data_3C9L # _model_server_result.job_id ZMa-L3zh490DhMdQmKbNqA _model_server_result.datetime_utc '2024-11-08 03:48:19' _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 3c9l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1332}' # _entry.id 3C9L # _exptl.entry_id 3C9L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 5 _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 3C9L _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 3C9L _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 _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 5 _struct_asym.id F _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 # 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 A 1335 NAG 2 n B NAG 2 B 2 NAG A 1336 NAG 2 n B BMA 3 B 3 BMA A 1337 BMA 2 n C NAG 1 C 1 NAG A 1338 NAG 2 n C NAG 2 C 2 NAG A 1339 NAG 2 n C BMA 3 C 3 BMA A 1340 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 110 A CYS 110 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 E C ACE . A ACE 0 1_555 A N MET 1 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A ND2 ASN 2 A ASN 2 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 15 A ASN 15 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A NZ LYS 296 A LYS 296 1_555 F C15 RET . A RET 1332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale5 A SG CYS 322 A CYS 322 1_555 G C1 PLM . A PLM 1333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? covale ? covale6 A SG CYS 323 A CYS 323 1_555 H C1 PLM . A PLM 1334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? covale ? covale7 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale10 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 3C9L _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 D 3 ZN A 1 1349 1349 ZN ZN . E 4 ACE A 1 0 0 ACE ACE . F 5 RET A 1 1332 1332 RET RET . G 6 PLM A 1 1333 1333 PLM PLM . H 6 PLM A 1 1334 1334 PLM PLM . I 7 PEF A 1 1341 1341 PEF PEF . J 8 LDA A 1 1342 1342 LDA LDA . K 9 C8E A 1 1343 1343 C8E C8E . L 9 C8E A 1 1344 1344 C8E C8E . M 9 C8E A 1 1345 1345 C8E C8E . N 9 C8E A 1 1346 1346 C8E C8E . O 9 C8E A 1 1347 1347 C8E C8E . P 9 C8E A 1 1348 1348 C8E C8E . Q 10 HOH A 1 1350 14 HOH HOH . Q 10 HOH A 2 1351 15 HOH HOH . Q 10 HOH A 3 1352 1 HOH HOH . Q 10 HOH A 4 1353 2 HOH HOH . Q 10 HOH A 5 1354 3 HOH HOH . Q 10 HOH A 6 1355 4 HOH HOH . Q 10 HOH A 7 1356 5 HOH HOH . Q 10 HOH A 8 1357 6 HOH HOH . Q 10 HOH A 9 1358 7 HOH HOH . Q 10 HOH A 10 1359 8 HOH HOH . Q 10 HOH A 11 1360 9 HOH HOH . Q 10 HOH A 12 1361 10 HOH HOH . Q 10 HOH A 13 1362 11 HOH HOH . Q 10 HOH A 14 1363 14 HOH HOH . Q 10 HOH A 15 1364 15 HOH HOH . Q 10 HOH A 16 1365 16 HOH HOH . Q 10 HOH A 17 1366 17 HOH HOH . Q 10 HOH A 18 1367 18 HOH HOH . Q 10 HOH A 19 1368 19 HOH HOH . Q 10 HOH A 20 1369 20 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 . . . F 5 -18.074 53.693 -1.661 1 53.11 ? C1 RET 1332 A 1 HETATM 2 C C2 RET . . . F 5 -18.184 52.169 -1.644 1 56.05 ? C2 RET 1332 A 1 HETATM 3 C C3 RET . . . F 5 -16.97 51.446 -1.085 1 57.26 ? C3 RET 1332 A 1 HETATM 4 C C4 RET . . . F 5 -15.706 51.911 -1.793 1 52.82 ? C4 RET 1332 A 1 HETATM 5 C C5 RET . . . F 5 -15.563 53.42 -1.777 1 52.45 ? C5 RET 1332 A 1 HETATM 6 C C6 RET . . . F 5 -16.645 54.234 -1.724 1 53.3 ? C6 RET 1332 A 1 HETATM 7 C C7 RET . . . F 5 -16.52 55.725 -1.737 1 51.52 ? C7 RET 1332 A 1 HETATM 8 C C8 RET . . . F 5 -15.831 56.387 -0.799 1 52.96 ? C8 RET 1332 A 1 HETATM 9 C C9 RET . . . F 5 -15.632 57.854 -0.698 1 50.78 ? C9 RET 1332 A 1 HETATM 10 C C10 RET . . . F 5 -14.774 58.257 0.281 1 51.67 ? C10 RET 1332 A 1 HETATM 11 C C11 RET . . . F 5 -14.401 59.647 0.576 1 53.12 ? C11 RET 1332 A 1 HETATM 12 C C12 RET . . . F 5 -13.681 60.134 1.611 1 51.38 ? C12 RET 1332 A 1 HETATM 13 C C13 RET . . . F 5 -13.067 59.492 2.806 1 53.64 ? C13 RET 1332 A 1 HETATM 14 C C14 RET . . . F 5 -12.181 60.234 3.52 1 54.58 ? C14 RET 1332 A 1 HETATM 15 C C15 RET . . . F 5 -11.481 59.812 4.743 1 51.74 ? C15 RET 1332 A 1 HETATM 16 C C16 RET . . . F 5 -18.855 54.168 -2.88 1 51.07 ? C16 RET 1332 A 1 HETATM 17 C C17 RET . . . F 5 -18.72 54.235 -0.388 1 45.35 ? C17 RET 1332 A 1 HETATM 18 C C18 RET . . . F 5 -14.151 53.957 -1.839 1 48.05 ? C18 RET 1332 A 1 HETATM 19 C C19 RET . . . F 5 -16.365 58.789 -1.618 1 46.02 ? C19 RET 1332 A 1 HETATM 20 C C20 RET . . . F 5 -13.443 58.107 3.249 1 50.58 ? C20 RET 1332 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #