data_2X72 # _model_server_result.job_id fUk9t3RDanVMnsHdMmvgpA _model_server_result.datetime_utc '2024-11-26 17:47:46' _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 2x72 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":410}' # _entry.id 2X72 # _exptl.entry_id 2X72 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 7 _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 120 _cell.entry_id 2X72 _cell.length_a 243.986 _cell.length_b 243.986 _cell.length_c 109.156 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2X72 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 109.156 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN 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 3 n C NAG 1 C 1 NAG A 1333 NAG 3 n C NAG 2 C 2 NAG A 1334 NAG 3 n C BMA 3 C 3 BMA A 1335 BMA 3 n C MAN 4 C 4 MAN A 1336 MAN 3 n C MAN 5 C 5 MAN A 1337 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 A SG CYS 323 A CYS 322 1_555 G C1 PLM . A PLM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.674 ? covale ? covale4 A SG CYS 324 A CYS 323 1_555 F C1 PLM . A PLM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.692 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale8 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _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 696 n n C1 C6 RET sing 697 n n C1 C16 RET sing 698 n n C1 C17 RET sing 699 n n C2 C3 RET sing 700 n n C2 H21 RET sing 701 n n C2 H22 RET sing 702 n n C3 C4 RET sing 703 n n C3 H31 RET sing 704 n n C3 H32 RET sing 705 n n C4 C5 RET sing 706 n n C4 H41 RET sing 707 n n C4 H42 RET sing 708 n n C5 C6 RET doub 709 n n C5 C18 RET sing 710 n n C6 C7 RET sing 711 n n C7 C8 RET doub 712 e n C7 H7 RET sing 713 n n C8 C9 RET sing 714 n n C8 H8 RET sing 715 n n C9 C10 RET doub 716 e n C9 C19 RET sing 717 n n C10 C11 RET sing 718 n n C10 H10 RET sing 719 n n C11 C12 RET doub 720 e n C11 H11 RET sing 721 n n C12 C13 RET sing 722 n n C12 H12 RET sing 723 n n C13 C14 RET doub 724 e n C13 C20 RET sing 725 n n C14 C15 RET sing 726 n n C14 H14 RET sing 727 n n C15 O1 RET doub 728 n n C15 H15 RET sing 729 n n C16 H161 RET sing 730 n n C16 H162 RET sing 731 n n C16 H163 RET sing 732 n n C17 H171 RET sing 733 n n C17 H172 RET sing 734 n n C17 H173 RET sing 735 n n C18 H181 RET sing 736 n n C18 H182 RET sing 737 n n C18 H183 RET sing 738 n n C19 H191 RET sing 739 n n C19 H192 RET sing 740 n n C19 H193 RET sing 741 n n C20 H201 RET sing 742 n n C20 H202 RET sing 743 n n C20 H203 RET sing 744 n n # _atom_sites.entry_id 2X72 _atom_sites.fract_transf_matrix[1][1] 0.004099 _atom_sites.fract_transf_matrix[1][2] 0.002366 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004733 _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] 0.009161 _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 D 4 PEF A 1 401 1329 PEF PEF . E 5 BOG A 1 402 1330 BOG BOG . F 6 PLM A 1 403 1331 PLM PLM . G 6 PLM A 1 404 1332 PLM PLM . H 7 RET A 1 410 1338 RET RET . I 8 LPP A 1 411 1340 LPP LPP . J 9 ACT A 1 412 1351 ACT ACT . K 10 HOH A 1 501 2014 HOH HOH . K 10 HOH A 2 502 2011 HOH HOH . K 10 HOH A 3 503 2009 HOH HOH . K 10 HOH A 4 504 2018 HOH HOH . K 10 HOH A 5 505 2007 HOH HOH . K 10 HOH A 6 506 2013 HOH HOH . K 10 HOH A 7 507 2003 HOH HOH . K 10 HOH A 8 508 2004 HOH HOH . K 10 HOH A 9 509 2001 HOH HOH . K 10 HOH A 10 510 2002 HOH HOH . K 10 HOH A 11 511 2010 HOH HOH . K 10 HOH A 12 512 2016 HOH HOH . K 10 HOH A 13 513 2012 HOH HOH . K 10 HOH A 14 514 2006 HOH HOH . K 10 HOH A 15 515 2017 HOH HOH . K 10 HOH A 16 516 2015 HOH HOH . L 10 HOH B 1 401 2005 HOH HOH . L 10 HOH B 2 402 2008 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 7 39.003 -30.972 33.378 0.75 86.59 ? C1 RET 410 A 1 HETATM 2 C C2 RET . . . H 7 39.687 -29.602 33.321 0.75 83.32 ? C2 RET 410 A 1 HETATM 3 C C3 RET . . . H 7 39.037 -28.598 34.262 0.75 84.18 ? C3 RET 410 A 1 HETATM 4 C C4 RET . . . H 7 37.604 -28.396 33.829 0.75 81.49 ? C4 RET 410 A 1 HETATM 5 C C5 RET . . . H 7 36.915 -29.699 33.906 0.75 90.1 ? C5 RET 410 A 1 HETATM 6 C C6 RET . . . H 7 37.567 -30.877 33.765 0.75 86.39 ? C6 RET 410 A 1 HETATM 7 C C7 RET . . . H 7 37.045 -32.229 33.955 0.75 78.84 ? C7 RET 410 A 1 HETATM 8 C C8 RET . . . H 7 35.958 -32.549 34.679 0.75 84.66 ? C8 RET 410 A 1 HETATM 9 C C9 RET . . . H 7 35.465 -33.891 34.775 0.75 84.62 ? C9 RET 410 A 1 HETATM 10 C C10 RET . . . H 7 34.287 -34.136 35.379 0.75 83.3 ? C10 RET 410 A 1 HETATM 11 C C11 RET . . . H 7 33.675 -35.42 35.317 0.75 80.83 ? C11 RET 410 A 1 HETATM 12 C C12 RET . . . H 7 32.558 -35.734 36 0.75 86.31 ? C12 RET 410 A 1 HETATM 13 C C13 RET . . . H 7 31.943 -37.019 35.814 0.75 87.25 ? C13 RET 410 A 1 HETATM 14 C C14 RET . . . H 7 31.115 -37.573 36.727 0.75 79.98 ? C14 RET 410 A 1 HETATM 15 C C15 RET . . . H 7 30.551 -38.894 36.569 0.75 77.82 ? C15 RET 410 A 1 HETATM 16 O O1 RET . . . H 7 29.91 -39.431 37.473 0.75 82.05 ? O1 RET 410 A 1 HETATM 17 C C16 RET . . . H 7 39.624 -31.937 34.389 0.75 89.68 ? C16 RET 410 A 1 HETATM 18 C C17 RET . . . H 7 39.153 -31.63 32.002 0.75 86.47 ? C17 RET 410 A 1 HETATM 19 C C18 RET . . . H 7 35.45 -29.515 34.129 0.75 87.5 ? C18 RET 410 A 1 HETATM 20 C C19 RET . . . H 7 36.247 -34.987 34.126 0.75 85.58 ? C19 RET 410 A 1 HETATM 21 C C20 RET . . . H 7 32.303 -37.72 34.551 0.75 73.93 ? C20 RET 410 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #