data_7VGU # _model_server_result.job_id DJmwDkUDuqjSBxyFOGy1mA _model_server_result.datetime_utc '2024-11-13 04:55:50' _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 7vgu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7VGU # _exptl.entry_id 7VGU _exptl.method 'X-RAY DIFFRACTION' # _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 131.5 _cell.angle_gamma 90 _cell.entry_id 7VGU _cell.length_a 104.3 _cell.length_b 51.1 _cell.length_c 78.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VGU _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B C15 RET . A RET 301 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.31 ? covale ? covale2 A NZ LYS 242 A LYS 235 1_555 B C15 RET . A RET 301 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.309 ? # _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 327 n n C1 C6 RET sing 328 n n C1 C16 RET sing 329 n n C1 C17 RET sing 330 n n C2 C3 RET sing 331 n n C2 H21 RET sing 332 n n C2 H22 RET sing 333 n n C3 C4 RET sing 334 n n C3 H31 RET sing 335 n n C3 H32 RET sing 336 n n C4 C5 RET sing 337 n n C4 H41 RET sing 338 n n C4 H42 RET sing 339 n n C5 C6 RET doub 340 n n C5 C18 RET sing 341 n n C6 C7 RET sing 342 n n C7 C8 RET doub 343 e n C7 H7 RET sing 344 n n C8 C9 RET sing 345 n n C8 H8 RET sing 346 n n C9 C10 RET doub 347 e n C9 C19 RET sing 348 n n C10 C11 RET sing 349 n n C10 H10 RET sing 350 n n C11 C12 RET doub 351 e n C11 H11 RET sing 352 n n C12 C13 RET sing 353 n n C12 H12 RET sing 354 n n C13 C14 RET doub 355 e n C13 C20 RET sing 356 n n C14 C15 RET sing 357 n n C14 H14 RET sing 358 n n C15 O1 RET doub 359 n n C15 H15 RET sing 360 n n C16 H161 RET sing 361 n n C16 H162 RET sing 362 n n C16 H163 RET sing 363 n n C17 H171 RET sing 364 n n C17 H172 RET sing 365 n n C17 H173 RET sing 366 n n C18 H181 RET sing 367 n n C18 H182 RET sing 368 n n C18 H183 RET sing 369 n n C19 H191 RET sing 370 n n C19 H192 RET sing 371 n n C19 H193 RET sing 372 n n C20 H201 RET sing 373 n n C20 H202 RET sing 374 n n C20 H203 RET sing 375 n n # _atom_sites.entry_id 7VGU _atom_sites.fract_transf_matrix[1][1] 0.009588 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008483 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019569 _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] 0.017031 _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 RET A 1 301 1 RET RET . C 3 HEX A 1 302 1 HEX HEX . D 3 HEX A 1 303 2 HEX HEX . E 3 HEX A 1 304 3 HEX HEX . F 3 HEX A 1 305 4 HEX HEX . G 4 D10 A 1 306 2 D10 D10 . H 4 D10 A 1 307 3 D10 D10 . I 4 D10 A 1 308 4 D10 D10 . J 5 BR A 1 309 1 BR BR . K 5 BR A 1 310 2 BR BR . L 5 BR A 1 311 3 BR BR . M 6 HOH A 1 401 552 HOH HOH . M 6 HOH A 2 402 404 HOH HOH . M 6 HOH A 3 403 524 HOH HOH . M 6 HOH A 4 404 507 HOH HOH . M 6 HOH A 5 405 401 HOH HOH . M 6 HOH A 6 406 411 HOH HOH . M 6 HOH A 7 407 405 HOH HOH . M 6 HOH A 8 408 410 HOH HOH . M 6 HOH A 9 409 417 HOH HOH . M 6 HOH A 10 410 420 HOH HOH . M 6 HOH A 11 411 501 HOH HOH . M 6 HOH A 12 412 435 HOH HOH . M 6 HOH A 13 413 408 HOH HOH . M 6 HOH A 14 414 504 HOH HOH . M 6 HOH A 15 415 402 HOH HOH . M 6 HOH A 16 416 406 HOH HOH . M 6 HOH A 17 417 447 HOH HOH . M 6 HOH A 18 418 528 HOH HOH . M 6 HOH A 19 419 512 HOH HOH . M 6 HOH A 20 420 514 HOH HOH . M 6 HOH A 21 421 439 HOH HOH . M 6 HOH A 22 422 503 HOH HOH . M 6 HOH A 23 423 407 HOH HOH . M 6 HOH A 24 424 429 HOH HOH . M 6 HOH A 25 425 461 HOH HOH . M 6 HOH A 26 426 523 HOH HOH . M 6 HOH A 27 427 434 HOH HOH . M 6 HOH A 28 428 508 HOH HOH . M 6 HOH A 29 429 454 HOH HOH . M 6 HOH A 30 430 511 HOH HOH . M 6 HOH A 31 431 544 HOH HOH . M 6 HOH A 32 432 462 HOH HOH . M 6 HOH A 33 433 467 HOH HOH . M 6 HOH A 34 434 502 HOH HOH . M 6 HOH A 35 435 422 HOH HOH . M 6 HOH A 36 436 513 HOH HOH . M 6 HOH A 37 437 526 HOH HOH . M 6 HOH A 38 438 510 HOH HOH . M 6 HOH A 39 439 403 HOH HOH . M 6 HOH A 40 440 424 HOH HOH . M 6 HOH A 41 441 442 HOH HOH . M 6 HOH A 42 442 509 HOH HOH . M 6 HOH A 43 443 438 HOH HOH . M 6 HOH A 44 444 492 HOH HOH . M 6 HOH A 45 445 433 HOH HOH . M 6 HOH A 46 446 455 HOH HOH . M 6 HOH A 47 447 421 HOH HOH . M 6 HOH A 48 448 458 HOH HOH . M 6 HOH A 49 449 425 HOH HOH . M 6 HOH A 50 450 412 HOH HOH . M 6 HOH A 51 451 457 HOH HOH . M 6 HOH A 52 452 517 HOH HOH . M 6 HOH A 53 453 491 HOH HOH . M 6 HOH A 54 454 515 HOH HOH . M 6 HOH A 55 455 436 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 . A . B 2 -4.964 7.614 24.103 0.81 28.29 ? C1 RET 301 A 1 HETATM 2 C C1 RET . B . B 2 -5.013 7.454 24.2 0.19 28.29 ? C1 RET 301 A 1 HETATM 3 C C2 RET . A . B 2 -4.083 8.471 23.159 0.81 21.84 ? C2 RET 301 A 1 HETATM 4 C C2 RET . B . B 2 -4.279 8.486 23.309 0.19 21.84 ? C2 RET 301 A 1 HETATM 5 C C3 RET . A . B 2 -2.598 8.435 23.381 0.81 24.26 ? C3 RET 301 A 1 HETATM 6 C C3 RET . B . B 2 -2.779 8.506 23.37 0.19 24.26 ? C3 RET 301 A 1 HETATM 7 C C4 RET . A . B 2 -2.28 8.81 24.792 0.81 23.8 ? C4 RET 301 A 1 HETATM 8 C C4 RET . B . B 2 -2.341 8.72 24.783 0.19 23.8 ? C4 RET 301 A 1 HETATM 9 C C5 RET . A . B 2 -3.253 8.323 25.821 0.81 20.33 ? C5 RET 301 A 1 HETATM 10 C C5 RET . B . B 2 -3.138 7.977 25.811 0.19 20.33 ? C5 RET 301 A 1 HETATM 11 C C6 RET . A . B 2 -4.37 7.588 25.514 0.81 21.34 ? C6 RET 301 A 1 HETATM 12 C C6 RET . B . B 2 -4.291 7.282 25.534 0.19 21.34 ? C6 RET 301 A 1 HETATM 13 C C7 RET . A . B 2 -4.912 6.633 26.495 0.81 18.43 ? C7 RET 301 A 1 HETATM 14 C C7 RET . B . B 2 -5.032 6.655 26.64 0.19 18.43 ? C7 RET 301 A 1 HETATM 15 C C8 RET . A . B 2 -6.143 6.149 26.679 0.81 19.11 ? C8 RET 301 A 1 HETATM 16 C C8 RET . B . B 2 -5.819 5.579 26.711 0.19 19.11 ? C8 RET 301 A 1 HETATM 17 C C9 RET . A . B 2 -6.585 5.212 27.677 0.81 23.57 ? C9 RET 301 A 1 HETATM 18 C C9 RET . B . B 2 -6.469 5.094 27.904 0.19 23.57 ? C9 RET 301 A 1 HETATM 19 C C10 RET . A . B 2 -7.692 4.479 27.429 0.81 18.14 ? C10 RET 301 A 1 HETATM 20 C C10 RET . B . B 2 -7.557 4.288 27.8 0.19 18.14 ? C10 RET 301 A 1 HETATM 21 C C11 RET . A . B 2 -8.31 3.498 28.265 0.81 26.47 ? C11 RET 301 A 1 HETATM 22 C C11 RET . B . B 2 -8.304 3.731 28.89 0.19 26.47 ? C11 RET 301 A 1 HETATM 23 C C12 RET . A . B 2 -9.347 2.699 27.829 0.81 25.15 ? C12 RET 301 A 1 HETATM 24 C C12 RET . B . B 2 -9.367 2.845 28.814 0.19 25.15 ? C12 RET 301 A 1 HETATM 25 C C13 RET . A . B 2 -10.015 1.685 28.618 0.81 23.27 ? C13 RET 301 A 1 HETATM 26 C C13 RET . B . B 2 -10.064 2.346 29.991 0.19 23.27 ? C13 RET 301 A 1 HETATM 27 C C14 RET . A . B 2 -10.905 0.89 28.029 0.81 28.68 ? C14 RET 301 A 1 HETATM 28 C C14 RET . B . B 2 -11.159 1.596 29.873 0.19 28.68 ? C14 RET 301 A 1 HETATM 29 C C15 RET . A . B 2 -11.654 -0.171 28.65 0.81 25.95 ? C15 RET 301 A 1 HETATM 30 C C15 RET . B . B 2 -11.896 1.11 28.735 0.19 25.95 ? C15 RET 301 A 1 HETATM 31 C C16 RET . A . B 2 -6.379 8.211 24.106 0.81 24.75 ? C16 RET 301 A 1 HETATM 32 C C16 RET . B . B 2 -6.456 7.927 24.426 0.19 24.75 ? C16 RET 301 A 1 HETATM 33 C C17 RET . A . B 2 -4.968 6.183 23.513 0.81 21.22 ? C17 RET 301 A 1 HETATM 34 C C17 RET . B . B 2 -5.001 6.118 23.418 0.19 21.22 ? C17 RET 301 A 1 HETATM 35 C C18 RET . A . B 2 -2.593 8.375 27.203 0.81 18.58 ? C18 RET 301 A 1 HETATM 36 C C18 RET . B . B 2 -2.622 8.301 27.218 0.19 18.58 ? C18 RET 301 A 1 HETATM 37 C C19 RET . A . B 2 -5.798 5.108 28.948 0.81 21.66 ? C19 RET 301 A 1 HETATM 38 C C19 RET . B . B 2 -5.892 5.507 29.229 0.19 21.66 ? C19 RET 301 A 1 HETATM 39 C C20 RET . A . B 2 -9.655 1.584 30.07 0.81 19.93 ? C20 RET 301 A 1 HETATM 40 C C20 RET . B . B 2 -9.419 2.77 31.269 0.19 19.93 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 40 #