data_3QBK
#
_model_server_result.job_id            EPbTMEC-qgLxY-DERI8VNQ 
_model_server_result.datetime_utc      '2024-11-02 13:27:37' 
_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          3qbk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":292}' 
#
_entry.id    3QBK 
#
_exptl.entry_id    3QBK 
_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    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          127.8 
_cell.angle_gamma         90 
_cell.entry_id            3QBK 
_cell.length_a            152.15 
_cell.length_b            99.72 
_cell.length_c            99.97 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QBK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_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 
_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    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
? 2 D N N 
? 2 I N N 
? 2 L 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 256 A LYS 256 1_555 D C15 RET . A RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
covale ? covale2 B NZ LYS 256 B LYS 256 1_555 I C15 RET . B RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? 
covale ? covale3 C NZ LYS 256 D LYS 256 1_555 L C15 RET . D RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? 
#
_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 406 n n 
C1 C6 RET sing 407 n n 
C1 C16 RET sing 408 n n 
C1 C17 RET sing 409 n n 
C2 C3 RET sing 410 n n 
C2 H21 RET sing 411 n n 
C2 H22 RET sing 412 n n 
C3 C4 RET sing 413 n n 
C3 H31 RET sing 414 n n 
C3 H32 RET sing 415 n n 
C4 C5 RET sing 416 n n 
C4 H41 RET sing 417 n n 
C4 H42 RET sing 418 n n 
C5 C6 RET doub 419 n n 
C5 C18 RET sing 420 n n 
C6 C7 RET sing 421 n n 
C7 C8 RET doub 422 e n 
C7 H7 RET sing 423 n n 
C8 C9 RET sing 424 n n 
C8 H8 RET sing 425 n n 
C9 C10 RET doub 426 e n 
C9 C19 RET sing 427 n n 
C10 C11 RET sing 428 n n 
C10 H10 RET sing 429 n n 
C11 C12 RET doub 430 e n 
C11 H11 RET sing 431 n n 
C12 C13 RET sing 432 n n 
C12 H12 RET sing 433 n n 
C13 C14 RET doub 434 e n 
C13 C20 RET sing 435 n n 
C14 C15 RET sing 436 n n 
C14 H14 RET sing 437 n n 
C15 O1 RET doub 438 n n 
C15 H15 RET sing 439 n n 
C16 H161 RET sing 440 n n 
C16 H162 RET sing 441 n n 
C16 H163 RET sing 442 n n 
C17 H171 RET sing 443 n n 
C17 H172 RET sing 444 n n 
C17 H173 RET sing 445 n n 
C18 H181 RET sing 446 n n 
C18 H182 RET sing 447 n n 
C18 H183 RET sing 448 n n 
C19 H191 RET sing 449 n n 
C19 H192 RET sing 450 n n 
C19 H193 RET sing 451 n n 
C20 H201 RET sing 452 n n 
C20 H202 RET sing 453 n n 
C20 H203 RET sing 454 n n 
#
_atom_sites.entry_id                     3QBK 
_atom_sites.fract_transf_matrix[1][1]    0.006572 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005098 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010028 
_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]    0.01266 
_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
D 2 RET A 1 292 292 RET RET . 
E 3 22B A 1 300 300 22B 22B . 
F 4 BR A 1 401 401 BR BR . 
G 4 BR A 1 402 402 BR BR . 
H 4 BR A 1 293 293 BR BR . 
I 2 RET B 1 292 292 RET RET . 
J 3 22B B 1 300 300 22B 22B . 
K 4 BR B 1 401 401 BR BR . 
L 2 RET D 1 292 292 RET RET . 
M 4 BR D 1 402 402 BR BR . 
N 4 BR D 1 401 401 BR BR . 
O 5 HOH A 1 501 501 HOH HOH . 
O 5 HOH A 2 502 502 HOH HOH . 
O 5 HOH A 3 503 503 HOH HOH . 
O 5 HOH A 4 504 504 HOH HOH . 
O 5 HOH A 5 505 505 HOH HOH . 
O 5 HOH A 6 506 506 HOH HOH . 
O 5 HOH A 7 507 507 HOH HOH . 
O 5 HOH A 8 508 508 HOH HOH . 
O 5 HOH A 9 509 509 HOH HOH . 
O 5 HOH A 10 510 510 HOH HOH . 
O 5 HOH A 11 511 511 HOH HOH . 
O 5 HOH A 12 512 512 HOH HOH . 
O 5 HOH A 13 513 513 HOH HOH . 
O 5 HOH A 14 514 514 HOH HOH . 
O 5 HOH A 15 515 515 HOH HOH . 
O 5 HOH A 16 516 516 HOH HOH . 
O 5 HOH A 17 517 517 HOH HOH . 
O 5 HOH A 18 518 518 HOH HOH . 
O 5 HOH A 19 519 519 HOH HOH . 
O 5 HOH A 20 520 520 HOH HOH . 
O 5 HOH A 21 521 521 HOH HOH . 
O 5 HOH A 22 522 522 HOH HOH . 
O 5 HOH A 23 523 523 HOH HOH . 
O 5 HOH A 24 524 524 HOH HOH . 
O 5 HOH A 25 525 525 HOH HOH . 
O 5 HOH A 26 526 526 HOH HOH . 
O 5 HOH A 27 527 527 HOH HOH . 
O 5 HOH A 28 528 528 HOH HOH . 
O 5 HOH A 29 529 529 HOH HOH . 
O 5 HOH A 30 530 530 HOH HOH . 
O 5 HOH A 31 531 531 HOH HOH . 
O 5 HOH A 32 532 532 HOH HOH . 
O 5 HOH A 33 533 533 HOH HOH . 
O 5 HOH A 34 534 534 HOH HOH . 
O 5 HOH A 35 535 535 HOH HOH . 
O 5 HOH A 36 536 536 HOH HOH . 
O 5 HOH A 37 537 537 HOH HOH . 
O 5 HOH A 38 538 538 HOH HOH . 
O 5 HOH A 39 539 539 HOH HOH . 
O 5 HOH A 40 540 540 HOH HOH . 
O 5 HOH A 41 541 541 HOH HOH . 
O 5 HOH A 42 542 542 HOH HOH . 
O 5 HOH A 43 543 543 HOH HOH . 
O 5 HOH A 44 544 544 HOH HOH . 
O 5 HOH A 45 545 545 HOH HOH . 
O 5 HOH A 46 546 546 HOH HOH . 
O 5 HOH A 47 547 547 HOH HOH . 
O 5 HOH A 48 548 548 HOH HOH . 
O 5 HOH A 49 549 549 HOH HOH . 
O 5 HOH A 50 552 552 HOH HOH . 
O 5 HOH A 51 565 565 HOH HOH . 
O 5 HOH A 52 600 600 HOH HOH . 
P 5 HOH B 1 501 501 HOH HOH . 
P 5 HOH B 2 502 502 HOH HOH . 
P 5 HOH B 3 503 503 HOH HOH . 
P 5 HOH B 4 504 504 HOH HOH . 
P 5 HOH B 5 505 505 HOH HOH . 
P 5 HOH B 6 506 506 HOH HOH . 
P 5 HOH B 7 507 507 HOH HOH . 
P 5 HOH B 8 508 508 HOH HOH . 
P 5 HOH B 9 509 509 HOH HOH . 
P 5 HOH B 10 510 510 HOH HOH . 
P 5 HOH B 11 511 511 HOH HOH . 
P 5 HOH B 12 512 512 HOH HOH . 
P 5 HOH B 13 513 513 HOH HOH . 
P 5 HOH B 14 514 514 HOH HOH . 
P 5 HOH B 15 515 515 HOH HOH . 
P 5 HOH B 16 516 516 HOH HOH . 
P 5 HOH B 17 517 517 HOH HOH . 
P 5 HOH B 18 518 518 HOH HOH . 
P 5 HOH B 19 519 519 HOH HOH . 
P 5 HOH B 20 520 520 HOH HOH . 
P 5 HOH B 21 521 521 HOH HOH . 
P 5 HOH B 22 522 522 HOH HOH . 
P 5 HOH B 23 523 523 HOH HOH . 
P 5 HOH B 24 524 524 HOH HOH . 
P 5 HOH B 25 525 525 HOH HOH . 
P 5 HOH B 26 526 526 HOH HOH . 
P 5 HOH B 27 527 527 HOH HOH . 
P 5 HOH B 28 528 528 HOH HOH . 
P 5 HOH B 29 529 529 HOH HOH . 
P 5 HOH B 30 530 530 HOH HOH . 
P 5 HOH B 31 531 531 HOH HOH . 
P 5 HOH B 32 532 532 HOH HOH . 
P 5 HOH B 33 533 533 HOH HOH . 
P 5 HOH B 34 534 534 HOH HOH . 
P 5 HOH B 35 535 535 HOH HOH . 
P 5 HOH B 36 536 536 HOH HOH . 
P 5 HOH B 37 537 537 HOH HOH . 
P 5 HOH B 38 538 538 HOH HOH . 
P 5 HOH B 39 539 539 HOH HOH . 
P 5 HOH B 40 540 540 HOH HOH . 
P 5 HOH B 41 541 541 HOH HOH . 
P 5 HOH B 42 542 542 HOH HOH . 
P 5 HOH B 43 543 543 HOH HOH . 
P 5 HOH B 44 544 544 HOH HOH . 
P 5 HOH B 45 545 545 HOH HOH . 
P 5 HOH B 46 546 546 HOH HOH . 
P 5 HOH B 47 547 547 HOH HOH . 
P 5 HOH B 48 548 548 HOH HOH . 
P 5 HOH B 49 549 549 HOH HOH . 
P 5 HOH B 50 550 550 HOH HOH . 
P 5 HOH B 51 551 551 HOH HOH . 
P 5 HOH B 52 552 552 HOH HOH . 
P 5 HOH B 53 553 553 HOH HOH . 
P 5 HOH B 54 554 554 HOH HOH . 
P 5 HOH B 55 555 555 HOH HOH . 
P 5 HOH B 56 556 556 HOH HOH . 
P 5 HOH B 57 557 557 HOH HOH . 
P 5 HOH B 58 558 558 HOH HOH . 
P 5 HOH B 59 559 559 HOH HOH . 
P 5 HOH B 60 560 560 HOH HOH . 
P 5 HOH B 61 561 561 HOH HOH . 
P 5 HOH B 62 562 562 HOH HOH . 
P 5 HOH B 63 563 563 HOH HOH . 
P 5 HOH B 64 564 564 HOH HOH . 
P 5 HOH B 65 565 551 HOH HOH . 
Q 5 HOH D 1 501 501 HOH HOH . 
Q 5 HOH D 2 502 502 HOH HOH . 
Q 5 HOH D 3 503 503 HOH HOH . 
Q 5 HOH D 4 504 504 HOH HOH . 
Q 5 HOH D 5 505 505 HOH HOH . 
Q 5 HOH D 6 506 506 HOH HOH . 
Q 5 HOH D 7 507 507 HOH HOH . 
Q 5 HOH D 8 508 508 HOH HOH . 
Q 5 HOH D 9 509 509 HOH HOH . 
Q 5 HOH D 10 510 510 HOH HOH . 
Q 5 HOH D 11 511 511 HOH HOH . 
Q 5 HOH D 12 512 512 HOH HOH . 
Q 5 HOH D 13 515 515 HOH HOH . 
Q 5 HOH D 14 516 516 HOH HOH . 
Q 5 HOH D 15 517 517 HOH HOH . 
Q 5 HOH D 16 518 518 HOH HOH . 
Q 5 HOH D 17 520 520 HOH HOH . 
Q 5 HOH D 18 521 521 HOH HOH . 
Q 5 HOH D 19 522 522 HOH HOH . 
Q 5 HOH D 20 523 523 HOH HOH . 
Q 5 HOH D 21 525 525 HOH HOH . 
Q 5 HOH D 22 529 529 HOH HOH . 
Q 5 HOH D 23 530 530 HOH HOH . 
Q 5 HOH D 24 531 531 HOH HOH . 
Q 5 HOH D 25 532 532 HOH HOH . 
Q 5 HOH D 26 536 536 HOH HOH . 
Q 5 HOH D 27 539 539 HOH HOH . 
Q 5 HOH D 28 540 540 HOH HOH . 
Q 5 HOH D 29 543 543 HOH HOH . 
Q 5 HOH D 30 544 544 HOH HOH . 
Q 5 HOH D 31 545 545 HOH HOH . 
Q 5 HOH D 32 547 547 HOH HOH . 
Q 5 HOH D 33 552 552 HOH HOH . 
Q 5 HOH D 34 553 553 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 . . . L 2 10.325 -4.909 32.967 1 44.72 ? C1 RET 292 D 1 
HETATM 2 C C2 RET . . . L 2 10.817 -6.077 33.899 1 43.53 ? C2 RET 292 D 1 
HETATM 3 C C3 RET . . . L 2 11.791 -5.798 34.949 1 43.51 ? C3 RET 292 D 1 
HETATM 4 C C4 RET . . . L 2 11.571 -4.512 35.719 1 40.42 ? C4 RET 292 D 1 
HETATM 5 C C5 RET . . . L 2 11.01 -3.347 34.92 1 42.13 ? C5 RET 292 D 1 
HETATM 6 C C6 RET . . . L 2 10.437 -3.451 33.642 1 42.99 ? C6 RET 292 D 1 
HETATM 7 C C7 RET . . . L 2 9.958 -2.123 32.999 1 42.5 ? C7 RET 292 D 1 
HETATM 8 C C8 RET . . . L 2 9.438 -1.867 31.773 1 41.67 ? C8 RET 292 D 1 
HETATM 9 C C9 RET . . . L 2 8.857 -0.612 31.299 1 41.82 ? C9 RET 292 D 1 
HETATM 10 C C10 RET . . . L 2 8.402 -0.618 30.005 1 42.59 ? C10 RET 292 D 1 
HETATM 11 C C11 RET . . . L 2 7.715 0.44 29.273 1 43.36 ? C11 RET 292 D 1 
HETATM 12 C C12 RET . . . L 2 7.343 0.204 28.008 1 43 ? C12 RET 292 D 1 
HETATM 13 C C13 RET . . . L 2 6.614 1.087 27.075 1 43.04 ? C13 RET 292 D 1 
HETATM 14 C C14 RET . . . L 2 6.452 0.577 25.824 1 43.76 ? C14 RET 292 D 1 
HETATM 15 C C15 RET . . . L 2 5.905 1.167 24.6 1 46.7 ? C15 RET 292 D 1 
HETATM 16 C C16 RET . . . L 2 11.213 -5.11 31.709 1 44.54 ? C16 RET 292 D 1 
HETATM 17 C C17 RET . . . L 2 8.878 -5.274 32.587 1 42.94 ? C17 RET 292 D 1 
HETATM 18 C C18 RET . . . L 2 11.197 -2.039 35.687 1 40.71 ? C18 RET 292 D 1 
HETATM 19 C C19 RET . . . L 2 8.685 0.583 32.221 1 40.88 ? C19 RET 292 D 1 
HETATM 20 C C20 RET . . . L 2 6.13 2.467 27.477 1 42.3 ? C20 RET 292 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           20 
#