data_9F9B # _model_server_result.job_id WM59x860p6oM5jl4T9cp2g _model_server_result.datetime_utc '2025-01-22 17:08:13' _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 9f9b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":318}' # _entry.id 9F9B # _exptl.entry_id 9F9B _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 ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 9F9B _cell.length_a 62.58 _cell.length_b 62.58 _cell.length_c 111.81 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9F9B _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 _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 S _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 213 _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 S _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 318 _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 1.345 _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 437 n n C1 C6 RET sing 438 n n C1 C16 RET sing 439 n n C1 C17 RET sing 440 n n C2 C3 RET sing 441 n n C2 H21 RET sing 442 n n C2 H22 RET sing 443 n n C3 C4 RET sing 444 n n C3 H31 RET sing 445 n n C3 H32 RET sing 446 n n C4 C5 RET sing 447 n n C4 H41 RET sing 448 n n C4 H42 RET sing 449 n n C5 C6 RET doub 450 n n C5 C18 RET sing 451 n n C6 C7 RET sing 452 n n C7 C8 RET doub 453 e n C7 H7 RET sing 454 n n C8 C9 RET sing 455 n n C8 H8 RET sing 456 n n C9 C10 RET doub 457 e n C9 C19 RET sing 458 n n C10 C11 RET sing 459 n n C10 H10 RET sing 460 n n C11 C12 RET doub 461 e n C11 H11 RET sing 462 n n C12 C13 RET sing 463 n n C12 H12 RET sing 464 n n C13 C14 RET doub 465 e n C13 C20 RET sing 466 n n C14 C15 RET sing 467 n n C14 H14 RET sing 468 n n C15 O1 RET doub 469 n n C15 H15 RET sing 470 n n C16 H161 RET sing 471 n n C16 H162 RET sing 472 n n C16 H163 RET sing 473 n n C17 H171 RET sing 474 n n C17 H172 RET sing 475 n n C17 H173 RET sing 476 n n C18 H181 RET sing 477 n n C18 H182 RET sing 478 n n C18 H183 RET sing 479 n n C19 H191 RET sing 480 n n C19 H192 RET sing 481 n n C19 H193 RET sing 482 n n C20 H201 RET sing 483 n n C20 H202 RET sing 484 n n C20 H203 RET sing 485 n n # _atom_sites.entry_id 9F9B _atom_sites.fract_transf_matrix[1][1] 0.01598 _atom_sites.fract_transf_matrix[1][2] 0.009226 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018452 _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] 0.008944 _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 LI1 A 1 301 303 LI1 LI1 . C 2 LI1 A 1 302 305 LI1 LI1 . D 2 LI1 A 1 303 306 LI1 LI1 . E 2 LI1 A 1 304 307 LI1 LI1 . F 2 LI1 A 1 305 308 LI1 LI1 . G 3 OLC A 1 306 309 OLC OLC . H 3 OLC A 1 307 310 OLC OLC . I 3 OLC A 1 308 311 OLC OLC . J 3 OLC A 1 309 312 OLC OLC . K 2 LI1 A 1 310 313 LI1 LI1 . L 2 LI1 A 1 311 314 LI1 LI1 . M 2 LI1 A 1 312 315 LI1 LI1 . N 2 LI1 A 1 313 316 LI1 LI1 . O 2 LI1 A 1 314 317 LI1 LI1 . P 2 LI1 A 1 315 318 LI1 LI1 . Q 2 LI1 A 1 316 319 LI1 LI1 . R 2 LI1 A 1 317 320 LI1 LI1 . S 4 RET A 1 318 216 RET LYR . T 5 HOH A 1 401 432 HOH HOH . T 5 HOH A 2 402 479 HOH HOH . T 5 HOH A 3 403 403 HOH HOH . T 5 HOH A 4 404 441 HOH HOH . T 5 HOH A 5 405 434 HOH HOH . T 5 HOH A 6 406 402 HOH HOH . T 5 HOH A 7 407 412 HOH HOH . T 5 HOH A 8 408 400 HOH HOH . T 5 HOH A 9 409 486 HOH HOH . T 5 HOH A 10 410 485 HOH HOH . T 5 HOH A 11 411 401 HOH HOH . T 5 HOH A 12 412 404 HOH HOH . T 5 HOH A 13 413 421 HOH HOH . T 5 HOH A 14 414 414 HOH HOH . T 5 HOH A 15 415 417 HOH HOH . T 5 HOH A 16 416 431 HOH HOH . T 5 HOH A 17 417 487 HOH HOH . T 5 HOH A 18 418 416 HOH HOH . T 5 HOH A 19 419 481 HOH HOH . T 5 HOH A 20 420 456 HOH HOH . T 5 HOH A 21 421 478 HOH HOH . T 5 HOH A 22 422 407 HOH HOH . T 5 HOH A 23 423 476 HOH HOH . T 5 HOH A 24 424 415 HOH HOH . T 5 HOH A 25 425 475 HOH HOH . T 5 HOH A 26 426 483 HOH HOH . T 5 HOH A 27 427 411 HOH HOH . T 5 HOH A 28 428 418 HOH HOH . T 5 HOH A 29 429 422 HOH HOH . T 5 HOH A 30 430 420 HOH HOH . T 5 HOH A 31 431 419 HOH HOH . T 5 HOH A 32 432 482 HOH HOH . T 5 HOH A 33 433 480 HOH HOH . T 5 HOH A 34 434 426 HOH HOH . T 5 HOH A 35 435 409 HOH HOH . T 5 HOH A 36 436 484 HOH HOH . T 5 HOH A 37 437 444 HOH HOH . T 5 HOH A 38 438 453 HOH HOH . T 5 HOH A 39 439 452 HOH HOH . T 5 HOH A 40 440 477 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 . . . S 4 15.089 46.443 29.763 1 38.93 ? C1 RET 318 A 1 HETATM 2 C C2 RET . . . S 4 14.62 47.356 28.625 1 42.64 ? C2 RET 318 A 1 HETATM 3 C C3 RET . . . S 4 15.26 48.718 28.611 1 45.3 ? C3 RET 318 A 1 HETATM 4 C C4 RET . . . S 4 15.027 49.44 29.933 1 36.14 ? C4 RET 318 A 1 HETATM 5 C C5 RET . . . S 4 15.251 48.578 31.132 1 34.02 ? C5 RET 318 A 1 HETATM 6 C C6 RET . . . S 4 15.395 47.231 31.057 1 25.35 ? C6 RET 318 A 1 HETATM 7 C C7 RET . . . S 4 15.858 46.481 32.251 1 29.15 ? C7 RET 318 A 1 HETATM 8 C C8 RET . . . S 4 15.982 45.193 32.448 1 31.3 ? C8 RET 318 A 1 HETATM 9 C C9 RET . . . S 4 16.478 44.495 33.626 1 27.35 ? C9 RET 318 A 1 HETATM 10 C C10 RET . . . S 4 16.655 43.161 33.555 1 30.98 ? C10 RET 318 A 1 HETATM 11 C C11 RET . . . S 4 17.193 42.284 34.567 1 30.18 ? C11 RET 318 A 1 HETATM 12 C C12 RET . . . S 4 17.327 40.98 34.324 1 29.43 ? C12 RET 318 A 1 HETATM 13 C C13 RET . . . S 4 17.791 39.953 35.234 1 32.98 ? C13 RET 318 A 1 HETATM 14 C C14 RET . . . S 4 17.83 38.684 34.778 1 32.81 ? C14 RET 318 A 1 HETATM 15 C C15 RET . . . S 4 17.671 37.488 35.53 1 28.02 ? C15 RET 318 A 1 HETATM 16 C C16 RET . . . S 4 16.311 45.632 29.315 1 38.55 ? C16 RET 318 A 1 HETATM 17 C C17 RET . . . S 4 13.9 45.496 29.958 1 32.4 ? C17 RET 318 A 1 HETATM 18 C C18 RET . . . S 4 15.259 49.352 32.434 1 31.19 ? C18 RET 318 A 1 HETATM 19 C C19 RET . . . S 4 16.843 45.299 34.836 1 30.45 ? C19 RET 318 A 1 HETATM 20 C C20 RET . . . S 4 18.076 40.337 36.67 1 28.43 ? C20 RET 318 A 1 HETATM 21 H H21 RET . . . S 4 14.795 46.929 27.762 1 51.11 ? H21 RET 318 A 1 HETATM 22 H H22 RET . . . S 4 13.65 47.478 28.676 1 51.11 ? H22 RET 318 A 1 HETATM 23 H H31 RET . . . S 4 14.897 49.253 27.875 1 54.31 ? H31 RET 318 A 1 HETATM 24 H H32 RET . . . S 4 16.222 48.636 28.446 1 54.31 ? H32 RET 318 A 1 HETATM 25 H H41 RET . . . S 4 14.11 49.781 29.962 1 43.31 ? H41 RET 318 A 1 HETATM 26 H H42 RET . . . S 4 15.621 50.216 29.992 1 43.31 ? H42 RET 318 A 1 HETATM 27 H H7 RET . . . S 4 16.403 47.052 32.83 1 34.92 ? H7 RET 318 A 1 HETATM 28 H H8 RET . . . S 4 16.094 44.674 31.625 1 37.51 ? H8 RET 318 A 1 HETATM 29 H H10 RET . . . S 4 16.392 42.718 32.722 1 37.12 ? H10 RET 318 A 1 HETATM 30 H H11 RET . . . S 4 17.76 42.675 35.263 1 36.17 ? H11 RET 318 A 1 HETATM 31 H H12 RET . . . S 4 17.086 40.673 33.426 1 35.27 ? H12 RET 318 A 1 HETATM 32 H H14 RET . . . S 4 17.982 38.517 33.826 1 39.31 ? H14 RET 318 A 1 HETATM 33 H H15 RET . . . S 4 17.628 37.573 36.504 1 33.56 ? H15 RET 318 A 1 HETATM 34 H H161 RET . . . S 4 16.338 45.518 28.343 1 46.2 ? H161 RET 318 A 1 HETATM 35 H H162 RET . . . S 4 17.151 46.064 29.575 1 46.2 ? H162 RET 318 A 1 HETATM 36 H H163 RET . . . S 4 16.319 44.735 29.708 1 46.2 ? H163 RET 318 A 1 HETATM 37 H H171 RET . . . S 4 13.128 45.976 30.322 1 38.83 ? H171 RET 318 A 1 HETATM 38 H H172 RET . . . S 4 14.127 44.773 30.579 1 38.83 ? H172 RET 318 A 1 HETATM 39 H H173 RET . . . S 4 13.632 45.091 29.108 1 38.83 ? H173 RET 318 A 1 HETATM 40 H H181 RET . . . S 4 14.716 50.166 32.413 1 37.37 ? H181 RET 318 A 1 HETATM 41 H H182 RET . . . S 4 16.15 49.651 32.71 1 37.37 ? H182 RET 318 A 1 HETATM 42 H H183 RET . . . S 4 14.919 48.843 33.198 1 37.37 ? H183 RET 318 A 1 HETATM 43 H H191 RET . . . S 4 17.674 45.793 34.678 1 36.49 ? H191 RET 318 A 1 HETATM 44 H H192 RET . . . S 4 16.133 45.94 35.045 1 36.49 ? H192 RET 318 A 1 HETATM 45 H H193 RET . . . S 4 16.971 44.711 35.608 1 36.49 ? H193 RET 318 A 1 HETATM 46 H H201 RET . . . S 4 17.436 41.004 36.993 1 34.06 ? H201 RET 318 A 1 HETATM 47 H H202 RET . . . S 4 18.02 39.561 37.264 1 34.06 ? H202 RET 318 A 1 HETATM 48 H H203 RET . . . S 4 18.973 40.719 36.765 1 34.06 ? H203 RET 318 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 48 #