data_1KME # _model_server_result.job_id '_IVfzcZ4UDim1Mo2eXBYLw' _model_server_result.datetime_utc '2024-12-10 09:46:48' _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 1kme # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":302}' # _entry.id 1KME # _exptl.entry_id 1KME _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.58 _cell.angle_gamma 90 _cell.entry_id 1KME _cell.length_a 45 _cell.length_b 108.9 _cell.length_c 55.9 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KME _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,I 1 1 B,F,G,H,J 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 ? 2 C N N ? 2 H 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 216 A LYS 216 1_555 C C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 B NZ LYS 216 B LYS 216 1_555 H C15 RET . B RET 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _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 267 n n C1 C6 RET sing 268 n n C1 C16 RET sing 269 n n C1 C17 RET sing 270 n n C2 C3 RET sing 271 n n C2 H21 RET sing 272 n n C2 H22 RET sing 273 n n C3 C4 RET sing 274 n n C3 H31 RET sing 275 n n C3 H32 RET sing 276 n n C4 C5 RET sing 277 n n C4 H41 RET sing 278 n n C4 H42 RET sing 279 n n C5 C6 RET doub 280 n n C5 C18 RET sing 281 n n C6 C7 RET sing 282 n n C7 C8 RET doub 283 e n C7 H7 RET sing 284 n n C8 C9 RET sing 285 n n C8 H8 RET sing 286 n n C9 C10 RET doub 287 e n C9 C19 RET sing 288 n n C10 C11 RET sing 289 n n C10 H10 RET sing 290 n n C11 C12 RET doub 291 e n C11 H11 RET sing 292 n n C12 C13 RET sing 293 n n C12 H12 RET sing 294 n n C13 C14 RET doub 295 e n C13 C20 RET sing 296 n n C14 C15 RET sing 297 n n C14 H14 RET sing 298 n n C15 O1 RET doub 299 n n C15 H15 RET sing 300 n n C16 H161 RET sing 301 n n C16 H162 RET sing 302 n n C16 H163 RET sing 303 n n C17 H171 RET sing 304 n n C17 H172 RET sing 305 n n C17 H173 RET sing 306 n n C18 H181 RET sing 307 n n C18 H182 RET sing 308 n n C18 H183 RET sing 309 n n C19 H191 RET sing 310 n n C19 H192 RET sing 311 n n C19 H193 RET sing 312 n n C20 H201 RET sing 313 n n C20 H202 RET sing 314 n n C20 H203 RET sing 315 n n # _atom_sites.entry_id 1KME _atom_sites.fract_transf_matrix[1][1] 0.022222 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.009699 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009183 _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] 0.019519 _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 RET A 1 301 301 RET RET . D 3 SQU A 1 401 401 SQU SQU . E 3 SQU A 1 402 402 SQU SQU . F 4 BGC B 1 501 501 BGC BGC . G 4 BGC B 1 502 502 BGC BGC . H 2 RET B 1 302 302 RET RET . I 5 HOH A 1 403 403 HOH HOH . I 5 HOH A 2 404 404 HOH HOH . I 5 HOH A 3 405 405 HOH HOH . I 5 HOH A 4 406 406 HOH HOH . I 5 HOH A 5 407 407 HOH HOH . I 5 HOH A 6 408 408 HOH HOH . I 5 HOH A 7 409 409 HOH HOH . I 5 HOH A 8 410 410 HOH HOH . I 5 HOH A 9 411 411 HOH HOH . I 5 HOH A 10 412 412 HOH HOH . I 5 HOH A 11 413 413 HOH HOH . I 5 HOH A 12 414 414 HOH HOH . I 5 HOH A 13 415 415 HOH HOH . I 5 HOH A 14 416 416 HOH HOH . I 5 HOH A 15 417 417 HOH HOH . I 5 HOH A 16 418 418 HOH HOH . I 5 HOH A 17 419 419 HOH HOH . I 5 HOH A 18 420 420 HOH HOH . I 5 HOH A 19 421 421 HOH HOH . I 5 HOH A 20 422 422 HOH HOH . I 5 HOH A 21 423 423 HOH HOH . I 5 HOH A 22 424 424 HOH HOH . I 5 HOH A 23 425 425 HOH HOH . I 5 HOH A 24 426 426 HOH HOH . I 5 HOH A 25 427 427 HOH HOH . I 5 HOH A 26 428 428 HOH HOH . I 5 HOH A 27 429 429 HOH HOH . I 5 HOH A 28 430 430 HOH HOH . I 5 HOH A 29 431 431 HOH HOH . I 5 HOH A 30 432 432 HOH HOH . I 5 HOH A 31 433 433 HOH HOH . I 5 HOH A 32 434 434 HOH HOH . I 5 HOH A 33 435 435 HOH HOH . I 5 HOH A 34 436 436 HOH HOH . I 5 HOH A 35 437 437 HOH HOH . I 5 HOH A 36 438 438 HOH HOH . I 5 HOH A 37 439 439 HOH HOH . I 5 HOH A 38 440 440 HOH HOH . I 5 HOH A 39 441 441 HOH HOH . I 5 HOH A 40 442 442 HOH HOH . I 5 HOH A 41 443 443 HOH HOH . I 5 HOH A 42 444 444 HOH HOH . I 5 HOH A 43 445 445 HOH HOH . I 5 HOH A 44 446 446 HOH HOH . I 5 HOH A 45 447 447 HOH HOH . I 5 HOH A 46 448 448 HOH HOH . I 5 HOH A 47 449 449 HOH HOH . I 5 HOH A 48 450 450 HOH HOH . I 5 HOH A 49 451 451 HOH HOH . I 5 HOH A 50 452 452 HOH HOH . I 5 HOH A 51 453 453 HOH HOH . I 5 HOH A 52 454 454 HOH HOH . I 5 HOH A 53 455 455 HOH HOH . J 5 HOH B 1 503 503 HOH HOH . J 5 HOH B 2 504 504 HOH HOH . J 5 HOH B 3 505 505 HOH HOH . J 5 HOH B 4 506 506 HOH HOH . J 5 HOH B 5 507 507 HOH HOH . J 5 HOH B 6 508 508 HOH HOH . J 5 HOH B 7 509 509 HOH HOH . J 5 HOH B 8 510 510 HOH HOH . J 5 HOH B 9 511 511 HOH HOH . J 5 HOH B 10 512 512 HOH HOH . J 5 HOH B 11 513 513 HOH HOH . J 5 HOH B 12 514 514 HOH HOH . J 5 HOH B 13 515 515 HOH HOH . J 5 HOH B 14 516 516 HOH HOH . J 5 HOH B 15 517 517 HOH HOH . J 5 HOH B 16 518 518 HOH HOH . J 5 HOH B 17 519 519 HOH HOH . J 5 HOH B 18 520 520 HOH HOH . J 5 HOH B 19 521 521 HOH HOH . J 5 HOH B 20 522 522 HOH HOH . J 5 HOH B 21 523 523 HOH HOH . J 5 HOH B 22 524 524 HOH HOH . J 5 HOH B 23 525 525 HOH HOH . J 5 HOH B 24 526 526 HOH HOH . J 5 HOH B 25 527 527 HOH HOH . J 5 HOH B 26 528 528 HOH HOH . J 5 HOH B 27 529 529 HOH HOH . J 5 HOH B 28 530 530 HOH HOH . J 5 HOH B 29 531 531 HOH HOH . J 5 HOH B 30 532 532 HOH HOH . J 5 HOH B 31 533 533 HOH HOH . J 5 HOH B 32 534 534 HOH HOH . J 5 HOH B 33 535 535 HOH HOH . J 5 HOH B 34 536 536 HOH HOH . J 5 HOH B 35 537 537 HOH HOH . J 5 HOH B 36 538 538 HOH HOH . J 5 HOH B 37 539 539 HOH HOH . J 5 HOH B 38 540 540 HOH HOH . J 5 HOH B 39 541 541 HOH HOH . J 5 HOH B 40 542 542 HOH HOH . J 5 HOH B 41 543 543 HOH HOH . J 5 HOH B 42 544 544 HOH HOH . J 5 HOH B 43 545 545 HOH HOH . J 5 HOH B 44 546 546 HOH HOH . J 5 HOH B 45 547 547 HOH HOH . J 5 HOH B 46 548 548 HOH HOH . J 5 HOH B 47 549 549 HOH HOH . J 5 HOH B 48 550 550 HOH HOH . J 5 HOH B 49 551 551 HOH HOH . J 5 HOH B 50 552 552 HOH HOH . J 5 HOH B 51 553 553 HOH HOH . J 5 HOH B 52 554 554 HOH HOH . J 5 HOH B 53 555 555 HOH HOH . J 5 HOH B 54 556 556 HOH HOH . J 5 HOH B 55 557 557 HOH HOH . J 5 HOH B 56 558 558 HOH HOH . J 5 HOH B 57 559 559 HOH HOH . J 5 HOH B 58 560 560 HOH HOH . J 5 HOH B 59 561 561 HOH HOH . J 5 HOH B 60 562 562 HOH HOH . J 5 HOH B 61 563 563 HOH HOH . J 5 HOH B 62 564 564 HOH HOH . J 5 HOH B 63 565 565 HOH HOH . J 5 HOH B 64 566 566 HOH HOH . J 5 HOH B 65 567 567 HOH HOH . J 5 HOH B 66 568 568 HOH HOH . J 5 HOH B 67 569 569 HOH HOH . J 5 HOH B 68 570 570 HOH HOH . J 5 HOH B 69 571 571 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 . . . H 2 18.78 48.592 32.524 1 15.11 ? C1 RET 302 B 1 HETATM 2 C C2 RET . . . H 2 19.629 47.378 32.988 1 14.79 ? C2 RET 302 B 1 HETATM 3 C C3 RET . . . H 2 20.204 47.393 34.358 1 14.48 ? C3 RET 302 B 1 HETATM 4 C C4 RET . . . H 2 20.715 48.746 34.875 1 13.96 ? C4 RET 302 B 1 HETATM 5 C C5 RET . . . H 2 19.902 49.999 34.469 1 14.6 ? C5 RET 302 B 1 HETATM 6 C C6 RET . . . H 2 18.996 49.94 33.375 1 14.78 ? C6 RET 302 B 1 HETATM 7 C C7 RET . . . H 2 18.265 51.223 33.092 1 13.8 ? C7 RET 302 B 1 HETATM 8 C C8 RET . . . H 2 17.322 51.543 32.147 1 9.92 ? C8 RET 302 B 1 HETATM 9 C C9 RET . . . H 2 16.661 52.813 31.934 1 10.58 ? C9 RET 302 B 1 HETATM 10 C C10 RET . . . H 2 15.767 52.749 30.897 1 10.25 ? C10 RET 302 B 1 HETATM 11 C C11 RET . . . H 2 14.982 53.921 30.504 1 11.41 ? C11 RET 302 B 1 HETATM 12 C C12 RET . . . H 2 14.175 53.657 29.445 1 12.68 ? C12 RET 302 B 1 HETATM 13 C C13 RET . . . H 2 13.293 54.632 28.831 1 13.25 ? C13 RET 302 B 1 HETATM 14 C C14 RET . . . H 2 12.623 54.049 27.778 1 14.53 ? C14 RET 302 B 1 HETATM 15 C C15 RET . . . H 2 11.673 54.715 26.93 1 14.41 ? C15 RET 302 B 1 HETATM 16 C C16 RET . . . H 2 19.164 48.802 31.01 1 15.2 ? C16 RET 302 B 1 HETATM 17 C C17 RET . . . H 2 17.301 48.029 32.62 1 14.49 ? C17 RET 302 B 1 HETATM 18 C C18 RET . . . H 2 20.277 51.124 35.406 1 13.79 ? C18 RET 302 B 1 HETATM 19 C C19 RET . . . H 2 16.954 54.04 32.778 1 9.57 ? C19 RET 302 B 1 HETATM 20 C C20 RET . . . H 2 13.174 56.056 29.308 1 11.45 ? C20 RET 302 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #