data_7VFU # _model_server_result.job_id ppZ4_GFu18FqZsNkNYdaUQ _model_server_result.datetime_utc '2024-11-04 22:34:18' _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 7vfu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":2404}' # _entry.id 7VFU # _exptl.entry_id 7VFU _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 486.726 _entity.id 8 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'CHOLESTEROL HEMISUCCINATE' _entity.pdbx_number_of_molecules 3 _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 7VFU _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VFU _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA _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 ? _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 ? 8 K N N ? 8 S N N ? 8 BA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 6 3 2 BMA NAG C1 O1 . O3 HO3 . 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 5 n E NAG 1 C 1 NAG B 1235 NAG 5 n E NAG 2 C 2 NAG B 1236 NAG 5 n E BMA 3 C 3 BMA B 1237 BMA 5 n F NAG 1 F 1 NAG B 1241 NAG 5 n F NAG 2 F 2 NAG B 1242 NAG 5 n F BMA 3 F 3 BMA B 1243 BMA 6 n G NAG 1 G 1 NAG B 1247 NAG 6 n G NAG 2 G 2 NAG B 1248 NAG 6 n G BMA 3 G 3 BMA B 1249 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 253 A CYS 253 1_555 A SG CYS 277 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 268 A CYS 268 1_555 A SG CYS 283 A CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 1311 A CYS 1311 1_555 A SG CYS 1322 A CYS 1322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 A SG CYS 1670 A CYS 1670 1_555 A SG CYS 1679 A CYS 1679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 B SG CYS 1 E CYS 1 1_555 B SG CYS 16 E CYS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 B SG CYS 8 E CYS 8 1_555 B SG CYS 20 E CYS 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 15 E CYS 15 1_555 B SG CYS 25 E CYS 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 D SG CYS 303 B CYS 303 1_555 D SG CYS 1044 B CYS 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf9 D SG CYS 354 B CYS 354 1_555 D SG CYS 1059 B CYS 1059 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf10 D SG CYS 404 B CYS 404 1_555 D SG CYS 1071 B CYS 1071 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 D SG CYS 667 B CYS 667 1_555 D SG CYS 697 B CYS 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf12 D SG CYS 904 B CYS 904 1_555 D SG CYS 974 B CYS 974 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf13 D SG CYS 996 B CYS 996 1_555 D SG CYS 1026 B CYS 1026 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 D SG CYS 999 B CYS 999 1_555 D SG CYS 1024 B CYS 1024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 D ND2 ASN 92 B ASN 92 1_555 FA C1 NAG . B NAG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 D ND2 ASN 184 B ASN 184 1_555 MA C1 NAG . B NAG 1208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 D ND2 ASN 324 B ASN 324 1_555 GA C1 NAG . B NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 D ND2 ASN 348 B ASN 348 1_555 HA C1 NAG . B NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 D ND2 ASN 468 B ASN 468 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 D ND2 ASN 604 B ASN 604 1_555 IA C1 NAG . B NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 D ND2 ASN 613 B ASN 613 1_555 JA C1 NAG . B NAG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 D ND2 ASN 675 B ASN 675 1_555 KA C1 NAG . B NAG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale9 D ND2 ASN 824 B ASN 824 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 D ND2 ASN 888 B ASN 888 1_555 LA C1 NAG . B NAG 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 D ND2 ASN 895 B ASN 895 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale12 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale13 E O4 NAG . C NAG 2 1_555 E C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale14 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale15 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale16 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale17 G O3 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc1 A OD2 ASP 122 A ASP 122 1_555 DA CA CA . A CA 2423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc2 A OE1 GLU 314 A GLU 314 1_555 EA CA CA . A CA 2424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? metalc ? metalc3 A OE2 GLU 314 A GLU 314 1_555 EA CA CA . A CA 2424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc4 A OE1 GLU 663 A GLU 663 1_555 EA CA CA . A CA 2424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? metalc ? metalc5 A OE2 GLU 1365 A GLU 1365 1_555 EA CA CA . A CA 2424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc6 DA CA CA . A CA 2423 1_555 D OG SER 263 B SER 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc7 DA CA CA . A CA 2423 1_555 D OG1 THR 331 B THR 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? # _chem_comp.formula 'C31 H50 O4' _chem_comp.formula_weight 486.726 _chem_comp.id Y01 _chem_comp.mon_nstd_flag . _chem_comp.name 'CHOLESTEROL HEMISUCCINATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7VFU _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 H 7 R16 A 1 2401 2402 R16 R16 . I 7 R16 A 1 2402 2403 R16 R16 . J 7 R16 A 1 2403 2404 R16 R16 . K 8 Y01 A 1 2404 2405 Y01 Y01 . L 7 R16 A 1 2405 2406 R16 R16 . M 7 R16 A 1 2406 2407 R16 R16 . N 7 R16 A 1 2407 2408 R16 R16 . O 7 R16 A 1 2408 2409 R16 R16 . P 7 R16 A 1 2409 2410 R16 R16 . Q 7 R16 A 1 2410 2411 R16 R16 . R 7 R16 A 1 2411 2413 R16 R16 . S 8 Y01 A 1 2412 2414 Y01 Y01 . T 7 R16 A 1 2413 2415 R16 R16 . U 7 R16 A 1 2414 2416 R16 R16 . V 7 R16 A 1 2415 2417 R16 R16 . W 7 R16 A 1 2416 2419 R16 R16 . X 7 R16 A 1 2417 2421 R16 R16 . Y 7 R16 A 1 2418 2422 R16 R16 . Z 7 R16 A 1 2419 2423 R16 R16 . AA 7 R16 A 1 2420 2424 R16 R16 . BA 8 Y01 A 1 2421 2426 Y01 Y01 . CA 9 PT5 A 1 2422 2427 PT5 PT5 . DA 10 CA A 1 2423 1201 CA CA . EA 10 CA A 1 2424 1 CA CA . FA 11 NAG B 1 1201 1238 NAG NAG . GA 11 NAG B 1 1202 1239 NAG NAG . HA 11 NAG B 1 1203 1240 NAG NAG . IA 11 NAG B 1 1204 1244 NAG NAG . JA 11 NAG B 1 1205 1245 NAG NAG . KA 11 NAG B 1 1206 1246 NAG NAG . LA 11 NAG B 1 1207 1250 NAG NAG . MA 11 NAG B 1 1208 1251 NAG NAG . # 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 CAA Y01 . . . K 8 153.765 185.182 185.373 1 53.2 ? CAA Y01 2404 A 1 HETATM 2 C CBA Y01 . . . K 8 155.27 184.876 185.289 1 53.2 ? CBA Y01 2404 A 1 HETATM 3 C CAB Y01 . . . K 8 155.751 184.297 186.622 1 53.2 ? CAB Y01 2404 A 1 HETATM 4 C CAN Y01 . . . K 8 155.556 183.863 184.151 1 53.2 ? CAN Y01 2404 A 1 HETATM 5 C CAJ Y01 . . . K 8 154.399 182.829 183.962 1 53.2 ? CAJ Y01 2404 A 1 HETATM 6 C CAO Y01 . . . K 8 153.85 182.839 182.497 1 53.2 ? CAO Y01 2404 A 1 HETATM 7 C CBB Y01 . . . K 8 152.264 182.572 182.341 1 53.2 ? CBB Y01 2404 A 1 HETATM 8 C CAC Y01 . . . K 8 151.726 182.008 183.677 1 53.2 ? CAC Y01 2404 A 1 HETATM 9 C CBE Y01 . . . K 8 151.45 183.717 181.957 1 53.2 ? CBE Y01 2404 A 1 HETATM 10 C CAP Y01 . . . K 8 152.266 185.039 181.916 1 53.2 ? CAP Y01 2404 A 1 HETATM 11 C CAQ Y01 . . . K 8 151.277 186.081 180.962 1 53.2 ? CAQ Y01 2404 A 1 HETATM 12 C CBG Y01 . . . K 8 150.27 185.065 180.15 1 53.2 ? CBG Y01 2404 A 1 HETATM 13 C CBI Y01 . . . K 8 150.822 183.63 180.433 1 53.2 ? CBI Y01 2404 A 1 HETATM 14 C CAE Y01 . . . K 8 152.013 183.478 179.5 1 53.2 ? CAE Y01 2404 A 1 HETATM 15 C CAU Y01 . . . K 8 149.905 182.635 180.037 1 53.2 ? CAU Y01 2404 A 1 HETATM 16 C CAS Y01 . . . K 8 149.404 182.835 178.473 1 53.2 ? CAS Y01 2404 A 1 HETATM 17 C CBF Y01 . . . K 8 148.884 184.242 178.211 1 53.2 ? CBF Y01 2404 A 1 HETATM 18 C CBD Y01 . . . K 8 149.896 185.278 178.681 1 53.2 ? CBD Y01 2404 A 1 HETATM 19 C CAK Y01 . . . K 8 149.345 186.802 178.495 1 53.2 ? CAK Y01 2404 A 1 HETATM 20 C CAI Y01 . . . K 8 148.74 187.055 177.122 1 53.2 ? CAI Y01 2404 A 1 HETATM 21 C CAZ Y01 . . . K 8 148.706 185.759 176.043 1 53.2 ? CAZ Y01 2404 A 1 HETATM 22 C CAV Y01 . . . K 8 148.13 185.969 174.621 1 53.2 ? CAV Y01 2404 A 1 HETATM 23 C CBH Y01 . . . K 8 148.465 184.408 176.6 1 53.2 ? CBH Y01 2404 A 1 HETATM 24 C CAD Y01 . . . K 8 149.37 183.425 175.861 1 53.2 ? CAD Y01 2404 A 1 HETATM 25 C CAT Y01 . . . K 8 146.998 183.98 176.415 1 53.2 ? CAT Y01 2404 A 1 HETATM 26 C CAR Y01 . . . K 8 146.463 184.2 174.995 1 53.2 ? CAR Y01 2404 A 1 HETATM 27 C CBC Y01 . . . K 8 146.659 185.593 174.5 1 53.2 ? CBC Y01 2404 A 1 HETATM 28 O OAW Y01 . . . K 8 146.304 185.597 173.106 1 53.2 ? OAW Y01 2404 A 1 HETATM 29 C CAY Y01 . . . K 8 145.205 186.418 172.717 1 53.2 ? CAY Y01 2404 A 1 HETATM 30 O OAG Y01 . . . K 8 144.64 187.077 173.527 1 53.2 ? OAG Y01 2404 A 1 HETATM 31 C CAM Y01 . . . K 8 144.735 186.467 171.248 1 53.2 ? CAM Y01 2404 A 1 HETATM 32 C CAL Y01 . . . K 8 145.305 187.751 170.615 1 53.2 ? CAL Y01 2404 A 1 HETATM 33 C CAX Y01 . . . K 8 144.435 188.971 170.957 1 53.2 ? CAX Y01 2404 A 1 HETATM 34 O OAH Y01 . . . K 8 144.719 189.682 171.955 1 53.2 ? OAH Y01 2404 A 1 HETATM 35 O OAF Y01 . . . K 8 143.44 189.263 170.247 1 53.2 ? OAF Y01 2404 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 35 #