data_5EN0 # _model_server_result.job_id -ghg3ovg8mbV63RbRHMAiA _model_server_result.datetime_utc '2025-07-09 17:43:29' _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 5en0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5EN0 # _exptl.entry_id 5EN0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation 'N2C, T94I, D282C' _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 5EN0 _cell.length_a 242.269 _cell.length_b 242.269 _cell.length_c 111.147 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EN0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . 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 3 n C NAG 1 C 1 NAG S 301 NAG 3 n C NAG 2 C 2 NAG S 302 NAG 3 n C BMA 3 C 3 BMA S 303 BMA 3 n C MAN 4 C 4 MAN S 304 MAN # 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 disulf ? disulf1 A SG CYS 3 A CYS 2 1_555 A SG CYS 283 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 A NZ LYS 297 A LYS 296 1_555 D C15 RET . A RET 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.277 ? covale ? covale4 A SG CYS 323 A CYS 322 1_555 H C1 PLM . A PLM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? covale ? covale5 A SG CYS 324 A CYS 323 1_555 I C1 PLM . A PLM 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.659 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale8 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? # _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 464 n n C1 C6 RET sing 465 n n C1 C16 RET sing 466 n n C1 C17 RET sing 467 n n C2 C3 RET sing 468 n n C2 H21 RET sing 469 n n C2 H22 RET sing 470 n n C3 C4 RET sing 471 n n C3 H31 RET sing 472 n n C3 H32 RET sing 473 n n C4 C5 RET sing 474 n n C4 H41 RET sing 475 n n C4 H42 RET sing 476 n n C5 C6 RET doub 477 n n C5 C18 RET sing 478 n n C6 C7 RET sing 479 n n C7 C8 RET doub 480 e n C7 H7 RET sing 481 n n C8 C9 RET sing 482 n n C8 H8 RET sing 483 n n C9 C10 RET doub 484 e n C9 C19 RET sing 485 n n C10 C11 RET sing 486 n n C10 H10 RET sing 487 n n C11 C12 RET doub 488 e n C11 H11 RET sing 489 n n C12 C13 RET sing 490 n n C12 H12 RET sing 491 n n C13 C14 RET doub 492 e n C13 C20 RET sing 493 n n C14 C15 RET sing 494 n n C14 H14 RET sing 495 n n C15 O1 RET doub 496 n n C15 H15 RET sing 497 n n C16 H161 RET sing 498 n n C16 H162 RET sing 499 n n C16 H163 RET sing 500 n n C17 H171 RET sing 501 n n C17 H172 RET sing 502 n n C17 H173 RET sing 503 n n C18 H181 RET sing 504 n n C18 H182 RET sing 505 n n C18 H183 RET sing 506 n n C19 H191 RET sing 507 n n C19 H192 RET sing 508 n n C19 H193 RET sing 509 n n C20 H201 RET sing 510 n n C20 H202 RET sing 511 n n C20 H203 RET sing 512 n n # _atom_sites.entry_id 5EN0 _atom_sites.fract_transf_matrix[1][1] 0.004128 _atom_sites.fract_transf_matrix[1][2] 0.002383 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004766 _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] 0.008997 _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 4 RET A 1 401 401 RET RET . E 5 ACT A 1 402 102 ACT ACT . F 5 ACT A 1 403 103 ACT ACT . G 6 BOG A 1 404 204 BOG BOG . H 7 PLM A 1 405 205 PLM PLM . I 7 PLM A 1 406 206 PLM PLM . J 6 BOG A 1 411 601 BOG BOG . K 8 SO4 A 1 412 801 SO4 SO4 . L 9 HOH A 1 501 41 HOH HOH . L 9 HOH A 2 502 3 HOH HOH . L 9 HOH A 3 503 43 HOH HOH . L 9 HOH A 4 504 21 HOH HOH . L 9 HOH A 5 505 44 HOH HOH . L 9 HOH A 6 506 5 HOH HOH . L 9 HOH A 7 507 4 HOH HOH . L 9 HOH A 8 508 8 HOH HOH . L 9 HOH A 9 509 45 HOH HOH . L 9 HOH A 10 510 1 HOH HOH . L 9 HOH A 11 511 35 HOH HOH . L 9 HOH A 12 512 19 HOH HOH . L 9 HOH A 13 513 27 HOH HOH . L 9 HOH A 14 514 10 HOH HOH . L 9 HOH A 15 515 39 HOH HOH . L 9 HOH A 16 516 40 HOH HOH . L 9 HOH A 17 517 12 HOH HOH . L 9 HOH A 18 518 13 HOH HOH . L 9 HOH A 19 519 46 HOH HOH . L 9 HOH A 20 520 18 HOH HOH . L 9 HOH A 21 521 20 HOH HOH . L 9 HOH A 22 522 7 HOH HOH . L 9 HOH A 23 523 11 HOH HOH . L 9 HOH A 24 524 32 HOH HOH . L 9 HOH A 25 525 23 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 . . . D 4 -43.281 -16.648 34.526 1 109.17 ? C1 RET 401 A 1 HETATM 2 C C2 RET . . . D 4 -43.614 -18.109 34.87 1 93.34 ? C2 RET 401 A 1 HETATM 3 C C3 RET . . . D 4 -44.698 -18.644 33.938 1 92.14 ? C3 RET 401 A 1 HETATM 4 C C4 RET . . . D 4 -45.994 -17.858 34.125 1 91.73 ? C4 RET 401 A 1 HETATM 5 C C5 RET . . . D 4 -45.791 -16.355 34.092 1 100.4 ? C5 RET 401 A 1 HETATM 6 C C6 RET . . . D 4 -44.582 -15.808 34.368 1 117.88 ? C6 RET 401 A 1 HETATM 7 C C7 RET . . . D 4 -44.473 -14.323 34.361 1 118.61 ? C7 RET 401 A 1 HETATM 8 C C8 RET . . . D 4 -45.119 -13.588 35.277 1 111.4 ? C8 RET 401 A 1 HETATM 9 C C9 RET . . . D 4 -44.929 -12.12 35.411 1 105.19 ? C9 RET 401 A 1 HETATM 10 C C10 RET . . . D 4 -45.804 -11.531 36.251 1 96.56 ? C10 RET 401 A 1 HETATM 11 C C11 RET . . . D 4 -45.683 -10.151 36.696 1 86.77 ? C11 RET 401 A 1 HETATM 12 C C12 RET . . . D 4 -46.513 -9.78 37.654 1 85.12 ? C12 RET 401 A 1 HETATM 13 C C13 RET . . . D 4 -46.278 -8.522 38.366 1 93.63 ? C13 RET 401 A 1 HETATM 14 C C14 RET . . . D 4 -47.25 -8.183 39.239 1 95.33 ? C14 RET 401 A 1 HETATM 15 C C15 RET . . . D 4 -47.164 -6.98 40.081 1 88.46 ? C15 RET 401 A 1 HETATM 16 C C16 RET . . . D 4 -42.418 -16.567 33.257 1 109.72 ? C16 RET 401 A 1 HETATM 17 C C17 RET . . . D 4 -42.423 -16.092 35.668 1 109.34 ? C17 RET 401 A 1 HETATM 18 C C18 RET . . . D 4 -47.015 -15.489 33.931 1 94.26 ? C18 RET 401 A 1 HETATM 19 C C19 RET . . . D 4 -43.788 -11.381 34.724 1 94.75 ? C19 RET 401 A 1 HETATM 20 C C20 RET . . . D 4 -44.886 -7.911 38.332 1 99.38 ? C20 RET 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 20 #