data_8R98 # _model_server_result.job_id yQy7oJJbUPPMEBDKyPa9ow _model_server_result.datetime_utc '2024-12-11 15:51:04' _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 8r98 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"IA","auth_seq_id":404}' # _entry.id 8R98 # _exptl.entry_id 8R98 _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 10 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.87 _cell.angle_gamma 90 _cell.entry_id 8R98 _cell.length_a 150.108 _cell.length_b 84.964 _cell.length_c 296.943 _cell.Z_PDB 40 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8R98 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 pentameric 5 author_and_software_defined_assembly 1 PISA pentameric 5 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,B,C,D,E,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA 1 1 F,G,H,I,J,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB 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 P N N ? 4 V N N ? 4 Z N N ? 4 EA N N ? 4 IA N N ? 4 MA N N ? 4 UA N N ? 4 ZA N N ? 4 DB N N ? 4 HB 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 242 A LYS 242 1_555 P C15 RET . A RET 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale2 B NZ LYS 242 B LYS 242 1_555 V C15 RET . B RET 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale3 C NZ LYS 242 C LYS 242 1_555 Z C15 RET . C RET 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale4 D NZ LYS 242 D LYS 242 1_555 EA C15 RET . D RET 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale5 E NZ LYS 242 E LYS 242 1_555 IA C15 RET . E RET 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale6 F NZ LYS 242 H LYS 242 1_555 MA C15 RET . H RET 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale7 G NZ LYS 242 G LYS 242 1_555 UA C15 RET . G RET 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale8 H NZ LYS 242 F LYS 242 1_555 ZA C15 RET . F RET 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale9 I NZ LYS 242 I LYS 242 1_555 DB C15 RET . I RET 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale10 J NZ LYS 242 K LYS 242 1_555 HB C15 RET . K RET 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? # _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 393 n n C1 C6 RET sing 394 n n C1 C16 RET sing 395 n n C1 C17 RET sing 396 n n C2 C3 RET sing 397 n n C2 H21 RET sing 398 n n C2 H22 RET sing 399 n n C3 C4 RET sing 400 n n C3 H31 RET sing 401 n n C3 H32 RET sing 402 n n C4 C5 RET sing 403 n n C4 H41 RET sing 404 n n C4 H42 RET sing 405 n n C5 C6 RET doub 406 n n C5 C18 RET sing 407 n n C6 C7 RET sing 408 n n C7 C8 RET doub 409 e n C7 H7 RET sing 410 n n C8 C9 RET sing 411 n n C8 H8 RET sing 412 n n C9 C10 RET doub 413 e n C9 C19 RET sing 414 n n C10 C11 RET sing 415 n n C10 H10 RET sing 416 n n C11 C12 RET doub 417 e n C11 H11 RET sing 418 n n C12 C13 RET sing 419 n n C12 H12 RET sing 420 n n C13 C14 RET doub 421 e n C13 C20 RET sing 422 n n C14 C15 RET sing 423 n n C14 H14 RET sing 424 n n C15 O1 RET doub 425 n n C15 H15 RET sing 426 n n C16 H161 RET sing 427 n n C16 H162 RET sing 428 n n C16 H163 RET sing 429 n n C17 H171 RET sing 430 n n C17 H172 RET sing 431 n n C17 H173 RET sing 432 n n C18 H181 RET sing 433 n n C18 H182 RET sing 434 n n C18 H183 RET sing 435 n n C19 H191 RET sing 436 n n C19 H192 RET sing 437 n n C19 H193 RET sing 438 n n C20 H201 RET sing 439 n n C20 H202 RET sing 440 n n C20 H203 RET sing 441 n n # _atom_sites.entry_id 8R98 _atom_sites.fract_transf_matrix[1][1] 0.006662 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000802 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01177 _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] 0.003392 _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 K 2 LFA A 1 401 401 LFA LFA . L 2 LFA A 1 402 401 LFA LFA . M 2 LFA A 1 403 11 LFA LFA . N 2 LFA A 1 404 12 LFA LFA . O 3 PO4 A 1 405 2 PO4 PO4 . P 4 RET A 1 406 242 RET LYR . Q 2 LFA B 1 401 402 LFA LFA . R 2 LFA B 1 402 401 LFA LFA . S 2 LFA B 1 403 402 LFA LFA . T 2 LFA B 1 404 14 LFA LFA . U 3 PO4 B 1 405 3 PO4 PO4 . V 4 RET B 1 406 242 RET LYR . W 2 LFA C 1 401 401 LFA LFA . X 2 LFA C 1 402 9 LFA LFA . Y 3 PO4 C 1 403 4 PO4 PO4 . Z 4 RET C 1 404 242 RET LYR . AA 5 OLA D 1 401 401 OLA OLA . BA 2 LFA D 1 402 10 LFA LFA . CA 2 LFA D 1 403 13 LFA LFA . DA 3 PO4 D 1 404 5 PO4 PO4 . EA 4 RET D 1 405 242 RET LYR . FA 2 LFA E 1 401 401 LFA LFA . GA 2 LFA E 1 402 8 LFA LFA . HA 3 PO4 E 1 403 1 PO4 PO4 . IA 4 RET E 1 404 242 RET LYR . JA 2 LFA H 1 401 403 LFA LFA . KA 2 LFA H 1 402 3 LFA LFA . LA 3 PO4 H 1 403 9 PO4 PO4 . MA 4 RET H 1 404 242 RET LYR . NA 2 LFA G 1 401 401 LFA LFA . OA 2 LFA G 1 402 402 LFA LFA . PA 2 LFA G 1 403 1 LFA LFA . QA 2 LFA G 1 404 2 LFA LFA . RA 2 LFA G 1 405 5 LFA LFA . SA 2 LFA G 1 406 6 LFA LFA . TA 3 PO4 G 1 407 7 PO4 PO4 . UA 4 RET G 1 408 242 RET LYR . VA 2 LFA F 1 401 400 LFA LFA . WA 2 LFA F 1 402 401 LFA LFA . XA 2 LFA F 1 403 402 LFA LFA . YA 3 PO4 F 1 404 8 PO4 PO4 . ZA 4 RET F 1 405 242 RET LYR . AB 5 OLA I 1 401 401 OLA OLA . BB 2 LFA I 1 402 4 LFA LFA . CB 3 PO4 I 1 403 10 PO4 PO4 . DB 4 RET I 1 404 242 RET LYR . EB 2 LFA K 1 401 401 LFA LFA . FB 2 LFA K 1 402 7 LFA LFA . GB 3 PO4 K 1 403 6 PO4 PO4 . HB 4 RET K 1 404 242 RET LYR . # 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 . . . IA 4 -41.729 31.905 24.057 1 96.95 ? C1 RET 404 E 1 HETATM 2 C C2 RET . . . IA 4 -42.166 32.768 22.871 1 100.37 ? C2 RET 404 E 1 HETATM 3 C C3 RET . . . IA 4 -41.418 34.045 22.762 1 101.21 ? C3 RET 404 E 1 HETATM 4 C C4 RET . . . IA 4 -41.612 34.878 24.023 1 100.7 ? C4 RET 404 E 1 HETATM 5 C C5 RET . . . IA 4 -41.593 34.078 25.294 1 99.94 ? C5 RET 404 E 1 HETATM 6 C C6 RET . . . IA 4 -41.48 32.735 25.306 1 98.41 ? C6 RET 404 E 1 HETATM 7 C C7 RET . . . IA 4 -41.166 32.046 26.532 1 106.15 ? C7 RET 404 E 1 HETATM 8 C C8 RET . . . IA 4 -40.783 30.745 26.668 1 109.75 ? C8 RET 404 E 1 HETATM 9 C C9 RET . . . IA 4 -40.275 30.146 27.824 1 110.37 ? C9 RET 404 E 1 HETATM 10 C C10 RET . . . IA 4 -39.973 28.772 27.891 1 107.02 ? C10 RET 404 E 1 HETATM 11 C C11 RET . . . IA 4 -39.607 28.018 28.992 1 109.42 ? C11 RET 404 E 1 HETATM 12 C C12 RET . . . IA 4 -39.303 26.67 29.027 1 108.15 ? C12 RET 404 E 1 HETATM 13 C C13 RET . . . IA 4 -39.056 25.843 30.152 1 111.68 ? C13 RET 404 E 1 HETATM 14 C C14 RET . . . IA 4 -38.8 24.514 29.986 1 114.05 ? C14 RET 404 E 1 HETATM 15 C C15 RET . . . IA 4 -38.698 23.528 31.125 1 122.29 ? C15 RET 404 E 1 HETATM 16 C C16 RET . . . IA 4 -42.838 30.875 24.322 1 97.55 ? C16 RET 404 E 1 HETATM 17 C C17 RET . . . IA 4 -40.446 31.156 23.66 1 93.06 ? C17 RET 404 E 1 HETATM 18 C C18 RET . . . IA 4 -41.672 34.927 26.532 1 103.16 ? C18 RET 404 E 1 HETATM 19 C C19 RET . . . IA 4 -40.019 30.957 29.041 1 109.39 ? C19 RET 404 E 1 HETATM 20 C C20 RET . . . IA 4 -39.151 26.48 31.47 1 114.36 ? C20 RET 404 E 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #