data_7XJD
#
_model_server_result.job_id            7G78tYPAG0VnaKC6gazJCw 
_model_server_result.datetime_utc      '2024-11-21 14:19:38' 
_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          7xjd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    7XJD 
#
_exptl.entry_id    7XJD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.436 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RETINAL 
_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         120 
_cell.entry_id            7XJD 
_cell.length_a            60.57 
_cell.length_b            60.57 
_cell.length_c            110.89 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7XJD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,K,L,M,N,O,P,Q,R,S,T,U 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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_635 -y+1,x-y-2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 121.14 -104.910317 0 
3 'crystal symmetry operation' 3_865 -x+y+3,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 151.425 52.455159 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            NZ 
_struct_conn.ptnr1_label_comp_id            LYS 
_struct_conn.ptnr1_label_seq_id             212 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             LYS 
_struct_conn.ptnr1_auth_seq_id              216 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            B 
_struct_conn.ptnr2_label_atom_id            C15 
_struct_conn.ptnr2_label_comp_id            RET 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             RET 
_struct_conn.ptnr2_auth_seq_id              301 
_struct_conn.ptnr2_symmetry                 1_555 
_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                1.351 
_struct_conn.pdbx_value_order               ? 
#
_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 376 n n 
C1 C6 RET sing 377 n n 
C1 C16 RET sing 378 n n 
C1 C17 RET sing 379 n n 
C2 C3 RET sing 380 n n 
C2 H21 RET sing 381 n n 
C2 H22 RET sing 382 n n 
C3 C4 RET sing 383 n n 
C3 H31 RET sing 384 n n 
C3 H32 RET sing 385 n n 
C4 C5 RET sing 386 n n 
C4 H41 RET sing 387 n n 
C4 H42 RET sing 388 n n 
C5 C6 RET doub 389 n n 
C5 C18 RET sing 390 n n 
C6 C7 RET sing 391 n n 
C7 C8 RET doub 392 e n 
C7 H7 RET sing 393 n n 
C8 C9 RET sing 394 n n 
C8 H8 RET sing 395 n n 
C9 C10 RET doub 396 e n 
C9 C19 RET sing 397 n n 
C10 C11 RET sing 398 n n 
C10 H10 RET sing 399 n n 
C11 C12 RET doub 400 e n 
C11 H11 RET sing 401 n n 
C12 C13 RET sing 402 n n 
C12 H12 RET sing 403 n n 
C13 C14 RET doub 404 e n 
C13 C20 RET sing 405 n n 
C14 C15 RET sing 406 n n 
C14 H14 RET sing 407 n n 
C15 O1 RET doub 408 n n 
C15 H15 RET sing 409 n n 
C16 H161 RET sing 410 n n 
C16 H162 RET sing 411 n n 
C16 H163 RET sing 412 n n 
C17 H171 RET sing 413 n n 
C17 H172 RET sing 414 n n 
C17 H173 RET sing 415 n n 
C18 H181 RET sing 416 n n 
C18 H182 RET sing 417 n n 
C18 H183 RET sing 418 n n 
C19 H191 RET sing 419 n n 
C19 H192 RET sing 420 n n 
C19 H193 RET sing 421 n n 
C20 H201 RET sing 422 n n 
C20 H202 RET sing 423 n n 
C20 H203 RET sing 424 n n 
#
_atom_sites.entry_id                     7XJD 
_atom_sites.fract_transf_matrix[1][1]    0.01651 
_atom_sites.fract_transf_matrix[1][2]    0.009532 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019064 
_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]    0.009018 
_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
B 2 RET A 1 301 301 RET RET . 
C 3 L2P A 1 302 302 L2P L2P . 
D 3 L2P A 1 303 303 L2P L2P . 
E 3 L2P A 1 304 304 L2P L2P . 
F 3 L2P A 1 305 305 L2P L2P . 
G 3 L2P A 1 306 306 L2P L2P . 
H 4 SQU A 1 312 312 SQU SQU . 
I 3 L2P A 1 313 313 L2P L2P . 
J 3 L2P A 1 315 315 L2P L2P . 
K 3 L2P A 1 320 320 L2P L2P . 
L 3 L2P A 1 322 322 L2P L2P . 
M 3 L2P A 1 323 323 L2P L2P . 
N 3 L2P A 1 324 324 L2P L2P . 
O 3 L2P A 1 327 327 L2P L2P . 
P 3 L2P A 1 328 328 L2P L2P . 
Q 3 L2P A 1 333 333 L2P L2P . 
R 4 SQU A 1 341 341 SQU SQU . 
S 4 SQU A 1 342 342 SQU SQU . 
T 4 SQU A 1 343 343 SQU SQU . 
U 5 HOH A 1 401 401 HOH HOH . 
U 5 HOH A 2 402 402 HOH HOH . 
U 5 HOH A 3 403 403 HOH HOH . 
U 5 HOH A 4 404 404 HOH HOH . 
U 5 HOH A 5 405 405 HOH HOH . 
U 5 HOH A 6 406 406 HOH HOH . 
U 5 HOH A 7 407 407 HOH HOH . 
U 5 HOH A 8 411 411 HOH HOH . 
U 5 HOH A 9 412 412 HOH HOH . 
U 5 HOH A 10 415 415 HOH HOH . 
U 5 HOH A 11 416 416 HOH HOH . 
U 5 HOH A 12 419 419 HOH HOH . 
U 5 HOH A 13 420 420 HOH HOH . 
U 5 HOH A 14 450 450 HOH HOH . 
U 5 HOH A 15 451 451 HOH HOH . 
U 5 HOH A 16 453 453 HOH HOH . 
U 5 HOH A 17 454 454 HOH HOH . 
U 5 HOH A 18 455 455 HOH HOH . 
U 5 HOH A 19 456 456 HOH HOH . 
U 5 HOH A 20 457 457 HOH HOH . 
U 5 HOH A 21 458 458 HOH HOH . 
U 5 HOH A 22 459 459 HOH HOH . 
U 5 HOH A 23 460 460 HOH HOH . 
U 5 HOH A 24 501 501 HOH HOH . 
U 5 HOH A 25 502 502 HOH HOH . 
U 5 HOH A 26 511 511 HOH HOH . 
U 5 HOH A 27 512 512 HOH HOH . 
U 5 HOH A 28 513 513 HOH HOH . 
U 5 HOH A 29 514 514 HOH HOH . 
U 5 HOH A 30 530 530 HOH HOH . 
U 5 HOH A 31 531 531 HOH HOH . 
U 5 HOH A 32 532 532 HOH HOH . 
U 5 HOH A 33 533 533 HOH HOH . 
U 5 HOH A 34 534 534 HOH HOH . 
U 5 HOH A 35 535 535 HOH HOH . 
U 5 HOH A 36 536 536 HOH HOH . 
U 5 HOH A 37 537 537 HOH HOH . 
U 5 HOH A 38 538 538 HOH HOH . 
U 5 HOH A 39 539 539 HOH HOH . 
U 5 HOH A 40 540 540 HOH HOH . 
U 5 HOH A 41 541 541 HOH HOH . 
U 5 HOH A 42 542 542 HOH HOH . 
U 5 HOH A 43 543 543 HOH HOH . 
U 5 HOH A 44 544 544 HOH HOH . 
U 5 HOH A 45 545 545 HOH HOH . 
U 5 HOH A 46 546 546 HOH HOH . 
U 5 HOH A 47 547 547 HOH HOH . 
U 5 HOH A 48 548 548 HOH HOH . 
U 5 HOH A 49 549 549 HOH HOH . 
U 5 HOH A 50 550 550 HOH HOH . 
U 5 HOH A 51 551 551 HOH HOH . 
U 5 HOH A 52 552 552 HOH HOH . 
U 5 HOH A 53 553 553 HOH HOH . 
U 5 HOH A 54 554 554 HOH HOH . 
U 5 HOH A 55 555 555 HOH HOH . 
U 5 HOH A 56 556 556 HOH HOH . 
U 5 HOH A 57 557 557 HOH HOH . 
U 5 HOH A 58 558 558 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 . . . B 2 75.936 -7.335 -20.922 1 16.95 ? C1 RET 301 A 1 
HETATM 2 C C2 RET . . . B 2 76.03 -6.355 -19.725 1 17.7 ? C2 RET 301 A 1 
HETATM 3 C C3 RET . . . B 2 76.874 -5.139 -20.016 1 17.21 ? C3 RET 301 A 1 
HETATM 4 C C4 RET . . . B 2 76.255 -4.335 -21.132 1 16.2 ? C4 RET 301 A 1 
HETATM 5 C C5 RET . . . B 2 75.843 -5.219 -22.278 1 15.51 ? C5 RET 301 A 1 
HETATM 6 C C6 RET . . . B 2 75.769 -6.595 -22.249 1 16.04 ? C6 RET 301 A 1 
HETATM 7 C C7 RET . . . B 2 75.368 -7.287 -23.462 1 15.86 ? C7 RET 301 A 1 
HETATM 8 C C8 RET . . . B 2 75.251 -8.639 -23.698 1 15.5 ? C8 RET 301 A 1 
HETATM 9 C C9 RET . . . B 2 74.664 -9.28 -24.868 1 15.34 ? C9 RET 301 A 1 
HETATM 10 C C10 RET . . . B 2 74.575 -10.64 -24.722 1 15.65 ? C10 RET 301 A 1 
HETATM 11 C C11 RET . . . B 2 73.935 -11.405 -25.79 1 15.58 ? C11 RET 301 A 1 
HETATM 12 C C12 RET . . . B 2 73.805 -12.772 -25.558 1 16.4 ? C12 RET 301 A 1 
HETATM 13 C C13 RET . . . B 2 73.407 -13.808 -26.494 1 16.47 ? C13 RET 301 A 1 
HETATM 14 C C14 RET . . . B 2 73.436 -15.067 -25.91 1 16.49 ? C14 RET 301 A 1 
HETATM 15 C C15 RET . . . B 2 73.602 -16.169 -26.79 1 16.39 ? C15 RET 301 A 1 
HETATM 16 C C16 RET . . . B 2 77.222 -8.137 -21.109 1 17.28 ? C16 RET 301 A 1 
HETATM 17 C C17 RET . . . B 2 74.702 -8.166 -20.504 1 16.74 ? C17 RET 301 A 1 
HETATM 18 C C18 RET . . . B 2 75.76 -4.386 -23.547 1 15.83 ? C18 RET 301 A 1 
HETATM 19 C C19 RET . . . B 2 74.336 -8.448 -26.048 1 15.8 ? C19 RET 301 A 1 
HETATM 20 C C20 RET . . . B 2 73.002 -13.365 -27.842 1 17.02 ? C20 RET 301 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#