data_1GZM # _model_server_result.job_id OxtUbbaFDfZa1L-W45FTFw _model_server_result.datetime_utc '2024-11-26 21:21:26' _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 1gzm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":1332}' # _entry.id 1GZM # _exptl.entry_id 1GZM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 3 _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 90 _cell.angle_gamma 120 _cell.entry_id 1GZM _cell.length_a 103.82 _cell.length_b 103.82 _cell.length_c 76.59 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GZM _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 S N 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 # 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 C NAG 1 C 1 NAG A 1335 NAG 2 n C NAG 2 C 2 NAG A 1336 NAG 2 n C BMA 3 C 3 BMA A 1337 BMA 2 n D NAG 1 D 1 NAG A 1338 NAG 2 n D NAG 2 D 2 NAG A 1339 NAG 2 n D BMA 3 D 3 BMA A 1340 BMA 2 n E NAG 1 E 1 NAG B 1335 NAG 2 n E NAG 2 E 2 NAG B 1336 NAG 2 n E BMA 3 E 3 BMA B 1350 BMA 2 n F NAG 1 F 1 NAG B 1337 NAG 2 n F NAG 2 F 2 NAG B 1338 NAG 2 n F BMA 3 F 3 BMA B 1339 BMA # 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 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 B SG CYS 111 B CYS 110 1_555 B SG CYS 188 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A ND2 ASN 3 A ASN 2 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 A ND2 ASN 16 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale4 A NZ LYS 297 A LYS 296 1_555 G C15 RET . A RET 1332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 A SG CYS 323 A CYS 322 1_555 H C1 PLM . A PLM 1333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.794 ? covale ? covale6 A SG CYS 324 A CYS 323 1_555 I C1 PLM . A PLM 1334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? covale ? covale7 B C ACE 1 B ACE 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 B ND2 ASN 3 B ASN 2 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale9 B ND2 ASN 16 B ASN 15 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 B NZ LYS 297 B LYS 296 1_555 S C15 RET . B RET 1332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale11 B SG CYS 323 B CYS 322 1_555 T C1 PLM . B PLM 1333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.801 ? covale ? covale12 B SG CYS 324 B CYS 323 1_555 U C1 PLM . B PLM 1334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? covale ? covale13 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale14 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale15 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale16 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale17 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale18 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale19 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale20 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? metalc ? metalc1 B ND2 ASN 152 B ASN 151 1_555 EA ZN ZN . B ZN 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? # _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 606 n n C1 C6 RET sing 607 n n C1 C16 RET sing 608 n n C1 C17 RET sing 609 n n C2 C3 RET sing 610 n n C2 H21 RET sing 611 n n C2 H22 RET sing 612 n n C3 C4 RET sing 613 n n C3 H31 RET sing 614 n n C3 H32 RET sing 615 n n C4 C5 RET sing 616 n n C4 H41 RET sing 617 n n C4 H42 RET sing 618 n n C5 C6 RET doub 619 n n C5 C18 RET sing 620 n n C6 C7 RET sing 621 n n C7 C8 RET doub 622 e n C7 H7 RET sing 623 n n C8 C9 RET sing 624 n n C8 H8 RET sing 625 n n C9 C10 RET doub 626 e n C9 C19 RET sing 627 n n C10 C11 RET sing 628 n n C10 H10 RET sing 629 n n C11 C12 RET doub 630 e n C11 H11 RET sing 631 n n C12 C13 RET sing 632 n n C12 H12 RET sing 633 n n C13 C14 RET doub 634 e n C13 C20 RET sing 635 n n C14 C15 RET sing 636 n n C14 H14 RET sing 637 n n C15 O1 RET doub 638 n n C15 H15 RET sing 639 n n C16 H161 RET sing 640 n n C16 H162 RET sing 641 n n C16 H163 RET sing 642 n n C17 H171 RET sing 643 n n C17 H172 RET sing 644 n n C17 H173 RET sing 645 n n C18 H181 RET sing 646 n n C18 H182 RET sing 647 n n C18 H183 RET sing 648 n n C19 H191 RET sing 649 n n C19 H192 RET sing 650 n n C19 H193 RET sing 651 n n C20 H201 RET sing 652 n n C20 H202 RET sing 653 n n C20 H203 RET sing 654 n n # _atom_sites.entry_id 1GZM _atom_sites.fract_transf_matrix[1][1] 0.009632 _atom_sites.fract_transf_matrix[1][2] 0.005561 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011122 _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] 0.013057 _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 G 3 RET A 1 1332 1332 RET RET . H 4 PLM A 1 1333 1333 PLM PLM . I 4 PLM A 1 1334 1334 PLM PLM . J 5 PEF A 1 1341 1341 PEF PEF . K 6 LDA A 1 1342 1342 LDA LDA . L 7 C8E A 1 1343 1343 C8E C8E . M 7 C8E A 1 1344 1344 C8E C8E . N 7 C8E A 1 1345 1345 C8E C8E . O 7 C8E A 1 1346 1346 C8E C8E . P 7 C8E A 1 1347 1347 C8E C8E . Q 7 C8E A 1 1348 1348 C8E C8E . R 8 ZN A 1 1349 1349 ZN ZN . S 3 RET B 1 1332 1332 RET RET . T 4 PLM B 1 1333 1333 PLM PLM . U 4 PLM B 1 1334 1334 PLM PLM . V 7 C8E B 1 1340 1340 C8E C8E . W 7 C8E B 1 1341 1341 C8E C8E . X 5 PEF B 1 1342 1342 PEF PEF . Y 6 LDA B 1 1343 1343 LDA LDA . Z 7 C8E B 1 1344 1344 C8E C8E . AA 7 C8E B 1 1345 1345 C8E C8E . BA 7 C8E B 1 1346 1346 C8E C8E . CA 7 C8E B 1 1347 1347 C8E C8E . DA 6 LDA B 1 1348 1348 LDA LDA . EA 8 ZN B 1 1349 1349 ZN ZN . FA 9 HOH A 1 2001 2001 HOH HOH . FA 9 HOH A 2 2002 2002 HOH HOH . FA 9 HOH A 3 2003 2003 HOH HOH . FA 9 HOH A 4 2004 2004 HOH HOH . FA 9 HOH A 5 2005 2005 HOH HOH . FA 9 HOH A 6 2006 2006 HOH HOH . FA 9 HOH A 7 2007 2007 HOH HOH . FA 9 HOH A 8 2008 2008 HOH HOH . FA 9 HOH A 9 2009 2009 HOH HOH . FA 9 HOH A 10 2010 2010 HOH HOH . FA 9 HOH A 11 2011 2011 HOH HOH . FA 9 HOH A 12 2012 2012 HOH HOH . FA 9 HOH A 13 2013 2013 HOH HOH . FA 9 HOH A 14 2014 2014 HOH HOH . FA 9 HOH A 15 2015 2015 HOH HOH . FA 9 HOH A 16 2016 2016 HOH HOH . FA 9 HOH A 17 2017 2017 HOH HOH . FA 9 HOH A 18 2018 2018 HOH HOH . FA 9 HOH A 19 2019 2019 HOH HOH . FA 9 HOH A 20 2020 2020 HOH HOH . GA 9 HOH B 1 2001 2001 HOH HOH . GA 9 HOH B 2 2002 2002 HOH HOH . GA 9 HOH B 3 2003 2003 HOH HOH . GA 9 HOH B 4 2004 2004 HOH HOH . GA 9 HOH B 5 2005 2005 HOH HOH . GA 9 HOH B 6 2006 2006 HOH HOH . GA 9 HOH B 7 2007 2007 HOH HOH . GA 9 HOH B 8 2008 2008 HOH HOH . GA 9 HOH B 9 2009 2009 HOH HOH . GA 9 HOH B 10 2010 2010 HOH HOH . GA 9 HOH B 11 2011 2011 HOH HOH . GA 9 HOH B 12 2012 2012 HOH HOH . GA 9 HOH B 13 2013 2013 HOH HOH . GA 9 HOH B 14 2014 2014 HOH HOH . GA 9 HOH B 15 2015 2015 HOH HOH . GA 9 HOH B 16 2016 2016 HOH HOH . GA 9 HOH B 17 2017 2017 HOH HOH . GA 9 HOH B 18 2018 2018 HOH HOH . GA 9 HOH B 19 2019 2019 HOH HOH . GA 9 HOH B 20 2020 2020 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 . . . S 3 18.098 6.252 -1.644 1 31.98 ? C1 RET 1332 B 1 HETATM 2 C C2 RET . . . S 3 18.196 7.787 -1.678 1 34.78 ? C2 RET 1332 B 1 HETATM 3 C C3 RET . . . S 3 16.999 8.535 -1.142 1 36.82 ? C3 RET 1332 B 1 HETATM 4 C C4 RET . . . S 3 15.671 8.047 -1.749 1 35.23 ? C4 RET 1332 B 1 HETATM 5 C C5 RET . . . S 3 15.551 6.532 -1.834 1 35.03 ? C5 RET 1332 B 1 HETATM 6 C C6 RET . . . S 3 16.638 5.703 -1.753 1 35.44 ? C6 RET 1332 B 1 HETATM 7 C C7 RET . . . S 3 16.55 4.191 -1.729 1 38.74 ? C7 RET 1332 B 1 HETATM 8 C C8 RET . . . S 3 15.814 3.479 -0.87 1 41.27 ? C8 RET 1332 B 1 HETATM 9 C C9 RET . . . S 3 15.681 2.042 -0.712 1 42.9 ? C9 RET 1332 B 1 HETATM 10 C C10 RET . . . S 3 14.805 1.644 0.256 1 43.23 ? C10 RET 1332 B 1 HETATM 11 C C11 RET . . . S 3 14.443 0.282 0.628 1 43 ? C11 RET 1332 B 1 HETATM 12 C C12 RET . . . S 3 13.658 -0.171 1.631 1 39.67 ? C12 RET 1332 B 1 HETATM 13 C C13 RET . . . S 3 13.081 0.446 2.85 1 38.91 ? C13 RET 1332 B 1 HETATM 14 C C14 RET . . . S 3 12.18 -0.316 3.542 1 38.03 ? C14 RET 1332 B 1 HETATM 15 C C15 RET . . . S 3 11.55 0.063 4.814 1 36.04 ? C15 RET 1332 B 1 HETATM 16 C C16 RET . . . S 3 18.945 5.772 -2.806 1 29.94 ? C16 RET 1332 B 1 HETATM 17 C C17 RET . . . S 3 18.791 5.72 -0.381 1 28.95 ? C17 RET 1332 B 1 HETATM 18 C C18 RET . . . S 3 14.091 6.141 -1.888 1 35.5 ? C18 RET 1332 B 1 HETATM 19 C C19 RET . . . S 3 16.51 1.136 -1.593 1 40.01 ? C19 RET 1332 B 1 HETATM 20 C C20 RET . . . S 3 13.475 1.823 3.348 1 39.67 ? C20 RET 1332 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #