data_5DYS # _model_server_result.job_id 4VMwUjxb0zK61kxzqooXXw _model_server_result.datetime_utc '2024-11-16 18:45:42' _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 5dys # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5DYS # _exptl.entry_id 5DYS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation 'N2C, D282C, T94I' _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 5DYS _cell.length_a 242.301 _cell.length_b 242.301 _cell.length_c 112.055 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYS _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 BMA BMA C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG S 301 NAG 2 n B NAG 2 B 2 NAG S 302 NAG 2 n B BMA 3 B 3 BMA S 303 BMA 2 n B MAN 4 B 4 MAN S 304 MAN 2 n B BMA 5 B 5 BMA S 305 MAN # 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 disulf ? disulf1 A SG CYS 3 A CYS 2 1_555 A SG CYS 283 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A NZ LYS 297 A LYS 296 1_555 C C15 RET . A RET 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.273 ? covale ? covale4 A SG CYS 323 A CYS 322 1_555 G C1 PLM . A PLM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.705 ? covale ? covale5 A SG CYS 324 A CYS 323 1_555 H C1 PLM . A PLM 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.692 ? covale ? covale6 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale7 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale8 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 B O6 BMA . B BMA 3 1_555 B C1 BMA . B BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? # _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 464 n n C1 C6 RET sing 465 n n C1 C16 RET sing 466 n n C1 C17 RET sing 467 n n C2 C3 RET sing 468 n n C2 H21 RET sing 469 n n C2 H22 RET sing 470 n n C3 C4 RET sing 471 n n C3 H31 RET sing 472 n n C3 H32 RET sing 473 n n C4 C5 RET sing 474 n n C4 H41 RET sing 475 n n C4 H42 RET sing 476 n n C5 C6 RET doub 477 n n C5 C18 RET sing 478 n n C6 C7 RET sing 479 n n C7 C8 RET doub 480 e n C7 H7 RET sing 481 n n C8 C9 RET sing 482 n n C8 H8 RET sing 483 n n C9 C10 RET doub 484 e n C9 C19 RET sing 485 n n C10 C11 RET sing 486 n n C10 H10 RET sing 487 n n C11 C12 RET doub 488 e n C11 H11 RET sing 489 n n C12 C13 RET sing 490 n n C12 H12 RET sing 491 n n C13 C14 RET doub 492 e n C13 C20 RET sing 493 n n C14 C15 RET sing 494 n n C14 H14 RET sing 495 n n C15 O1 RET doub 496 n n C15 H15 RET sing 497 n n C16 H161 RET sing 498 n n C16 H162 RET sing 499 n n C16 H163 RET sing 500 n n C17 H171 RET sing 501 n n C17 H172 RET sing 502 n n C17 H173 RET sing 503 n n C18 H181 RET sing 504 n n C18 H182 RET sing 505 n n C18 H183 RET sing 506 n n C19 H191 RET sing 507 n n C19 H192 RET sing 508 n n C19 H193 RET sing 509 n n C20 H201 RET sing 510 n n C20 H202 RET sing 511 n n C20 H203 RET sing 512 n n # _atom_sites.entry_id 5DYS _atom_sites.fract_transf_matrix[1][1] 0.004127 _atom_sites.fract_transf_matrix[1][2] 0.002383 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004766 _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] 0.008924 _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 3 RET A 1 401 401 RET RET . D 4 ACT A 1 402 102 ACT ACT . E 4 ACT A 1 403 103 ACT ACT . F 5 BOG A 1 404 204 BOG BOG . G 6 PLM A 1 405 205 PLM PLM . H 6 PLM A 1 406 206 PLM PLM . I 5 BOG A 1 412 601 BOG BOG . J 7 SO4 A 1 413 801 SO4 SO4 . K 8 HOH A 1 501 25 HOH HOH . K 8 HOH A 2 502 21 HOH HOH . K 8 HOH A 3 503 43 HOH HOH . K 8 HOH A 4 504 5 HOH HOH . K 8 HOH A 5 505 41 HOH HOH . K 8 HOH A 6 506 4 HOH HOH . K 8 HOH A 7 507 14 HOH HOH . K 8 HOH A 8 508 44 HOH HOH . K 8 HOH A 9 509 46 HOH HOH . K 8 HOH A 10 510 3 HOH HOH . K 8 HOH A 11 511 26 HOH HOH . K 8 HOH A 12 512 18 HOH HOH . K 8 HOH A 13 513 13 HOH HOH . K 8 HOH A 14 514 19 HOH HOH . K 8 HOH A 15 515 20 HOH HOH . K 8 HOH A 16 516 27 HOH HOH . K 8 HOH A 17 517 8 HOH HOH . K 8 HOH A 18 518 28 HOH HOH . K 8 HOH A 19 519 45 HOH HOH . K 8 HOH A 20 520 12 HOH HOH . K 8 HOH A 21 521 35 HOH HOH . K 8 HOH A 22 522 32 HOH HOH . K 8 HOH A 23 523 10 HOH HOH . K 8 HOH A 24 524 39 HOH HOH . K 8 HOH A 25 525 11 HOH HOH . K 8 HOH A 26 526 1 HOH HOH . K 8 HOH A 27 527 40 HOH HOH . K 8 HOH A 28 528 7 HOH HOH . K 8 HOH A 29 529 23 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 . . . C 3 -43.285 -16.241 34.783 1 74.6 ? C1 RET 401 A 1 HETATM 2 C C2 RET . . . C 3 -43.521 -17.749 34.895 1 75.05 ? C2 RET 401 A 1 HETATM 3 C C3 RET . . . C 3 -44.636 -18.22 33.976 1 76.22 ? C3 RET 401 A 1 HETATM 4 C C4 RET . . . C 3 -45.94 -17.536 34.33 1 74.78 ? C4 RET 401 A 1 HETATM 5 C C5 RET . . . C 3 -45.766 -16.038 34.302 1 74.07 ? C5 RET 401 A 1 HETATM 6 C C6 RET . . . C 3 -44.594 -15.451 34.645 1 75.51 ? C6 RET 401 A 1 HETATM 7 C C7 RET . . . C 3 -44.497 -13.969 34.647 1 73.47 ? C7 RET 401 A 1 HETATM 8 C C8 RET . . . C 3 -44.907 -13.262 35.695 1 67.4 ? C8 RET 401 A 1 HETATM 9 C C9 RET . . . C 3 -44.736 -11.798 35.767 1 66.79 ? C9 RET 401 A 1 HETATM 10 C C10 RET . . . C 3 -45.561 -11.164 36.629 1 67.65 ? C10 RET 401 A 1 HETATM 11 C C11 RET . . . C 3 -45.406 -9.791 37.12 1 61.64 ? C11 RET 401 A 1 HETATM 12 C C12 RET . . . C 3 -46.152 -9.459 38.183 1 66.97 ? C12 RET 401 A 1 HETATM 13 C C13 RET . . . C 3 -46.096 -8.15 38.894 1 68.72 ? C13 RET 401 A 1 HETATM 14 C C14 RET . . . C 3 -47.091 -7.874 39.776 1 66.22 ? C14 RET 401 A 1 HETATM 15 C C15 RET . . . C 3 -47.077 -6.748 40.713 1 62.53 ? C15 RET 401 A 1 HETATM 16 C C16 RET . . . C 3 -42.392 -15.904 33.586 1 72.21 ? C16 RET 401 A 1 HETATM 17 C C17 RET . . . C 3 -42.519 -15.841 36.041 1 77.17 ? C17 RET 401 A 1 HETATM 18 C C18 RET . . . C 3 -46.978 -15.226 33.972 1 72.58 ? C18 RET 401 A 1 HETATM 19 C C19 RET . . . C 3 -43.765 -11.081 34.86 1 68.75 ? C19 RET 401 A 1 HETATM 20 C C20 RET . . . C 3 -44.941 -7.209 38.669 1 73.48 ? C20 RET 401 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #