data_3DDL
#
_model_server_result.job_id            mC6Q50ZVvpMIOgMCqLmxDg 
_model_server_result.datetime_utc      '2024-11-23 12:59:58' 
_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          3ddl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1301}' 
#
_entry.id    3DDL 
#
_exptl.entry_id    3DDL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.436 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RETINAL 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         76.35 
_cell.angle_beta          74.93 
_cell.angle_gamma         64.08 
_cell.entry_id            3DDL 
_cell.length_a            52.74 
_cell.length_b            59.49 
_cell.length_c            59.72 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DDL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,K,L,DA 1 1 
B,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,EA 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
? 4 L N N 
? 4 AA 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 240 A LYS 240 1_555 L C15 RET . A RET 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? 
covale ? covale2 B NZ LYS 240 B LYS 240 1_555 AA C15 RET . B RET 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
#
_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 520 n n 
C1 C6 RET sing 521 n n 
C1 C16 RET sing 522 n n 
C1 C17 RET sing 523 n n 
C2 C3 RET sing 524 n n 
C2 H21 RET sing 525 n n 
C2 H22 RET sing 526 n n 
C3 C4 RET sing 527 n n 
C3 H31 RET sing 528 n n 
C3 H32 RET sing 529 n n 
C4 C5 RET sing 530 n n 
C4 H41 RET sing 531 n n 
C4 H42 RET sing 532 n n 
C5 C6 RET doub 533 n n 
C5 C18 RET sing 534 n n 
C6 C7 RET sing 535 n n 
C7 C8 RET doub 536 e n 
C7 H7 RET sing 537 n n 
C8 C9 RET sing 538 n n 
C8 H8 RET sing 539 n n 
C9 C10 RET doub 540 e n 
C9 C19 RET sing 541 n n 
C10 C11 RET sing 542 n n 
C10 H10 RET sing 543 n n 
C11 C12 RET doub 544 e n 
C11 H11 RET sing 545 n n 
C12 C13 RET sing 546 n n 
C12 H12 RET sing 547 n n 
C13 C14 RET doub 548 e n 
C13 C20 RET sing 549 n n 
C14 C15 RET sing 550 n n 
C14 H14 RET sing 551 n n 
C15 O1 RET doub 552 n n 
C15 H15 RET sing 553 n n 
C16 H161 RET sing 554 n n 
C16 H162 RET sing 555 n n 
C16 H163 RET sing 556 n n 
C17 H171 RET sing 557 n n 
C17 H172 RET sing 558 n n 
C17 H173 RET sing 559 n n 
C18 H181 RET sing 560 n n 
C18 H182 RET sing 561 n n 
C18 H183 RET sing 562 n n 
C19 H191 RET sing 563 n n 
C19 H192 RET sing 564 n n 
C19 H193 RET sing 565 n n 
C20 H201 RET sing 566 n n 
C20 H202 RET sing 567 n n 
C20 H203 RET sing 568 n n 
#
_atom_sites.entry_id                     3DDL 
_atom_sites.fract_transf_matrix[1][1]    0.018961 
_atom_sites.fract_transf_matrix[1][2]    -0.009215 
_atom_sites.fract_transf_matrix[1][3]    -0.003846 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01869 
_atom_sites.fract_transf_matrix[2][3]    -0.002659 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.017516 
_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
C 2 SXN A 1 1401 1401 SXN SXN . 
D 3 UNL A 1 1402 1402 UNL UNL . 
E 3 UNL A 1 1403 1403 UNL UNL . 
F 3 UNL A 1 1404 1404 UNL UNL . 
G 3 UNL A 1 1405 1405 UNL UNL . 
H 3 UNL A 1 1406 1406 UNL UNL . 
I 3 UNL A 1 1407 1407 UNL UNL . 
J 3 UNL A 1 1408 1408 UNL UNL . 
K 3 UNL A 1 1409 1409 UNL UNL . 
L 4 RET A 1 1301 1301 RET RET . 
M 2 SXN B 1 1401 1401 SXN SXN . 
N 3 UNL B 1 1402 1402 UNL UNL . 
O 3 UNL B 1 1403 1403 UNL UNL . 
P 3 UNL B 1 1404 1404 UNL UNL . 
Q 3 UNL B 1 1405 1405 UNL UNL . 
R 3 UNL B 1 1406 1406 UNL UNL . 
S 3 UNL B 1 1407 1407 UNL UNL . 
T 3 UNL B 1 1408 1408 UNL UNL . 
U 3 UNL B 1 1409 1409 UNL UNL . 
V 3 UNL B 1 1410 1410 UNL UNL . 
W 3 UNL B 1 1411 1411 UNL UNL . 
X 3 UNL B 1 1412 1412 UNL UNL . 
Y 3 UNL B 1 1413 1413 UNL UNL . 
Z 3 UNL B 1 1414 1414 UNL UNL . 
AA 4 RET B 1 1301 1301 RET RET . 
BA 5 PX4 B 1 1415 1415 PX4 PX4 . 
CA 6 PCW B 1 1416 1416 PCW PCW . 
DA 7 HOH A 1 402 402 HOH HOH . 
DA 7 HOH A 2 413 413 HOH HOH . 
DA 7 HOH A 3 414 414 HOH HOH . 
DA 7 HOH A 4 415 415 HOH HOH . 
DA 7 HOH A 5 416 416 HOH HOH . 
DA 7 HOH A 6 417 417 HOH HOH . 
DA 7 HOH A 7 418 418 HOH HOH . 
DA 7 HOH A 8 419 419 HOH HOH . 
DA 7 HOH A 9 420 420 HOH HOH . 
DA 7 HOH A 10 421 421 HOH HOH . 
DA 7 HOH A 11 422 422 HOH HOH . 
DA 7 HOH A 12 423 423 HOH HOH . 
DA 7 HOH A 13 424 424 HOH HOH . 
DA 7 HOH A 14 425 425 HOH HOH . 
DA 7 HOH A 15 426 426 HOH HOH . 
DA 7 HOH A 16 427 427 HOH HOH . 
DA 7 HOH A 17 428 428 HOH HOH . 
DA 7 HOH A 18 429 429 HOH HOH . 
DA 7 HOH A 19 430 430 HOH HOH . 
DA 7 HOH A 20 431 431 HOH HOH . 
DA 7 HOH A 21 432 432 HOH HOH . 
DA 7 HOH A 22 433 433 HOH HOH . 
DA 7 HOH A 23 434 434 HOH HOH . 
DA 7 HOH A 24 435 435 HOH HOH . 
DA 7 HOH A 25 436 436 HOH HOH . 
DA 7 HOH A 26 437 437 HOH HOH . 
DA 7 HOH A 27 438 438 HOH HOH . 
DA 7 HOH A 28 439 439 HOH HOH . 
DA 7 HOH A 29 440 440 HOH HOH . 
DA 7 HOH A 30 441 441 HOH HOH . 
DA 7 HOH A 31 442 442 HOH HOH . 
DA 7 HOH A 32 443 443 HOH HOH . 
DA 7 HOH A 33 501 501 HOH HOH . 
DA 7 HOH A 34 502 502 HOH HOH . 
EA 7 HOH B 1 402 402 HOH HOH . 
EA 7 HOH B 2 420 420 HOH HOH . 
EA 7 HOH B 3 421 421 HOH HOH . 
EA 7 HOH B 4 422 422 HOH HOH . 
EA 7 HOH B 5 423 423 HOH HOH . 
EA 7 HOH B 6 424 424 HOH HOH . 
EA 7 HOH B 7 425 425 HOH HOH . 
EA 7 HOH B 8 426 426 HOH HOH . 
EA 7 HOH B 9 427 427 HOH HOH . 
EA 7 HOH B 10 428 428 HOH HOH . 
EA 7 HOH B 11 429 429 HOH HOH . 
EA 7 HOH B 12 430 430 HOH HOH . 
EA 7 HOH B 13 431 431 HOH HOH . 
EA 7 HOH B 14 432 432 HOH HOH . 
EA 7 HOH B 15 433 433 HOH HOH . 
EA 7 HOH B 16 434 434 HOH HOH . 
EA 7 HOH B 17 435 435 HOH HOH . 
EA 7 HOH B 18 436 436 HOH HOH . 
EA 7 HOH B 19 437 437 HOH HOH . 
EA 7 HOH B 20 438 438 HOH HOH . 
EA 7 HOH B 21 439 439 HOH HOH . 
EA 7 HOH B 22 440 440 HOH HOH . 
EA 7 HOH B 23 441 441 HOH HOH . 
EA 7 HOH B 24 442 442 HOH HOH . 
EA 7 HOH B 25 443 443 HOH HOH . 
EA 7 HOH B 26 444 444 HOH HOH . 
EA 7 HOH B 27 501 501 HOH HOH . 
EA 7 HOH B 28 502 502 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 4 50.873 -0.913 48.035 1 35.36 ? C1 RET 1301 A 1 
HETATM 2 C C2 RET . . . L 4 50.309 -2.1 47.233 1 35.08 ? C2 RET 1301 A 1 
HETATM 3 C C3 RET . . . L 4 48.866 -2.422 47.481 1 37.08 ? C3 RET 1301 A 1 
HETATM 4 C C4 RET . . . L 4 48.563 -2.624 48.944 1 34.66 ? C4 RET 1301 A 1 
HETATM 5 C C5 RET . . . L 4 49.14 -1.537 49.873 1 36.73 ? C5 RET 1301 A 1 
HETATM 6 C C6 RET . . . L 4 50.165 -0.715 49.437 1 36.1 ? C6 RET 1301 A 1 
HETATM 7 C C7 RET . . . L 4 50.494 0.362 50.404 1 32.02 ? C7 RET 1301 A 1 
HETATM 8 C C8 RET . . . L 4 51.407 1.362 50.35 1 31.38 ? C8 RET 1301 A 1 
HETATM 9 C C9 RET . . . L 4 51.618 2.399 51.34 1 34.66 ? C9 RET 1301 A 1 
HETATM 10 C C10 RET . . . L 4 52.625 3.283 50.99 1 29.9 ? C10 RET 1301 A 1 
HETATM 11 C C11 RET . . . L 4 52.962 4.43 51.873 1 35.27 ? C11 RET 1301 A 1 
HETATM 12 C C12 RET . . . L 4 54.004 5.245 51.413 1 31.2 ? C12 RET 1301 A 1 
HETATM 13 C C13 RET . . . L 4 54.427 6.435 52.172 1 33.56 ? C13 RET 1301 A 1 
HETATM 14 C C14 RET . . . L 4 55.47 7.091 51.567 1 33.48 ? C14 RET 1301 A 1 
HETATM 15 C C15 RET . . . L 4 56.1 8.303 52.08 1 32.73 ? C15 RET 1301 A 1 
HETATM 16 C C16 RET . . . L 4 52.426 -1.162 48.224 1 35.55 ? C16 RET 1301 A 1 
HETATM 17 C C17 RET . . . L 4 50.651 0.31 47.024 1 31.74 ? C17 RET 1301 A 1 
HETATM 18 C C18 RET . . . L 4 48.368 -1.51 51.16 1 34.2 ? C18 RET 1301 A 1 
HETATM 19 C C19 RET . . . L 4 50.776 2.478 52.604 1 29.61 ? C19 RET 1301 A 1 
HETATM 20 C C20 RET . . . L 4 53.764 6.848 53.454 1 32.78 ? C20 RET 1301 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           28 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#