data_7AVN # _model_server_result.job_id vWk2-mQAHpcqoUdCFkV9kg _model_server_result.datetime_utc '2025-07-18 01:12:29' _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 7avn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":317}' # _entry.id 7AVN # _exptl.entry_id 7AVN _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 63.66 _cell.angle_beta 78.98 _cell.angle_gamma 80.33 _cell.entry_id 7AVN _cell.length_a 40.686 _cell.length_b 56.628 _cell.length_c 57.386 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7AVN _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,KA 1 1 B,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,LA 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 ? 5 S N N ? 5 JA 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 S C15 RET . A RET 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 sing covale ? covale2 B NZ LYS 200 B LYS 200 1_555 JA C15 RET . B RET 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 sing # _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 466 n n C1 C6 RET sing 467 n n C1 C16 RET sing 468 n n C1 C17 RET sing 469 n n C2 C3 RET sing 470 n n C2 H21 RET sing 471 n n C2 H22 RET sing 472 n n C3 C4 RET sing 473 n n C3 H31 RET sing 474 n n C3 H32 RET sing 475 n n C4 C5 RET sing 476 n n C4 H41 RET sing 477 n n C4 H42 RET sing 478 n n C5 C6 RET doub 479 n n C5 C18 RET sing 480 n n C6 C7 RET sing 481 n n C7 C8 RET doub 482 e n C7 H7 RET sing 483 n n C8 C9 RET sing 484 n n C8 H8 RET sing 485 n n C9 C10 RET doub 486 e n C9 C19 RET sing 487 n n C10 C11 RET sing 488 n n C10 H10 RET sing 489 n n C11 C12 RET doub 490 e n C11 H11 RET sing 491 n n C12 C13 RET sing 492 n n C12 H12 RET sing 493 n n C13 C14 RET doub 494 e n C13 C20 RET sing 495 n n C14 C15 RET sing 496 n n C14 H14 RET sing 497 n n C15 O1 RET doub 498 n n C15 H15 RET sing 499 n n C16 H161 RET sing 500 n n C16 H162 RET sing 501 n n C16 H163 RET sing 502 n n C17 H171 RET sing 503 n n C17 H172 RET sing 504 n n C17 H173 RET sing 505 n n C18 H181 RET sing 506 n n C18 H182 RET sing 507 n n C18 H183 RET sing 508 n n C19 H191 RET sing 509 n n C19 H192 RET sing 510 n n C19 H193 RET sing 511 n n C20 H201 RET sing 512 n n C20 H202 RET sing 513 n n C20 H203 RET sing 514 n n # _atom_sites.entry_id 7AVN _atom_sites.fract_transf_matrix[1][1] 0.024578 _atom_sites.fract_transf_matrix[1][2] -0.004186 _atom_sites.fract_transf_matrix[1][3] -0.003321 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017913 _atom_sites.fract_transf_matrix[2][3] -0.008419 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.019616 _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 10 LFA LFA . D 2 LFA A 1 302 11 LFA LFA . E 2 LFA A 1 303 12 LFA LFA . F 2 LFA A 1 304 16 LFA LFA . G 2 LFA A 1 305 19 LFA LFA . H 2 LFA A 1 306 21 LFA LFA . I 2 LFA A 1 307 22 LFA LFA . J 2 LFA A 1 308 23 LFA LFA . K 2 LFA A 1 309 29 LFA LFA . L 2 LFA A 1 310 30 LFA LFA . M 2 LFA A 1 311 31 LFA LFA . N 2 LFA A 1 312 33 LFA LFA . O 2 LFA A 1 313 34 LFA LFA . P 3 OLB A 1 314 2 OLB OLB . Q 4 OLC A 1 315 3 OLC OLC . R 4 OLC A 1 316 4 OLC OLC . S 5 RET A 1 317 200 RET LYR . T 2 LFA B 1 301 4 LFA LFA . U 2 LFA B 1 302 13 LFA LFA . V 2 LFA B 1 303 14 LFA LFA . W 2 LFA B 1 304 15 LFA LFA . X 2 LFA B 1 305 17 LFA LFA . Y 2 LFA B 1 306 18 LFA LFA . Z 2 LFA B 1 307 20 LFA LFA . AA 2 LFA B 1 308 24 LFA LFA . BA 2 LFA B 1 309 25 LFA LFA . CA 2 LFA B 1 310 26 LFA LFA . DA 2 LFA B 1 311 27 LFA LFA . EA 2 LFA B 1 312 28 LFA LFA . FA 2 LFA B 1 313 32 LFA LFA . GA 3 OLB B 1 314 1 OLB OLB . HA 4 OLC B 1 315 1 OLC OLC . IA 4 OLC B 1 316 2 OLC OLC . JA 5 RET B 1 317 200 RET LYR . KA 6 HOH A 1 401 105 HOH HOH . KA 6 HOH A 2 402 77 HOH HOH . KA 6 HOH A 3 403 142 HOH HOH . KA 6 HOH A 4 404 116 HOH HOH . KA 6 HOH A 5 405 146 HOH HOH . KA 6 HOH A 6 406 14 HOH HOH . KA 6 HOH A 7 407 135 HOH HOH . KA 6 HOH A 8 408 41 HOH HOH . KA 6 HOH A 9 409 8 HOH HOH . KA 6 HOH A 10 410 16 HOH HOH . KA 6 HOH A 11 411 63 HOH HOH . KA 6 HOH A 12 412 93 HOH HOH . KA 6 HOH A 13 413 156 HOH HOH . KA 6 HOH A 14 414 70 HOH HOH . KA 6 HOH A 15 415 34 HOH HOH . KA 6 HOH A 16 416 61 HOH HOH . KA 6 HOH A 17 417 163 HOH HOH . KA 6 HOH A 18 418 69 HOH HOH . KA 6 HOH A 19 419 17 HOH HOH . KA 6 HOH A 20 420 108 HOH HOH . KA 6 HOH A 21 421 158 HOH HOH . KA 6 HOH A 22 422 94 HOH HOH . KA 6 HOH A 23 423 62 HOH HOH . KA 6 HOH A 24 424 143 HOH HOH . KA 6 HOH A 25 425 13 HOH HOH . KA 6 HOH A 26 426 133 HOH HOH . KA 6 HOH A 27 427 159 HOH HOH . KA 6 HOH A 28 428 136 HOH HOH . KA 6 HOH A 29 429 65 HOH HOH . KA 6 HOH A 30 430 112 HOH HOH . KA 6 HOH A 31 431 27 HOH HOH . KA 6 HOH A 32 432 66 HOH HOH . KA 6 HOH A 33 433 12 HOH HOH . KA 6 HOH A 34 434 60 HOH HOH . KA 6 HOH A 35 435 38 HOH HOH . KA 6 HOH A 36 436 32 HOH HOH . KA 6 HOH A 37 437 122 HOH HOH . KA 6 HOH A 38 438 15 HOH HOH . KA 6 HOH A 39 439 98 HOH HOH . KA 6 HOH A 40 440 7 HOH HOH . KA 6 HOH A 41 441 75 HOH HOH . KA 6 HOH A 42 442 50 HOH HOH . KA 6 HOH A 43 443 21 HOH HOH . KA 6 HOH A 44 444 147 HOH HOH . KA 6 HOH A 45 445 71 HOH HOH . KA 6 HOH A 46 446 132 HOH HOH . KA 6 HOH A 47 447 155 HOH HOH . KA 6 HOH A 48 448 130 HOH HOH . KA 6 HOH A 49 449 40 HOH HOH . KA 6 HOH A 50 450 2 HOH HOH . KA 6 HOH A 51 451 37 HOH HOH . KA 6 HOH A 52 452 3 HOH HOH . KA 6 HOH A 53 453 56 HOH HOH . KA 6 HOH A 54 454 153 HOH HOH . KA 6 HOH A 55 455 24 HOH HOH . KA 6 HOH A 56 456 128 HOH HOH . KA 6 HOH A 57 457 96 HOH HOH . KA 6 HOH A 58 458 124 HOH HOH . KA 6 HOH A 59 459 74 HOH HOH . KA 6 HOH A 60 460 67 HOH HOH . KA 6 HOH A 61 461 36 HOH HOH . KA 6 HOH A 62 462 59 HOH HOH . KA 6 HOH A 63 463 72 HOH HOH . KA 6 HOH A 64 464 97 HOH HOH . KA 6 HOH A 65 465 42 HOH HOH . KA 6 HOH A 66 466 46 HOH HOH . KA 6 HOH A 67 467 109 HOH HOH . KA 6 HOH A 68 468 123 HOH HOH . KA 6 HOH A 69 469 113 HOH HOH . KA 6 HOH A 70 470 106 HOH HOH . KA 6 HOH A 71 471 127 HOH HOH . KA 6 HOH A 72 472 160 HOH HOH . KA 6 HOH A 73 473 68 HOH HOH . KA 6 HOH A 74 474 64 HOH HOH . KA 6 HOH A 75 475 154 HOH HOH . KA 6 HOH A 76 476 111 HOH HOH . KA 6 HOH A 77 477 137 HOH HOH . KA 6 HOH A 78 478 43 HOH HOH . KA 6 HOH A 79 479 51 HOH HOH . KA 6 HOH A 80 480 92 HOH HOH . KA 6 HOH A 81 481 102 HOH HOH . KA 6 HOH A 82 482 134 HOH HOH . KA 6 HOH A 83 483 110 HOH HOH . KA 6 HOH A 84 484 73 HOH HOH . LA 6 HOH B 1 401 101 HOH HOH . LA 6 HOH B 2 402 79 HOH HOH . LA 6 HOH B 3 403 26 HOH HOH . LA 6 HOH B 4 404 22 HOH HOH . LA 6 HOH B 5 405 95 HOH HOH . LA 6 HOH B 6 406 89 HOH HOH . LA 6 HOH B 7 407 157 HOH HOH . LA 6 HOH B 8 408 20 HOH HOH . LA 6 HOH B 9 409 48 HOH HOH . LA 6 HOH B 10 410 148 HOH HOH . LA 6 HOH B 11 411 100 HOH HOH . LA 6 HOH B 12 412 141 HOH HOH . LA 6 HOH B 13 413 6 HOH HOH . LA 6 HOH B 14 414 126 HOH HOH . LA 6 HOH B 15 415 19 HOH HOH . LA 6 HOH B 16 416 29 HOH HOH . LA 6 HOH B 17 417 23 HOH HOH . LA 6 HOH B 18 418 115 HOH HOH . LA 6 HOH B 19 419 86 HOH HOH . LA 6 HOH B 20 420 84 HOH HOH . LA 6 HOH B 21 421 149 HOH HOH . LA 6 HOH B 22 422 88 HOH HOH . LA 6 HOH B 23 423 162 HOH HOH . LA 6 HOH B 24 424 99 HOH HOH . LA 6 HOH B 25 425 39 HOH HOH . LA 6 HOH B 26 426 87 HOH HOH . LA 6 HOH B 27 427 131 HOH HOH . LA 6 HOH B 28 428 103 HOH HOH . LA 6 HOH B 29 429 55 HOH HOH . LA 6 HOH B 30 430 49 HOH HOH . LA 6 HOH B 31 431 78 HOH HOH . LA 6 HOH B 32 432 4 HOH HOH . LA 6 HOH B 33 433 90 HOH HOH . LA 6 HOH B 34 434 25 HOH HOH . LA 6 HOH B 35 435 85 HOH HOH . LA 6 HOH B 36 436 18 HOH HOH . LA 6 HOH B 37 437 57 HOH HOH . LA 6 HOH B 38 438 9 HOH HOH . LA 6 HOH B 39 439 120 HOH HOH . LA 6 HOH B 40 440 11 HOH HOH . LA 6 HOH B 41 441 31 HOH HOH . LA 6 HOH B 42 442 35 HOH HOH . LA 6 HOH B 43 443 114 HOH HOH . LA 6 HOH B 44 444 117 HOH HOH . LA 6 HOH B 45 445 125 HOH HOH . LA 6 HOH B 46 446 118 HOH HOH . LA 6 HOH B 47 447 150 HOH HOH . LA 6 HOH B 48 448 151 HOH HOH . LA 6 HOH B 49 449 30 HOH HOH . LA 6 HOH B 50 450 33 HOH HOH . LA 6 HOH B 51 451 5 HOH HOH . LA 6 HOH B 52 452 1 HOH HOH . LA 6 HOH B 53 453 82 HOH HOH . LA 6 HOH B 54 454 139 HOH HOH . LA 6 HOH B 55 455 107 HOH HOH . LA 6 HOH B 56 456 28 HOH HOH . LA 6 HOH B 57 457 80 HOH HOH . LA 6 HOH B 58 458 91 HOH HOH . LA 6 HOH B 59 459 104 HOH HOH . LA 6 HOH B 60 460 54 HOH HOH . LA 6 HOH B 61 461 58 HOH HOH . LA 6 HOH B 62 462 47 HOH HOH . LA 6 HOH B 63 463 119 HOH HOH . LA 6 HOH B 64 464 129 HOH HOH . LA 6 HOH B 65 465 152 HOH HOH . LA 6 HOH B 66 466 53 HOH HOH . LA 6 HOH B 67 467 83 HOH HOH . LA 6 HOH B 68 468 81 HOH HOH . LA 6 HOH B 69 469 140 HOH HOH . LA 6 HOH B 70 470 144 HOH HOH . LA 6 HOH B 71 471 161 HOH HOH . LA 6 HOH B 72 472 52 HOH HOH . LA 6 HOH B 73 473 138 HOH HOH . LA 6 HOH B 74 474 145 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 5 -9.249 -0.268 6.748 1 16.06 ? C1 RET 317 A 1 HETATM 2 C C2 RET . . . S 5 -10.643 -0.026 7.34 1 18.08 ? C2 RET 317 A 1 HETATM 3 C C3 RET . . . S 5 -11.519 -1.258 7.271 1 19.31 ? C3 RET 317 A 1 HETATM 4 C C4 RET . . . S 5 -11.874 -1.423 5.79 1 18.29 ? C4 RET 317 A 1 HETATM 5 C C5 RET . . . S 5 -10.609 -1.444 4.969 1 18.52 ? C5 RET 317 A 1 HETATM 6 C C6 RET . . . S 5 -9.391 -0.987 5.381 1 16.4 ? C6 RET 317 A 1 HETATM 7 C C7 RET . . . S 5 -8.244 -1.18 4.48 1 17.67 ? C7 RET 317 A 1 HETATM 8 C C8 RET . . . S 5 -6.966 -0.849 4.778 1 15.67 ? C8 RET 317 A 1 HETATM 9 C C9 RET . . . S 5 -5.886 -1.08 3.819 1 18.03 ? C9 RET 317 A 1 HETATM 10 C C10 RET . . . S 5 -4.559 -0.782 4.178 1 15.54 ? C10 RET 317 A 1 HETATM 11 C C11 RET . . . S 5 -3.428 -1.023 3.35 1 16.73 ? C11 RET 317 A 1 HETATM 12 C C12 RET . . . S 5 -2.224 -0.698 3.929 1 13.51 ? C12 RET 317 A 1 HETATM 13 C C13 RET . . . S 5 -0.974 -0.732 3.18 1 16.4 ? C13 RET 317 A 1 HETATM 14 C C14 RET . . . S 5 0.171 -0.188 3.779 1 15.75 ? C14 RET 317 A 1 HETATM 15 C C15 RET . . . S 5 1.411 -0.045 3.212 1 18.46 ? C15 RET 317 A 1 HETATM 16 C C16 RET . . . S 5 -8.64 1.127 6.516 1 16.57 ? C16 RET 317 A 1 HETATM 17 C C17 RET . . . S 5 -8.41 -1.085 7.697 1 17.59 ? C17 RET 317 A 1 HETATM 18 C C18 RET . . . S 5 -10.787 -2.068 3.601 1 17.45 ? C18 RET 317 A 1 HETATM 19 C C19 RET . . . S 5 -6.255 -1.777 2.514 1 17.51 ? C19 RET 317 A 1 HETATM 20 C C20 RET . . . S 5 -0.916 -1.316 1.782 1 17.07 ? C20 RET 317 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #