            8XX8 
_cell.length_a            90.22 
_cell.length_b            126.18 
_cell.length_c            97.61 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XX8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_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
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,QB 1 1 
C,D,E,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,NB,OB,PB 2 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
? 5 R N N 
? 5 Y N N 
? 5 HA N N 
? 5 RA N N 
? 5 BB N N 
? 5 KB N 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
covale ? covale1 A NZ LYS 220 A LYS 221 1_555 R C15 RET . A RET 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale2 B NZ LYS 220 B LYS 221 1_555 Y C15 RET . B RET 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale3 C NZ LYS 220 D LYS 221 1_555 HA C15 RET . D RET 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale4 D NZ LYS 220 E LYS 221 1_555 RA C15 RET . E RET 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale5 E NZ LYS 220 F LYS 221 1_555 BB C15 RET . F RET 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale6 F NZ LYS 220 C LYS 221 1_555 KB C15 RET . C RET 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
#
_chem_comp.formula           'C20 H28 O' 
_chem_comp.formula_weight    284.436 
_chem_comp.id                RET 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              RETINAL 
_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
C1 C2 RET sing 391 n n 
C1 C6 RET sing 392 n n 
C1 C16 RET sing 393 n n 
C1 C17 RET sing 394 n n 
C2 C3 RET sing 395 n n 
C2 H21 RET sing 396 n n 
C2 H22 RET sing 397 n n 
C3 C4 RET sing 398 n n 
C3 H31 RET sing 399 n n 
C3 H32 RET sing 400 n n 
C4 C5 RET sing 401 n n 
C4 H41 RET sing 402 n n 
C4 H42 RET sing 403 n n 
C5 C6 RET doub 404 n n 
C5 C18 RET sing 405 n n 
C6 C7 RET sing 406 n n 
C7 C8 RET doub 407 e n 
C7 H7 RET sing 408 n n 
C8 C9 RET sing 409 n n 
C8 H8 RET sing 410 n n 
C9 C10 RET doub 411 e n 
C9 C19 RET sing 412 n n 
C10 C11 RET sing 413 n n 
C10 H10 RET sing 414 n n 
C11 C12 RET doub 415 e n 
C11 H11 RET sing 416 n n 
C12 C13 RET sing 417 n n 
C12 H12 RET sing 418 n n 
C13 C14 RET doub 419 e n 
C13 C20 RET sing 420 n n 
C14 C15 RET sing 421 n n 
C14 H14 RET sing 422 n n 
C15 O1 RET doub 423 n n 
C15 H15 RET sing 424 n n 
C16 H161 RET sing 425 n n 
C16 H162 RET sing 426 n n 
C16 H163 RET sing 427 n n 
C17 H171 RET sing 428 n n 
C17 H172 RET sing 429 n n 
C17 H173 RET sing 430 n n 
C18 H181 RET sing 431 n n 
C18 H182 RET sing 432 n n 
C18 H183 RET sing 433 n n 
C19 H191 RET sing 434 n n 
C19 H192 RET sing 435 n n 
C19 H193 RET sing 436 n n 
C20 H201 RET sing 437 n n 
C20 H202 RET sing 438 n n 
C20 H203 RET sing 439 n n 
#
_atom_sites.entry_id                     8XX8 
_atom_sites.fract_transf_matrix[1][1]    0.011084 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002922 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007925 
_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]    0.010595 
_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
G 2 LFA A 1 301 313 LFA LFA . 
H 3 CL A 1 302 1 CL CL . 
I 4 OLA A 1 303 4 OLA OLA . 
J 4 OLA A 1 304 9 OLA OLA . 
K 4 OLA A 1 305 18 OLA OLA . 
L 4 OLA A 1 306 20 OLA OLA . 
M 4 OLA A 1 307 22 OLA OLA . 
N 4 OLA A 1 308 24 OLA OLA . 
O 4 OLA A 1 309 29 OLA OLA . 
P 4 OLA A 1 310 31 OLA OLA . 
Q 4 OLA A 1 311 34 OLA OLA . 
R 5 RET A 1 312 311 RET RET . 
S 2 LFA B 1 301 313 LFA LFA . 
T 3 CL B 1 302 2 CL CL . 
U 4 OLA B 1 303 5 OLA OLA . 
V 4 OLA B 1 304 6 OLA OLA . 
W 4 OLA B 1 305 7 OLA OLA . 
X 4 OLA B 1 306 27 OLA OLA . 
Y 5 RET B 1 307 311 RET RET . 
Z 2 LFA D 1 301 313 LFA LFA . 
AA 2 LFA D 1 302 314 LFA LFA . 
BA 2 LFA D 1 303 315 LFA LFA . 
CA 2 LFA D 1 304 316 LFA LFA . 
DA 3 CL D 1 305 4 CL CL . 
EA 4 OLA D 1 306 11 OLA OLA . 
FA 4 OLA D 1 307 15 OLA OLA . 
GA 4 OLA D 1 308 23 OLA OLA . 
HA 5 RET D 1 309 311 RET RET . 
IA 2 LFA E 1 301 315 LFA LFA . 
JA 3 CL E 1 302 5 CL CL . 
KA 4 OLA E 1 303 2 OLA OLA . 
LA 4 OLA E 1 304 3 OLA OLA . 
MA 4 OLA E 1 305 16 OLA OLA . 
NA 4 OLA E 1 306 17 OLA OLA . 
OA 4 OLA E 1 307 26 OLA OLA . 
PA 4 OLA E 1 308 28 OLA OLA . 
QA 4 OLA E 1 309 30 OLA OLA . 
RA 5 RET E 1 310 311 RET RET . 
SA 2 LFA F 1 301 314 LFA LFA . 
TA 2 LFA F 1 302 316 LFA LFA . 
UA 2 LFA F 1 303 313 LFA LFA . 
VA 2 LFA F 1 304 314 LFA LFA . 
WA 3 CL F 1 305 6 CL CL . 
XA 4 OLA F 1 306 1 OLA OLA . 
YA 4 OLA F 1 307 8 OLA OLA . 
ZA 4 OLA F 1 308 32 OLA OLA . 
AB 4 OLA F 1 309 40 OLA OLA . 
BB 5 RET F 1 310 311 RET RET . 
CB 3 CL C 1 301 3 CL CL . 
DB 4 OLA C 1 302 10 OLA OLA . 
EB 4 OLA C 1 303 12 OLA OLA . 
FB 4 OLA C 1 304 13 OLA OLA . 
GB 4 OLA C 1 305 14 OLA OLA . 
HB 4 OLA C 1 306 19 OLA OLA . 
IB 4 OLA C 1 307 21 OLA OLA . 
JB 4 OLA C 1 308 25 OLA OLA . 
KB 5 RET C 1 309 311 RET RET . 
LB 6 HOH A 1 401 9 HOH HOH . 
LB 6 HOH A 2 402 45 HOH HOH . 
LB 6 HOH A 3 403 42 HOH HOH . 
LB 6 HOH A 4 404 19 HOH HOH . 
LB 6 HOH A 5 405 1 HOH HOH . 
LB 6 HOH A 6 406 25 HOH HOH . 
LB 6 HOH A 7 407 49 HOH HOH . 
LB 6 HOH A 8 408 82 HOH HOH . 
LB 6 HOH A 9 409 51 HOH HOH . 
LB 6 HOH A 10 410 2 HOH HOH . 
LB 6 HOH A 11 411 83 HOH HOH . 
LB 6 HOH A 12 412 81 HOH HOH . 
LB 6 HOH A 13 413 89 HOH HOH . 
LB 6 HOH A 14 414 52 HOH HOH . 
LB 6 HOH A 15 415 84 HOH HOH . 
MB 6 HOH B 1 401 10 HOH HOH . 
MB 6 HOH B 2 402 31 HOH HOH . 
MB 6 HOH B 3 403 54 HOH HOH . 
MB 6 HOH B 4 404 3 HOH HOH . 
MB 6 HOH B 5 405 70 HOH HOH . 
MB 6 HOH B 6 406 20 HOH HOH . 
MB 6 HOH B 7 407 36 HOH HOH . 
MB 6 HOH B 8 408 15 HOH HOH . 
MB 6 HOH B 9 409 53 HOH HOH . 
MB 6 HOH B 10 410 69 HOH HOH . 
MB 6 HOH B 11 411 55 HOH HOH . 
MB 6 HOH B 12 412 44 HOH HOH . 
MB 6 HOH B 13 413 43 HOH HOH . 
NB 6 HOH D 1 401 11 HOH HOH . 
NB 6 HOH D 2 402 63 HOH HOH . 
NB 6 HOH D 3 403 79 HOH HOH . 
NB 6 HOH D 4 404 64 HOH HOH . 
NB 6 HOH D 5 405 62 HOH HOH . 
NB 6 HOH D 6 406 26 HOH HOH . 
NB 6 HOH D 7 407 28 HOH HOH . 
NB 6 HOH D 8 408 21 HOH HOH . 
NB 6 HOH D 9 409 4 HOH HOH . 
NB 6 HOH D 10 410 57 HOH HOH . 
NB 6 HOH D 11 411 5 HOH HOH . 
NB 6 HOH D 12 412 80 HOH HOH . 
NB 6 HOH D 13 413 88 HOH HOH . 
NB 6 HOH D 14 414 17 HOH HOH . 
NB 6 HOH D 15 415 27 HOH HOH . 
NB 6 HOH D 16 416 60 HOH HOH . 
NB 6 HOH D 17 417 61 HOH HOH . 
NB 6 HOH D 18 418 59 HOH HOH . 
NB 6 HOH D 19 419 74 HOH HOH . 
NB 6 HOH D 20 420 40 HOH HOH . 
NB 6 HOH D 21 421 71 HOH HOH . 
NB 6 HOH D 22 422 41 HOH HOH . 
NB 6 HOH D 23 423 58 HOH HOH . 
OB 6 HOH E 1 401 12 HOH HOH . 
OB 6 HOH E 2 402 87 HOH HOH . 
OB 6 HOH E 3 403 73 HOH HOH . 
OB 6 HOH E 4 404 67 HOH HOH . 
OB 6 HOH E 5 405 22 HOH HOH . 
OB 6 HOH E 6 406 72 HOH HOH . 
OB 6 HOH E 7 407 14 HOH HOH . 
OB 6 HOH E 8 408 30 HOH HOH . 
OB 6 HOH E 9 409 68 HOH HOH . 
OB 6 HOH E 10 410 34 HOH HOH . 
OB 6 HOH E 11 411 29 HOH HOH . 
OB 6 HOH E 12 412 6 HOH HOH . 
OB 6 HOH E 13 413 38 HOH HOH . 
PB 6 HOH F 1 401 8 HOH HOH . 
PB 6 HOH F 2 402 16 HOH HOH . 
PB 6 HOH F 3 403 39 HOH HOH . 
PB 6 HOH F 4 404 32 HOH HOH . 
PB 6 HOH F 5 405 78 HOH HOH . 
PB 6 HOH F 6 406 23 HOH HOH . 
PB 6 HOH F 7 407 18 HOH HOH . 
PB 6 HOH F 8 408 7 HOH HOH . 
PB 6 HOH F 9 409 66 HOH HOH . 
PB 6 HOH F 10 410 65 HOH HOH . 
QB 6 HOH C 1 401 13 HOH HOH . 
QB 6 HOH C 2 402 77 HOH HOH . 
QB 6 HOH C 3 403 35 HOH HOH . 
QB 6 HOH C 4 404 75 HOH HOH . 
QB 6 HOH C 5 405 33 HOH HOH . 
QB 6 HOH C 6 406 24 HOH HOH . 
QB 6 HOH C 7 407 37 HOH HOH . 
QB 6 HOH C 8 408 46 HOH HOH . 
QB 6 HOH C 9 409 47 HOH HOH . 
QB 6 HOH C 10 410 76 HOH HOH . 
QB 6 HOH C 11 411 48 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 C1 RET . . . BB 5 38.634 22.584 76.844 1 45.14 ? C1 RET 310 F 1 
HETATM 2 C C2 RET . . . BB 5 38.785 21.407 77.809 1 42.26 ? C2 RET 310 F 1 
HETATM 3 C C3 RET . . . BB 5 39.673 21.702 79.005 1 46.18 ? C3 RET 310 F 1 
HETATM 4 C C4 RET . . . BB 5 39.188 22.912 79.782 1 40.45 ? C4 RET 310 F 1 
HETATM 5 C C5 RET . . . BB 5 38.64 24.024 78.925 1 41.42 ? C5 RET 310 F 1 
HETATM 6 C C6 RET . . . BB 5 38.463 23.906 77.597 1 49.65 ? C6 RET 310 F 1 
HETATM 7 C C7 RET . . . BB 5 37.72 24.891 76.838 1 49.67 ? C7 RET 310 F 1 
HETATM 8 C C8 RET . . . BB 5 38.247 25.798 76.034 1 42.62 ? C8 RET 310 F 1 
HETATM 9 C C9 RET . . . BB 5 37.539 26.791 75.251 1 40.7 ? C9 RET 310 F 1 
HETATM 10 C C10 RET . . . BB 5 37.416 26.608 73.916 1 45.11 ? C10 RET 310 F 1 
HETATM 11 C C11 RET . . . BB 5 36.773 27.471 72.966 1 44.64 ? C11 RET 310 F 1 
HETATM 12 C C12 RET . . . BB 5 36.932 27.35 71.645 1 43.15 ? C12 RET 310 F 1 
HETATM 13 C C13 RET . . . BB 5 36.336 28.178 70.615 1 43.83 ? C13 RET 310 F 1 
HETATM 14 C C14 RET . . . BB 5 36.355 27.75 69.33 1 46.7 ? C14 RET 310 F 1 
HETATM 15 C C15 RET . . . BB 5 35.827 28.42 68.17 1 43.64 ? C15 RET 310 F 1 
HETATM 16 C C16 RET . . . BB 5 39.881 22.651 75.955 1 41.73 ? C16 RET 310 F 1 
HETATM 17 C C17 RET . . . BB 5 37.414 22.323 75.952 1 45.18 ? C17 RET 310 F 1 
HETATM 18 C C18 RET . . . BB 5 38.55 25.328 79.669 1 42.93 ? C18 RET 310 F 1 
HETATM 19 C C19 RET . . . BB 5 36.982 27.989 75.969 1 44.97 ? C19 RET 310 F 1 
HETATM 20 C C20 RET . . . BB 5 35.733 29.491 71.029 1 41.2 ? C20 RET 310 F 1 
#
_model_server_stats.io_time_ms              100 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           20 
#