data_9JOX # _model_server_result.job_id cmgWiRH6NTWslNWpNMZtVA _model_server_result.datetime_utc '2025-08-31 08:21:53' _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 9jox # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"KA","auth_seq_id":302}' # _entry.id 9JOX # _exptl.entry_id 9JOX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 284.436 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 5 _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 90 _cell.entry_id 9JOX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JOX _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 ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,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 _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 ? _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 ? 2 F N N ? 2 O N N ? 2 V N N ? 2 CA N N ? 2 KA 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 235 1_555 F C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.268 ? covale ? covale2 B NZ LYS 242 B LYS 235 1_555 O C15 RET . B RET 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.263 ? covale ? covale3 C NZ LYS 242 C LYS 235 1_555 V C15 RET . C RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.261 ? covale ? covale4 D NZ LYS 242 D LYS 235 1_555 CA C15 RET . D RET 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.249 ? covale ? covale5 E NZ LYS 242 E LYS 235 1_555 KA C15 RET . E RET 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.261 ? # _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 708 n n C1 C6 RET sing 709 n n C1 C16 RET sing 710 n n C1 C17 RET sing 711 n n C2 C3 RET sing 712 n n C2 H21 RET sing 713 n n C2 H22 RET sing 714 n n C3 C4 RET sing 715 n n C3 H31 RET sing 716 n n C3 H32 RET sing 717 n n C4 C5 RET sing 718 n n C4 H41 RET sing 719 n n C4 H42 RET sing 720 n n C5 C6 RET doub 721 n n C5 C18 RET sing 722 n n C6 C7 RET sing 723 n n C7 C8 RET doub 724 e n C7 H7 RET sing 725 n n C8 C9 RET sing 726 n n C8 H8 RET sing 727 n n C9 C10 RET doub 728 e n C9 C19 RET sing 729 n n C10 C11 RET sing 730 n n C10 H10 RET sing 731 n n C11 C12 RET doub 732 e n C11 H11 RET sing 733 n n C12 C13 RET sing 734 n n C12 H12 RET sing 735 n n C13 C14 RET doub 736 e n C13 C20 RET sing 737 n n C14 C15 RET sing 738 n n C14 H14 RET sing 739 n n C15 O1 RET doub 740 n n C15 H15 RET sing 741 n n C16 H161 RET sing 742 n n C16 H162 RET sing 743 n n C16 H163 RET sing 744 n n C17 H171 RET sing 745 n n C17 H172 RET sing 746 n n C17 H173 RET sing 747 n n C18 H181 RET sing 748 n n C18 H182 RET sing 749 n n C18 H183 RET sing 750 n n C19 H191 RET sing 751 n n C19 H192 RET sing 752 n n C19 H193 RET sing 753 n n C20 H201 RET sing 754 n n C20 H202 RET sing 755 n n C20 H203 RET sing 756 n n # _atom_sites.entry_id 9JOX _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 F 2 RET A 1 301 301 RET RET . G 3 CL A 1 302 303 CL CL . H 3 CL A 1 303 304 CL CL . I 4 PC1 A 1 304 501 PC1 PC1 . J 5 PLC A 1 305 502 PLC PLC . K 6 D12 A 1 306 507 D12 D12 . L 5 PLC A 1 307 502 PLC PLC . M 7 R16 A 1 308 506 R16 R16 . N 8 8K6 B 1 301 506 8K6 8K6 . O 2 RET B 1 302 301 RET RET . P 3 CL B 1 303 303 CL CL . Q 3 CL B 1 304 304 CL CL . R 4 PC1 B 1 305 501 PC1 PC1 . S 5 PLC B 1 306 502 PLC PLC . T 7 R16 B 1 307 506 R16 R16 . U 9 C14 B 1 308 507 C14 C14 . V 2 RET C 1 301 301 RET RET . W 3 CL C 1 302 303 CL CL . X 3 CL C 1 303 304 CL CL . Y 4 PC1 C 1 304 501 PC1 PC1 . Z 5 PLC C 1 305 502 PLC PLC . AA 8 8K6 C 1 306 507 8K6 8K6 . BA 7 R16 D 1 301 506 R16 R16 . CA 2 RET D 1 302 301 RET RET . DA 3 CL D 1 303 303 CL CL . EA 3 CL D 1 304 304 CL CL . FA 4 PC1 D 1 305 501 PC1 PC1 . GA 5 PLC D 1 306 502 PLC PLC . HA 7 R16 D 1 307 505 R16 R16 . IA 6 D12 D 1 308 507 D12 D12 . JA 7 R16 E 1 301 506 R16 R16 . KA 2 RET E 1 302 301 RET RET . LA 3 CL E 1 303 303 CL CL . MA 3 CL E 1 304 304 CL CL . NA 4 PC1 E 1 305 501 PC1 PC1 . OA 7 R16 E 1 306 505 R16 R16 . PA 9 C14 E 1 307 507 C14 C14 . QA 10 HOH A 1 401 411 HOH HOH . QA 10 HOH A 2 402 403 HOH HOH . QA 10 HOH A 3 403 429 HOH HOH . QA 10 HOH A 4 404 439 HOH HOH . QA 10 HOH A 5 405 422 HOH HOH . QA 10 HOH A 6 406 430 HOH HOH . QA 10 HOH A 7 407 418 HOH HOH . QA 10 HOH A 8 408 410 HOH HOH . QA 10 HOH A 9 409 424 HOH HOH . QA 10 HOH A 10 410 401 HOH HOH . QA 10 HOH A 11 411 417 HOH HOH . QA 10 HOH A 12 412 406 HOH HOH . QA 10 HOH A 13 413 407 HOH HOH . QA 10 HOH A 14 414 405 HOH HOH . QA 10 HOH A 15 415 419 HOH HOH . QA 10 HOH A 16 416 427 HOH HOH . QA 10 HOH A 17 417 415 HOH HOH . QA 10 HOH A 18 418 409 HOH HOH . QA 10 HOH A 19 419 404 HOH HOH . QA 10 HOH A 20 420 421 HOH HOH . QA 10 HOH A 21 421 402 HOH HOH . QA 10 HOH A 22 422 436 HOH HOH . QA 10 HOH A 23 423 434 HOH HOH . QA 10 HOH A 24 424 420 HOH HOH . QA 10 HOH A 25 425 426 HOH HOH . QA 10 HOH A 26 426 423 HOH HOH . QA 10 HOH A 27 427 428 HOH HOH . QA 10 HOH A 28 428 431 HOH HOH . QA 10 HOH A 29 429 438 HOH HOH . QA 10 HOH A 30 430 440 HOH HOH . QA 10 HOH A 31 431 408 HOH HOH . QA 10 HOH A 32 432 437 HOH HOH . RA 10 HOH B 1 401 403 HOH HOH . RA 10 HOH B 2 402 406 HOH HOH . RA 10 HOH B 3 403 413 HOH HOH . RA 10 HOH B 4 404 415 HOH HOH . RA 10 HOH B 5 405 428 HOH HOH . RA 10 HOH B 6 406 426 HOH HOH . RA 10 HOH B 7 407 405 HOH HOH . RA 10 HOH B 8 408 411 HOH HOH . RA 10 HOH B 9 409 421 HOH HOH . RA 10 HOH B 10 410 409 HOH HOH . RA 10 HOH B 11 411 412 HOH HOH . RA 10 HOH B 12 412 410 HOH HOH . RA 10 HOH B 13 413 422 HOH HOH . RA 10 HOH B 14 414 420 HOH HOH . RA 10 HOH B 15 415 418 HOH HOH . RA 10 HOH B 16 416 401 HOH HOH . RA 10 HOH B 17 417 425 HOH HOH . RA 10 HOH B 18 418 419 HOH HOH . RA 10 HOH B 19 419 412 HOH HOH . RA 10 HOH B 20 420 427 HOH HOH . RA 10 HOH B 21 421 404 HOH HOH . RA 10 HOH B 22 422 408 HOH HOH . RA 10 HOH B 23 423 417 HOH HOH . RA 10 HOH B 24 424 441 HOH HOH . RA 10 HOH B 25 425 429 HOH HOH . RA 10 HOH B 26 426 416 HOH HOH . RA 10 HOH B 27 427 430 HOH HOH . RA 10 HOH B 28 428 407 HOH HOH . SA 10 HOH C 1 401 404 HOH HOH . SA 10 HOH C 2 402 417 HOH HOH . SA 10 HOH C 3 403 428 HOH HOH . SA 10 HOH C 4 404 431 HOH HOH . SA 10 HOH C 5 405 423 HOH HOH . SA 10 HOH C 6 406 437 HOH HOH . SA 10 HOH C 7 407 402 HOH HOH . SA 10 HOH C 8 408 410 HOH HOH . SA 10 HOH C 9 409 414 HOH HOH . SA 10 HOH C 10 410 426 HOH HOH . SA 10 HOH C 11 411 408 HOH HOH . SA 10 HOH C 12 412 413 HOH HOH . SA 10 HOH C 13 413 438 HOH HOH . SA 10 HOH C 14 414 409 HOH HOH . SA 10 HOH C 15 415 419 HOH HOH . SA 10 HOH C 16 416 429 HOH HOH . SA 10 HOH C 17 417 436 HOH HOH . SA 10 HOH C 18 418 418 HOH HOH . SA 10 HOH C 19 419 407 HOH HOH . SA 10 HOH C 20 420 415 HOH HOH . SA 10 HOH C 21 421 406 HOH HOH . SA 10 HOH C 22 422 403 HOH HOH . SA 10 HOH C 23 423 411 HOH HOH . SA 10 HOH C 24 424 405 HOH HOH . SA 10 HOH C 25 425 424 HOH HOH . SA 10 HOH C 26 426 401 HOH HOH . SA 10 HOH C 27 427 435 HOH HOH . SA 10 HOH C 28 428 424 HOH HOH . SA 10 HOH C 29 429 412 HOH HOH . SA 10 HOH C 30 430 442 HOH HOH . SA 10 HOH C 31 431 425 HOH HOH . SA 10 HOH C 32 432 433 HOH HOH . SA 10 HOH C 33 433 416 HOH HOH . SA 10 HOH C 34 434 439 HOH HOH . SA 10 HOH C 35 435 430 HOH HOH . TA 10 HOH D 1 401 422 HOH HOH . TA 10 HOH D 2 402 426 HOH HOH . TA 10 HOH D 3 403 427 HOH HOH . TA 10 HOH D 4 404 412 HOH HOH . TA 10 HOH D 5 405 419 HOH HOH . TA 10 HOH D 6 406 409 HOH HOH . TA 10 HOH D 7 407 404 HOH HOH . TA 10 HOH D 8 408 406 HOH HOH . TA 10 HOH D 9 409 407 HOH HOH . TA 10 HOH D 10 410 405 HOH HOH . TA 10 HOH D 11 411 423 HOH HOH . TA 10 HOH D 12 412 401 HOH HOH . TA 10 HOH D 13 413 425 HOH HOH . TA 10 HOH D 14 414 431 HOH HOH . TA 10 HOH D 15 415 411 HOH HOH . TA 10 HOH D 16 416 402 HOH HOH . TA 10 HOH D 17 417 420 HOH HOH . TA 10 HOH D 18 418 417 HOH HOH . TA 10 HOH D 19 419 408 HOH HOH . TA 10 HOH D 20 420 410 HOH HOH . TA 10 HOH D 21 421 423 HOH HOH . TA 10 HOH D 22 422 413 HOH HOH . TA 10 HOH D 23 423 418 HOH HOH . TA 10 HOH D 24 424 430 HOH HOH . TA 10 HOH D 25 425 432 HOH HOH . TA 10 HOH D 26 426 428 HOH HOH . TA 10 HOH D 27 427 403 HOH HOH . TA 10 HOH D 28 428 424 HOH HOH . TA 10 HOH D 29 429 443 HOH HOH . TA 10 HOH D 30 430 421 HOH HOH . UA 10 HOH E 1 401 406 HOH HOH . UA 10 HOH E 2 402 412 HOH HOH . UA 10 HOH E 3 403 405 HOH HOH . UA 10 HOH E 4 404 415 HOH HOH . UA 10 HOH E 5 405 428 HOH HOH . UA 10 HOH E 6 406 403 HOH HOH . UA 10 HOH E 7 407 426 HOH HOH . UA 10 HOH E 8 408 425 HOH HOH . UA 10 HOH E 9 409 411 HOH HOH . UA 10 HOH E 10 410 404 HOH HOH . UA 10 HOH E 11 411 402 HOH HOH . UA 10 HOH E 12 412 420 HOH HOH . UA 10 HOH E 13 413 418 HOH HOH . UA 10 HOH E 14 414 416 HOH HOH . UA 10 HOH E 15 415 408 HOH HOH . UA 10 HOH E 16 416 410 HOH HOH . UA 10 HOH E 17 417 444 HOH HOH . UA 10 HOH E 18 418 409 HOH HOH . UA 10 HOH E 19 419 427 HOH HOH . UA 10 HOH E 20 420 413 HOH HOH . UA 10 HOH E 21 421 422 HOH HOH . UA 10 HOH E 22 422 419 HOH HOH . UA 10 HOH E 23 423 430 HOH HOH . UA 10 HOH E 24 424 431 HOH HOH . UA 10 HOH E 25 425 407 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 . . . KA 2 106.575 62.338 82.526 1 99.17 ? C1 RET 302 E 1 HETATM 2 C C2 RET . . . KA 2 107.381 62.022 81.264 1 115.87 ? C2 RET 302 E 1 HETATM 3 C C3 RET . . . KA 2 107.854 60.621 81.193 1 122.14 ? C3 RET 302 E 1 HETATM 4 C C4 RET . . . KA 2 108.666 60.284 82.445 1 104.58 ? C4 RET 302 E 1 HETATM 5 C C5 RET . . . KA 2 107.941 60.632 83.716 1 133.65 ? C5 RET 302 E 1 HETATM 6 C C6 RET . . . KA 2 106.841 61.423 83.709 1 122.19 ? C6 RET 302 E 1 HETATM 7 C C7 RET . . . KA 2 105.988 61.491 84.884 1 113.3 ? C7 RET 302 E 1 HETATM 8 C C8 RET . . . KA 2 105.035 62.411 85.202 1 118.35 ? C8 RET 302 E 1 HETATM 9 C C9 RET . . . KA 2 104.303 62.438 86.394 1 112.44 ? C9 RET 302 E 1 HETATM 10 C C10 RET . . . KA 2 103.224 63.316 86.576 1 106.66 ? C10 RET 302 E 1 HETATM 11 C C11 RET . . . KA 2 102.379 63.476 87.654 1 102.63 ? C11 RET 302 E 1 HETATM 12 C C12 RET . . . KA 2 101.352 64.368 87.644 1 105.97 ? C12 RET 302 E 1 HETATM 13 C C13 RET . . . KA 2 100.371 64.629 88.598 1 106.19 ? C13 RET 302 E 1 HETATM 14 C C14 RET . . . KA 2 99.416 65.598 88.22 1 90.71 ? C14 RET 302 E 1 HETATM 15 C C15 RET . . . KA 2 98.206 65.914 88.916 1 94.99 ? C15 RET 302 E 1 HETATM 16 C C16 RET . . . KA 2 106.917 63.774 82.935 1 99.52 ? C16 RET 302 E 1 HETATM 17 C C17 RET . . . KA 2 105.102 62.263 82.117 1 95.95 ? C17 RET 302 E 1 HETATM 18 C C18 RET . . . KA 2 108.531 59.979 84.943 1 100.89 ? C18 RET 302 E 1 HETATM 19 C C19 RET . . . KA 2 104.647 61.561 87.511 1 99.75 ? C19 RET 302 E 1 HETATM 20 C C20 RET . . . KA 2 100.466 63.894 89.899 1 87.67 ? C20 RET 302 E 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 618 _model_server_stats.encode_time_ms 52 _model_server_stats.element_count 20 #