data_3VI0
#
_model_server_result.job_id            5oDPk4bwR4_867qu8jbUrA 
_model_server_result.datetime_utc      '2024-11-28 05:19:54' 
_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          3vi0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    3VI0 
#
_exptl.entry_id    3VI0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.436 
_entity.id                          3 
_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            3VI0 
_cell.length_a            102.3 
_cell.length_b            102.3 
_cell.length_c            112.3 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VI0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        177 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 6 2 2' 
#
_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 
_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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.3 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.15 88.594399 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 2 2 1 MAN GLC C1 O1 . O2 HO2 . sing 
2 ? 2 3 2 SGA MAN C1 O1 . O6 HO6 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n B GLC 1 B 1 GLC ? 400 GLC 
2 n B MAN 2 B 2 MAN ? 410 MAN 
2 n B SGA 3 B 3 SGA ? 420 SGA 
#
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 229 A LYS 216 1_555 C C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? 
covale ? covale2 E O3 L2P . A L2P 303 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 SGA . B SGA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
#
_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 424 n n 
C1 C6 RET sing 425 n n 
C1 C16 RET sing 426 n n 
C1 C17 RET sing 427 n n 
C2 C3 RET sing 428 n n 
C2 H21 RET sing 429 n n 
C2 H22 RET sing 430 n n 
C3 C4 RET sing 431 n n 
C3 H31 RET sing 432 n n 
C3 H32 RET sing 433 n n 
C4 C5 RET sing 434 n n 
C4 H41 RET sing 435 n n 
C4 H42 RET sing 436 n n 
C5 C6 RET doub 437 n n 
C5 C18 RET sing 438 n n 
C6 C7 RET sing 439 n n 
C7 C8 RET doub 440 e n 
C7 H7 RET sing 441 n n 
C8 C9 RET sing 442 n n 
C8 H8 RET sing 443 n n 
C9 C10 RET doub 444 e n 
C9 C19 RET sing 445 n n 
C10 C11 RET sing 446 n n 
C10 H10 RET sing 447 n n 
C11 C12 RET doub 448 e n 
C11 H11 RET sing 449 n n 
C12 C13 RET sing 450 n n 
C12 H12 RET sing 451 n n 
C13 C14 RET doub 452 e n 
C13 C20 RET sing 453 n n 
C14 C15 RET sing 454 n n 
C14 H14 RET sing 455 n n 
C15 O1 RET doub 456 n n 
C15 H15 RET sing 457 n n 
C16 H161 RET sing 458 n n 
C16 H162 RET sing 459 n n 
C16 H163 RET sing 460 n n 
C17 H171 RET sing 461 n n 
C17 H172 RET sing 462 n n 
C17 H173 RET sing 463 n n 
C18 H181 RET sing 464 n n 
C18 H182 RET sing 465 n n 
C18 H183 RET sing 466 n n 
C19 H191 RET sing 467 n n 
C19 H192 RET sing 468 n n 
C19 H193 RET sing 469 n n 
C20 H201 RET sing 470 n n 
C20 H202 RET sing 471 n n 
C20 H203 RET sing 472 n n 
#
_atom_sites.entry_id                     3VI0 
_atom_sites.fract_transf_matrix[1][1]    0.009775 
_atom_sites.fract_transf_matrix[1][2]    0.005644 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011287 
_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]    0.008905 
_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 3 RET A 1 301 250 RET RET . 
D 4 SOG A 1 302 430 SOG SOG . 
E 5 L2P A 1 303 270 L2P L2P . 
F 6 HOH A 1 401 600 HOH HOH . 
F 6 HOH A 2 402 601 HOH HOH . 
F 6 HOH A 3 403 604 HOH HOH . 
F 6 HOH A 4 404 605 HOH HOH . 
F 6 HOH A 5 405 606 HOH HOH . 
F 6 HOH A 6 406 607 HOH HOH . 
F 6 HOH A 7 407 608 HOH HOH . 
F 6 HOH A 8 408 609 HOH HOH . 
F 6 HOH A 9 409 610 HOH HOH . 
F 6 HOH A 10 410 611 HOH HOH . 
F 6 HOH A 11 411 612 HOH HOH . 
F 6 HOH A 12 412 613 HOH HOH . 
F 6 HOH A 13 413 614 HOH HOH . 
F 6 HOH A 14 414 617 HOH HOH . 
F 6 HOH A 15 415 618 HOH HOH . 
F 6 HOH A 16 416 619 HOH HOH . 
F 6 HOH A 17 417 621 HOH HOH . 
F 6 HOH A 18 418 622 HOH HOH . 
F 6 HOH A 19 419 623 HOH HOH . 
F 6 HOH A 20 420 624 HOH HOH . 
F 6 HOH A 21 421 625 HOH HOH . 
F 6 HOH A 22 422 626 HOH HOH . 
F 6 HOH A 23 423 629 HOH HOH . 
F 6 HOH A 24 424 630 HOH HOH . 
F 6 HOH A 25 425 633 HOH HOH . 
F 6 HOH A 26 426 636 HOH HOH . 
F 6 HOH A 27 427 701 HOH HOH . 
F 6 HOH A 28 428 703 HOH HOH . 
F 6 HOH A 29 429 704 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 . . . C 3 39.173 16.236 21.623 1 31 ? C1 RET 301 A 1 
HETATM 2 C C2 RET . . . C 3 39.879 15.392 20.458 1 31.08 ? C2 RET 301 A 1 
HETATM 3 C C3 RET . . . C 3 39.442 13.948 20.469 1 31.33 ? C3 RET 301 A 1 
HETATM 4 C C4 RET . . . C 3 39.941 13.264 21.744 1 30.36 ? C4 RET 301 A 1 
HETATM 5 C C5 RET . . . C 3 39.416 13.975 22.991 1 29.55 ? C5 RET 301 A 1 
HETATM 6 C C6 RET . . . C 3 39.025 15.397 22.962 1 30.24 ? C6 RET 301 A 1 
HETATM 7 C C7 RET . . . C 3 38.413 15.996 24.259 1 30.02 ? C7 RET 301 A 1 
HETATM 8 C C8 RET . . . C 3 37.92 17.266 24.414 1 29.73 ? C8 RET 301 A 1 
HETATM 9 C C9 RET . . . C 3 37.267 17.712 25.642 1 29.81 ? C9 RET 301 A 1 
HETATM 10 C C10 RET . . . C 3 36.781 19.014 25.659 1 30.68 ? C10 RET 301 A 1 
HETATM 11 C C11 RET . . . C 3 36.044 19.603 26.777 1 31.34 ? C11 RET 301 A 1 
HETATM 12 C C12 RET . . . C 3 35.677 20.923 26.705 1 32.3 ? C12 RET 301 A 1 
HETATM 13 C C13 RET . . . C 3 34.824 21.58 27.764 1 32.72 ? C13 RET 301 A 1 
HETATM 14 C C14 RET . . . C 3 34.447 22.915 27.658 1 33.74 ? C14 RET 301 A 1 
HETATM 15 C C15 RET . . . C 3 34.979 23.831 26.632 1 35.65 ? C15 RET 301 A 1 
HETATM 16 C C16 RET . . . C 3 40.018 17.508 21.83 1 30.39 ? C16 RET 301 A 1 
HETATM 17 C C17 RET . . . C 3 37.79 16.653 21.079 1 30.86 ? C17 RET 301 A 1 
HETATM 18 C C18 RET . . . C 3 39.286 13.142 24.262 1 28.99 ? C18 RET 301 A 1 
HETATM 19 C C19 RET . . . C 3 37.127 16.742 26.819 1 29.56 ? C19 RET 301 A 1 
HETATM 20 C C20 RET . . . C 3 34.316 20.755 28.935 1 33.06 ? C20 RET 301 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           20 
#