data_5B34 # _model_server_result.job_id p7Yhb0J-gzayC6sYUV_0lA _model_server_result.datetime_utc '2024-11-26 20:44:03' _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 5b34 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5B34 # _exptl.entry_id 5B34 _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 90 _cell.angle_gamma 90 _cell.entry_id 5B34 _cell.length_a 46.2 _cell.length_b 103 _cell.length_c 128.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B34 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,N,O,P,Q,R,S,T _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 216 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 301 _struct_conn.ptnr2_symmetry 1_555 _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 1.298 _struct_conn.pdbx_value_order ? # _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 478 n n C1 C6 RET sing 479 n n C1 C16 RET sing 480 n n C1 C17 RET sing 481 n n C2 C3 RET sing 482 n n C2 H21 RET sing 483 n n C2 H22 RET sing 484 n n C3 C4 RET sing 485 n n C3 H31 RET sing 486 n n C3 H32 RET sing 487 n n C4 C5 RET sing 488 n n C4 H41 RET sing 489 n n C4 H42 RET sing 490 n n C5 C6 RET doub 491 n n C5 C18 RET sing 492 n n C6 C7 RET sing 493 n n C7 C8 RET doub 494 e n C7 H7 RET sing 495 n n C8 C9 RET sing 496 n n C8 H8 RET sing 497 n n C9 C10 RET doub 498 e n C9 C19 RET sing 499 n n C10 C11 RET sing 500 n n C10 H10 RET sing 501 n n C11 C12 RET doub 502 e n C11 H11 RET sing 503 n n C12 C13 RET sing 504 n n C12 H12 RET sing 505 n n C13 C14 RET doub 506 e n C13 C20 RET sing 507 n n C14 C15 RET sing 508 n n C14 H14 RET sing 509 n n C15 O1 RET doub 510 n n C15 H15 RET sing 511 n n C16 H161 RET sing 512 n n C16 H162 RET sing 513 n n C16 H163 RET sing 514 n n C17 H171 RET sing 515 n n C17 H172 RET sing 516 n n C17 H173 RET sing 517 n n C18 H181 RET sing 518 n n C18 H182 RET sing 519 n n C18 H183 RET sing 520 n n C19 H191 RET sing 521 n n C19 H192 RET sing 522 n n C19 H193 RET sing 523 n n C20 H201 RET sing 524 n n C20 H202 RET sing 525 n n C20 H203 RET sing 526 n n # _atom_sites.entry_id 5B34 _atom_sites.fract_transf_matrix[1][1] 0.021645 _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] 0.009709 _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] 0.00777 _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 1 301 300 RET RET . C 3 4QL A 1 302 1 4QL 13a . D 3 4QL A 1 303 2 4QL 13a . E 4 OCT A 1 304 100 OCT OCT . F 4 OCT A 1 305 200 OCT OCT . G 5 D12 A 1 306 402 D12 D12 . H 6 D10 A 1 307 406 D10 D10 . I 6 D10 A 1 308 407 D10 D10 . J 7 R16 A 1 309 411 R16 R16 . K 6 D10 A 1 310 250 D10 D10 . L 8 HP6 A 1 311 401 HP6 HP6 . M 8 HP6 A 1 312 251 HP6 HP6 . N 8 HP6 A 1 313 252 HP6 HP6 . O 9 DD9 A 1 314 253 DD9 DD9 . P 5 D12 A 1 315 254 D12 D12 . Q 5 D12 A 1 316 255 D12 D12 . R 5 D12 A 1 317 256 D12 D12 . S 9 DD9 A 1 318 257 DD9 DD9 . T 10 HOH A 1 401 533 HOH HOH . T 10 HOH A 2 402 405 HOH HOH . T 10 HOH A 3 403 423 HOH HOH . T 10 HOH A 4 404 402 HOH HOH . T 10 HOH A 5 405 403 HOH HOH . T 10 HOH A 6 406 537 HOH HOH . T 10 HOH A 7 407 530 HOH HOH . T 10 HOH A 8 408 400 HOH HOH . T 10 HOH A 9 409 545 HOH HOH . T 10 HOH A 10 410 401 HOH HOH . T 10 HOH A 11 411 527 HOH HOH . T 10 HOH A 12 412 526 HOH HOH . T 10 HOH A 13 413 418 HOH HOH . T 10 HOH A 14 414 547 HOH HOH . T 10 HOH A 15 415 532 HOH HOH . T 10 HOH A 16 416 536 HOH HOH . T 10 HOH A 17 417 419 HOH HOH . T 10 HOH A 18 418 501 HOH HOH . T 10 HOH A 19 419 406 HOH HOH . T 10 HOH A 20 420 521 HOH HOH . T 10 HOH A 21 421 529 HOH HOH . T 10 HOH A 22 422 514 HOH HOH . T 10 HOH A 23 423 531 HOH HOH . T 10 HOH A 24 424 404 HOH HOH . T 10 HOH A 25 425 543 HOH HOH . T 10 HOH A 26 426 522 HOH HOH . T 10 HOH A 27 427 523 HOH HOH . T 10 HOH A 28 428 535 HOH HOH . T 10 HOH A 29 429 541 HOH HOH . T 10 HOH A 30 430 433 HOH HOH . T 10 HOH A 31 431 429 HOH HOH . T 10 HOH A 32 432 542 HOH HOH . T 10 HOH A 33 433 539 HOH HOH . T 10 HOH A 34 434 546 HOH HOH . T 10 HOH A 35 435 540 HOH HOH . T 10 HOH A 36 436 528 HOH HOH . T 10 HOH A 37 437 524 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 . . . B 2 26.972 61.97 -3.025 1 56.97 ? C1 RET 301 A 1 HETATM 2 C C2 RET . . . B 2 27.931 61.506 -4.105 1 57.16 ? C2 RET 301 A 1 HETATM 3 C C3 RET . . . B 2 28.237 60.044 -4.071 1 57.85 ? C3 RET 301 A 1 HETATM 4 C C4 RET . . . B 2 28.861 59.585 -2.758 1 55.79 ? C4 RET 301 A 1 HETATM 5 C C5 RET . . . B 2 28.178 60.197 -1.567 1 57.6 ? C5 RET 301 A 1 HETATM 6 C C6 RET . . . B 2 27.312 61.271 -1.679 1 55.61 ? C6 RET 301 A 1 HETATM 7 C C7 RET . . . B 2 26.676 61.714 -0.421 1 52.67 ? C7 RET 301 A 1 HETATM 8 C C8 RET . . . B 2 25.711 62.628 -0.326 1 51.86 ? C8 RET 301 A 1 HETATM 9 C C9 RET . . . B 2 25.113 62.928 0.968 1 51.22 ? C9 RET 301 A 1 HETATM 10 C C10 RET . . . B 2 24.141 63.86 0.954 1 50.98 ? C10 RET 301 A 1 HETATM 11 C C11 RET . . . B 2 23.429 64.278 2.153 1 55.37 ? C11 RET 301 A 1 HETATM 12 C C12 RET . . . B 2 22.553 65.191 1.952 1 55.03 ? C12 RET 301 A 1 HETATM 13 C C13 RET . . . B 2 21.722 65.782 3.016 1 60.71 ? C13 RET 301 A 1 HETATM 14 C C14 RET . . . B 2 21.021 66.709 2.416 1 64.89 ? C14 RET 301 A 1 HETATM 15 C C15 RET . . . B 2 20.121 67.559 2.875 1 70.44 ? C15 RET 301 A 1 HETATM 16 C C16 RET . . . B 2 27.324 63.461 -2.954 1 58.68 ? C16 RET 301 A 1 HETATM 17 C C17 RET . . . B 2 25.458 61.76 -3.401 1 56.11 ? C17 RET 301 A 1 HETATM 18 C C18 RET . . . B 2 28.615 59.568 -0.269 1 50.5 ? C18 RET 301 A 1 HETATM 19 C C19 RET . . . B 2 25.498 62.18 2.215 1 50.48 ? C19 RET 301 A 1 HETATM 20 C C20 RET . . . B 2 21.73 65.377 4.43 1 57.72 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #