data_8Y81 # _model_server_result.job_id -vEt6NFD1xHTlxBIA4yABw _model_server_result.datetime_utc '2024-11-22 13:12:42' _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 8y81 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":601}' # _entry.id 8Y81 # _exptl.entry_id 8Y81 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 486.726 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CHOLESTEROL HEMISUCCINATE' _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 90 _cell.entry_id 8Y81 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y81 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,M,N,O _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 8 _struct_asym.id L _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 # 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 G NAG 1 D 1 NAG E 432 NAG 5 n G NAG 2 D 2 NAG E 433 NAG 5 n G BMA 3 D 3 BMA E 434 BMA 5 n H NAG 1 H 1 NAG F 417 NAG 5 n H NAG 2 H 2 NAG F 418 NAG 5 n H BMA 3 H 3 BMA F 419 BMA 6 n I NAG 1 T 1 NAG T 729 NAG 6 n I NAG 2 T 2 NAG T 730 NAG # 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 49 A CYS 49 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 A SG CYS 130 A CYS 130 1_555 A SG CYS 174 A CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 162 B CYS 162 1_555 B SG CYS 171 B CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 C SG CYS 25 C CYS 25 1_555 F SG CYS 25 G CYS 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 D SG CYS 40 E CYS 112 1_555 E SG CYS 128 F CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf6 D SG CYS 53 E CYS 125 1_555 D SG CYS 112 E CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 D SG CYS 158 E CYS 230 1_555 D SG CYS 217 E CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 D SG CYS 262 E CYS 334 1_555 D SG CYS 324 E CYS 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf9 E SG CYS 53 F CYS 125 1_555 E SG CYS 112 F CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 E SG CYS 158 F CYS 230 1_555 E SG CYS 217 F CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf11 E SG CYS 262 F CYS 334 1_555 E SG CYS 324 F CYS 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 65 A ASN 65 1_555 I C1 NAG . T NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 158 A ASN 158 1_555 J C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale3 A ND2 ASN 167 A ASN 167 1_555 K C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale4 D ND2 ASN 168 E ASN 240 1_555 N C1 NAG . E NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 D ND2 ASN 193 E ASN 265 1_555 G C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale6 E ND2 ASN 98 F ASN 170 1_555 O C1 NAG . F NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale7 E ND2 ASN 193 F ASN 265 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 G O4 NAG . D NAG 1 1_555 G C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale9 G O4 NAG . D NAG 2 1_555 G C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale10 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale11 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 I O4 NAG . T NAG 1 1_555 I C1 NAG . T NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 ? # 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 CAA CBA Y01 sing 428 n n CBA CAB Y01 sing 429 n n CBA CAN Y01 sing 430 n n CAN CAJ Y01 sing 431 n n CAJ CAO Y01 sing 432 n n CAO CBB Y01 sing 433 n n CBB CAC Y01 sing 434 n n CBB CBE Y01 sing 435 n n CBE CAP Y01 sing 436 n n CBE CBI Y01 sing 437 n n CAP CAQ Y01 sing 438 n n CAQ CBG Y01 sing 439 n n CBG CBI Y01 sing 440 n n CBG CBD Y01 sing 441 n n CBI CAE Y01 sing 442 n n CBI CAU Y01 sing 443 n n CAU CAS Y01 sing 444 n n CAS CBF Y01 sing 445 n n CBF CBD Y01 sing 446 n n CBF CBH Y01 sing 447 n n CBD CAK Y01 sing 448 n n CAK CAI Y01 sing 449 n n CAI CAZ Y01 doub 450 n n CAZ CAV Y01 sing 451 n n CAZ CBH Y01 sing 452 n n CAV CBC Y01 sing 453 n n CBH CAD Y01 sing 454 n n CBH CAT Y01 sing 455 n n CAT CAR Y01 sing 456 n n CAR CBC Y01 sing 457 n n CBC OAW Y01 sing 458 n n OAW CAY Y01 sing 459 n n CAY OAG Y01 doub 460 n n CAY CAM Y01 sing 461 n n CAM CAL Y01 sing 462 n n CAL CAX Y01 sing 463 n n CAX OAH Y01 sing 464 n n CAX OAF Y01 doub 465 n n CAA HAA1 Y01 sing 466 n n CAA HAA2 Y01 sing 467 n n CAA HAA3 Y01 sing 468 n n CBA HBA Y01 sing 469 n n CAB HAB1 Y01 sing 470 n n CAB HAB2 Y01 sing 471 n n CAB HAB3 Y01 sing 472 n n CAN HAN1 Y01 sing 473 n n CAN HAN2 Y01 sing 474 n n CAJ HAJ1 Y01 sing 475 n n CAJ HAJ2 Y01 sing 476 n n CAO HAO1 Y01 sing 477 n n CAO HAO2 Y01 sing 478 n n CBB HBB Y01 sing 479 n n CAC HAC1 Y01 sing 480 n n CAC HAC2 Y01 sing 481 n n CAC HAC3 Y01 sing 482 n n CBE HBE Y01 sing 483 n n CAP HAP1 Y01 sing 484 n n CAP HAP2 Y01 sing 485 n n CAQ HAQ1 Y01 sing 486 n n CAQ HAQ2 Y01 sing 487 n n CBG HBG Y01 sing 488 n n CBD HBD Y01 sing 489 n n CAE HAE1 Y01 sing 490 n n CAE HAE2 Y01 sing 491 n n CAE HAE3 Y01 sing 492 n n CAU HAU1 Y01 sing 493 n n CAU HAU2 Y01 sing 494 n n CAS HAS1 Y01 sing 495 n n CAS HAS2 Y01 sing 496 n n CBF HBF Y01 sing 497 n n CAK HAK1 Y01 sing 498 n n CAK HAK2 Y01 sing 499 n n CAI HAI Y01 sing 500 n n CAV HAV1 Y01 sing 501 n n CAV HAV2 Y01 sing 502 n n CBC HBC Y01 sing 503 n n CAD HAD1 Y01 sing 504 n n CAD HAD2 Y01 sing 505 n n CAD HAD3 Y01 sing 506 n n CAT HAT1 Y01 sing 507 n n CAT HAT2 Y01 sing 508 n n CAR HAR1 Y01 sing 509 n n CAR HAR2 Y01 sing 510 n n CAM HAM1 Y01 sing 511 n n CAM HAM2 Y01 sing 512 n n CAL HAL1 Y01 sing 513 n n CAL HAL2 Y01 sing 514 n n OAH HAH Y01 sing 515 n n # _atom_sites.entry_id 8Y81 _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 J 7 NAG A 1 301 731 NAG NAG . K 7 NAG A 1 302 732 NAG NAG . L 8 Y01 B 1 601 601 Y01 Y01 . M 7 NAG E 1 501 430 NAG NAG . N 7 NAG E 1 502 431 NAG NAG . O 7 NAG F 1 501 420 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 . . . L 8 179.227 142.655 134.023 1 56.38 ? CAA Y01 601 B 1 HETATM 2 C CBA Y01 . . . L 8 178.881 143.166 132.63 1 56.38 ? CBA Y01 601 B 1 HETATM 3 C CAB Y01 . . . L 8 177.431 143.651 132.618 1 56.38 ? CAB Y01 601 B 1 HETATM 4 C CAN Y01 . . . L 8 179.019 141.988 131.681 1 56.38 ? CAN Y01 601 B 1 HETATM 5 C CAJ Y01 . . . L 8 180.01 142.286 130.55 1 56.38 ? CAJ Y01 601 B 1 HETATM 6 C CAO Y01 . . . L 8 181.206 141.323 130.601 1 56.38 ? CAO Y01 601 B 1 HETATM 7 C CBB Y01 . . . L 8 181.337 140.264 129.469 1 56.38 ? CBB Y01 601 B 1 HETATM 8 C CAC Y01 . . . L 8 180.013 139.946 128.748 1 56.38 ? CAC Y01 601 B 1 HETATM 9 C CBE Y01 . . . L 8 182.36 140.592 128.354 1 56.38 ? CBE Y01 601 B 1 HETATM 10 C CAP Y01 . . . L 8 183.126 141.933 128.496 1 56.38 ? CAP Y01 601 B 1 HETATM 11 C CAQ Y01 . . . L 8 184.254 141.78 127.443 1 56.38 ? CAQ Y01 601 B 1 HETATM 12 C CBG Y01 . . . L 8 184.104 140.349 126.918 1 56.38 ? CBG Y01 601 B 1 HETATM 13 C CBI Y01 . . . L 8 183.496 139.58 128.135 1 56.38 ? CBI Y01 601 B 1 HETATM 14 C CAE Y01 . . . L 8 184.397 139.486 129.378 1 56.38 ? CAE Y01 601 B 1 HETATM 15 C CAU Y01 . . . L 8 183.168 138.169 127.667 1 56.38 ? CAU Y01 601 B 1 HETATM 16 C CAS Y01 . . . L 8 184.418 137.47 127.091 1 56.38 ? CAS Y01 601 B 1 HETATM 17 C CBF Y01 . . . L 8 184.989 138.274 125.919 1 56.38 ? CBF Y01 601 B 1 HETATM 18 C CBD Y01 . . . L 8 185.365 139.695 126.374 1 56.38 ? CBD Y01 601 B 1 HETATM 19 C CAK Y01 . . . L 8 185.805 140.506 125.143 1 56.38 ? CAK Y01 601 B 1 HETATM 20 C CAI Y01 . . . L 8 186.723 139.764 124.202 1 56.38 ? CAI Y01 601 B 1 HETATM 21 C CAZ Y01 . . . L 8 186.927 138.48 124.275 1 56.38 ? CAZ Y01 601 B 1 HETATM 22 C CAV Y01 . . . L 8 187.768 137.832 123.192 1 56.38 ? CAV Y01 601 B 1 HETATM 23 C CBH Y01 . . . L 8 186.147 137.579 125.194 1 56.38 ? CBH Y01 601 B 1 HETATM 24 C CAD Y01 . . . L 8 187.186 137.063 126.187 1 56.38 ? CAD Y01 601 B 1 HETATM 25 C CAT Y01 . . . L 8 185.561 136.363 124.462 1 56.38 ? CAT Y01 601 B 1 HETATM 26 C CAR Y01 . . . L 8 186.531 135.739 123.457 1 56.38 ? CAR Y01 601 B 1 HETATM 27 C CBC Y01 . . . L 8 186.909 136.813 122.444 1 56.38 ? CBC Y01 601 B 1 HETATM 28 O OAW Y01 . . . L 8 187.654 136.212 121.354 1 56.38 ? OAW Y01 601 B 1 HETATM 29 C CAY Y01 . . . L 8 186.999 135.341 120.569 1 56.38 ? CAY Y01 601 B 1 HETATM 30 O OAG Y01 . . . L 8 185.902 135.601 120.14 1 56.38 ? OAG Y01 601 B 1 HETATM 31 C CAM Y01 . . . L 8 187.617 134.02 120.21 1 56.38 ? CAM Y01 601 B 1 HETATM 32 C CAL Y01 . . . L 8 187.236 133.671 118.77 1 56.38 ? CAL Y01 601 B 1 HETATM 33 C CAX Y01 . . . L 8 187.255 132.176 118.566 1 56.38 ? CAX Y01 601 B 1 HETATM 34 O OAH Y01 . . . L 8 186.759 131.362 119.511 1 56.38 ? OAH Y01 601 B 1 HETATM 35 O OAF Y01 . . . L 8 187.716 131.709 117.552 1 56.38 ? OAF Y01 601 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 35 #