data_5JSI # _model_server_result.job_id UfWJBgrMg8LrppSvDviG8g _model_server_result.datetime_utc '2025-07-31 15:43:26' _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 5jsi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":323}' # _entry.id 5JSI # _exptl.entry_id 5JSI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 5 _entity.src_method man _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 63.61 _cell.angle_beta 78.48 _cell.angle_gamma 80.21 _cell.entry_id 5JSI _cell.length_a 40.793 _cell.length_b 56.771 _cell.length_c 57.286 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JSI _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,G,H,I,J,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,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 Y N N ? 5 WA 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 200 A LYS 200 1_555 Y C15 RET . A RET 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale2 B NZ LYS 200 B LYS 200 1_555 WA C15 RET . B RET 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? # _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 402 n n C1 C6 RET sing 403 n n C1 C16 RET sing 404 n n C1 C17 RET sing 405 n n C2 C3 RET sing 406 n n C2 H21 RET sing 407 n n C2 H22 RET sing 408 n n C3 C4 RET sing 409 n n C3 H31 RET sing 410 n n C3 H32 RET sing 411 n n C4 C5 RET sing 412 n n C4 H41 RET sing 413 n n C4 H42 RET sing 414 n n C5 C6 RET doub 415 n n C5 C18 RET sing 416 n n C6 C7 RET sing 417 n n C7 C8 RET doub 418 e n C7 H7 RET sing 419 n n C8 C9 RET sing 420 n n C8 H8 RET sing 421 n n C9 C10 RET doub 422 e n C9 C19 RET sing 423 n n C10 C11 RET sing 424 n n C10 H10 RET sing 425 n n C11 C12 RET doub 426 e n C11 H11 RET sing 427 n n C12 C13 RET sing 428 n n C12 H12 RET sing 429 n n C13 C14 RET doub 430 e n C13 C20 RET sing 431 n n C14 C15 RET sing 432 n n C14 H14 RET sing 433 n n C15 O1 RET doub 434 n n C15 H15 RET sing 435 n n C16 H161 RET sing 436 n n C16 H162 RET sing 437 n n C16 H163 RET sing 438 n n C17 H171 RET sing 439 n n C17 H172 RET sing 440 n n C17 H173 RET sing 441 n n C18 H181 RET sing 442 n n C18 H182 RET sing 443 n n C18 H183 RET sing 444 n n C19 H191 RET sing 445 n n C19 H192 RET sing 446 n n C19 H193 RET sing 447 n n C20 H201 RET sing 448 n n C20 H202 RET sing 449 n n C20 H203 RET sing 450 n n # _atom_sites.entry_id 5JSI _atom_sites.fract_transf_matrix[1][1] 0.024514 _atom_sites.fract_transf_matrix[1][2] -0.004229 _atom_sites.fract_transf_matrix[1][3] -0.003533 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017875 _atom_sites.fract_transf_matrix[2][3] -0.008398 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.019683 _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 LFA A 1 301 1 LFA LFA . D 2 LFA A 1 302 3 LFA LFA . E 2 LFA A 1 303 4 LFA LFA . F 2 LFA A 1 304 7 LFA LFA . G 2 LFA A 1 305 8 LFA LFA . H 2 LFA A 1 306 9 LFA LFA . I 2 LFA A 1 307 10 LFA LFA . J 2 LFA A 1 308 13 LFA LFA . K 2 LFA A 1 309 15 LFA LFA . L 2 LFA A 1 310 17 LFA LFA . M 2 LFA A 1 311 21 LFA LFA . N 2 LFA A 1 312 22 LFA LFA . O 3 IOD A 1 313 1 IOD IOD . P 3 IOD A 1 314 2 IOD IOD . Q 3 IOD A 1 315 3 IOD IOD . R 3 IOD A 1 316 4 IOD IOD . S 3 IOD A 1 317 12 IOD IOD . T 3 IOD A 1 318 13 IOD IOD . U 3 IOD A 1 319 19 IOD IOD . V 3 IOD A 1 320 20 IOD IOD . W 3 IOD A 1 321 21 IOD IOD . X 4 OLC A 1 322 1 OLC OLC . Y 5 RET A 1 323 200 RET LYR . Z 2 LFA B 1 301 2 LFA LFA . AA 2 LFA B 1 302 5 LFA LFA . BA 2 LFA B 1 303 6 LFA LFA . CA 2 LFA B 1 304 11 LFA LFA . DA 2 LFA B 1 305 12 LFA LFA . EA 2 LFA B 1 306 14 LFA LFA . FA 2 LFA B 1 307 16 LFA LFA . GA 2 LFA B 1 308 18 LFA LFA . HA 2 LFA B 1 309 19 LFA LFA . IA 2 LFA B 1 310 20 LFA LFA . JA 3 IOD B 1 311 5 IOD IOD . KA 3 IOD B 1 312 6 IOD IOD . LA 3 IOD B 1 313 7 IOD IOD . MA 3 IOD B 1 314 8 IOD IOD . NA 3 IOD B 1 315 9 IOD IOD . OA 3 IOD B 1 316 10 IOD IOD . PA 3 IOD B 1 317 11 IOD IOD . QA 3 IOD B 1 318 14 IOD IOD . RA 3 IOD B 1 319 15 IOD IOD . SA 3 IOD B 1 320 16 IOD IOD . TA 3 IOD B 1 321 17 IOD IOD . UA 3 IOD B 1 322 18 IOD IOD . VA 3 IOD B 1 323 22 IOD IOD . WA 5 RET B 1 324 200 RET LYR . XA 6 HOH A 1 401 8 HOH HOH . XA 6 HOH A 2 402 14 HOH HOH . XA 6 HOH A 3 403 30 HOH HOH . XA 6 HOH A 4 404 18 HOH HOH . XA 6 HOH A 5 405 36 HOH HOH . XA 6 HOH A 6 406 25 HOH HOH . XA 6 HOH A 7 407 16 HOH HOH . XA 6 HOH A 8 408 21 HOH HOH . XA 6 HOH A 9 409 32 HOH HOH . XA 6 HOH A 10 410 64 HOH HOH . XA 6 HOH A 11 411 5 HOH HOH . XA 6 HOH A 12 412 19 HOH HOH . XA 6 HOH A 13 413 51 HOH HOH . XA 6 HOH A 14 414 7 HOH HOH . XA 6 HOH A 15 415 6 HOH HOH . XA 6 HOH A 16 416 65 HOH HOH . XA 6 HOH A 17 417 70 HOH HOH . XA 6 HOH A 18 418 12 HOH HOH . XA 6 HOH A 19 419 1 HOH HOH . XA 6 HOH A 20 420 15 HOH HOH . XA 6 HOH A 21 421 62 HOH HOH . XA 6 HOH A 22 422 52 HOH HOH . XA 6 HOH A 23 423 59 HOH HOH . XA 6 HOH A 24 424 53 HOH HOH . XA 6 HOH A 25 425 26 HOH HOH . XA 6 HOH A 26 426 48 HOH HOH . XA 6 HOH A 27 427 76 HOH HOH . XA 6 HOH A 28 428 54 HOH HOH . XA 6 HOH A 29 429 47 HOH HOH . XA 6 HOH A 30 430 66 HOH HOH . XA 6 HOH A 31 431 68 HOH HOH . XA 6 HOH A 32 432 45 HOH HOH . XA 6 HOH A 33 433 42 HOH HOH . XA 6 HOH A 34 434 38 HOH HOH . XA 6 HOH A 35 435 57 HOH HOH . XA 6 HOH A 36 436 77 HOH HOH . XA 6 HOH A 37 437 46 HOH HOH . XA 6 HOH A 38 438 44 HOH HOH . YA 6 HOH B 1 401 39 HOH HOH . YA 6 HOH B 2 402 41 HOH HOH . YA 6 HOH B 3 403 40 HOH HOH . YA 6 HOH B 4 404 17 HOH HOH . YA 6 HOH B 5 405 9 HOH HOH . YA 6 HOH B 6 406 31 HOH HOH . YA 6 HOH B 7 407 27 HOH HOH . YA 6 HOH B 8 408 75 HOH HOH . YA 6 HOH B 9 409 24 HOH HOH . YA 6 HOH B 10 410 22 HOH HOH . YA 6 HOH B 11 411 20 HOH HOH . YA 6 HOH B 12 412 23 HOH HOH . YA 6 HOH B 13 413 4 HOH HOH . YA 6 HOH B 14 414 58 HOH HOH . YA 6 HOH B 15 415 28 HOH HOH . YA 6 HOH B 16 416 10 HOH HOH . YA 6 HOH B 17 417 3 HOH HOH . YA 6 HOH B 18 418 11 HOH HOH . YA 6 HOH B 19 419 13 HOH HOH . YA 6 HOH B 20 420 61 HOH HOH . YA 6 HOH B 21 421 74 HOH HOH . YA 6 HOH B 22 422 60 HOH HOH . YA 6 HOH B 23 423 2 HOH HOH . YA 6 HOH B 24 424 78 HOH HOH . YA 6 HOH B 25 425 33 HOH HOH . YA 6 HOH B 26 426 29 HOH HOH . YA 6 HOH B 27 427 49 HOH HOH . YA 6 HOH B 28 428 63 HOH HOH . YA 6 HOH B 29 429 69 HOH HOH . YA 6 HOH B 30 430 71 HOH HOH . YA 6 HOH B 31 431 72 HOH HOH . YA 6 HOH B 32 432 67 HOH HOH . YA 6 HOH B 33 433 43 HOH HOH . YA 6 HOH B 34 434 55 HOH HOH . YA 6 HOH B 35 435 56 HOH HOH . YA 6 HOH B 36 436 35 HOH HOH . YA 6 HOH B 37 437 34 HOH HOH . YA 6 HOH B 38 438 37 HOH HOH . YA 6 HOH B 39 439 73 HOH HOH . YA 6 HOH B 40 440 50 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 . . . Y 5 20.583 26.324 7.279 1 22.94 ? C1 RET 323 A 1 HETATM 2 C C2 RET . . . Y 5 21.987 26.152 7.909 1 24.6 ? C2 RET 323 A 1 HETATM 3 C C3 RET . . . Y 5 22.724 27.496 7.903 1 24.57 ? C3 RET 323 A 1 HETATM 4 C C4 RET . . . Y 5 23.053 27.742 6.443 1 24.56 ? C4 RET 323 A 1 HETATM 5 C C5 RET . . . Y 5 21.895 27.537 5.498 1 24.34 ? C5 RET 323 A 1 HETATM 6 C C6 RET . . . Y 5 20.682 27.025 5.938 1 24.1 ? C6 RET 323 A 1 HETATM 7 C C7 RET . . . Y 5 19.495 27.207 5.068 1 22.04 ? C7 RET 323 A 1 HETATM 8 C C8 RET . . . Y 5 18.227 26.908 5.311 1 24.37 ? C8 RET 323 A 1 HETATM 9 C C9 RET . . . Y 5 17.126 27.165 4.356 1 24.12 ? C9 RET 323 A 1 HETATM 10 C C10 RET . . . Y 5 15.874 26.758 4.764 1 21.48 ? C10 RET 323 A 1 HETATM 11 C C11 RET . . . Y 5 14.692 27.027 3.974 1 23.77 ? C11 RET 323 A 1 HETATM 12 C C12 RET . . . Y 5 13.518 26.687 4.43 1 20.16 ? C12 RET 323 A 1 HETATM 13 C C13 RET . . . Y 5 12.258 26.8 3.639 1 24 ? C13 RET 323 A 1 HETATM 14 C C14 RET . . . Y 5 11.185 26.271 4.298 1 22.36 ? C14 RET 323 A 1 HETATM 15 C C15 RET . . . Y 5 9.857 26.236 3.813 1 24.27 ? C15 RET 323 A 1 HETATM 16 C C16 RET . . . Y 5 20.04 24.907 7 1 19.17 ? C16 RET 323 A 1 HETATM 17 C C17 RET . . . Y 5 19.694 27.072 8.281 1 24.08 ? C17 RET 323 A 1 HETATM 18 C C18 RET . . . Y 5 22.099 28.229 4.178 1 23.61 ? C18 RET 323 A 1 HETATM 19 C C19 RET . . . Y 5 17.414 27.821 3.057 1 22.12 ? C19 RET 323 A 1 HETATM 20 C C20 RET . . . Y 5 12.221 27.42 2.261 1 24.3 ? C20 RET 323 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 388 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #