data_1Y8P
#
_model_server_result.job_id            LDepzQ6CszyKVlrGCZtruA 
_model_server_result.datetime_utc      '2024-11-23 05:55:42' 
_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          1y8p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":373}' 
#
_entry.id    1Y8P 
#
_exptl.entry_id    1Y8P 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              208.341 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIHYDROLIPOIC ACID' 
_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            1Y8P 
_cell.length_a            120.904 
_cell.length_b            120.904 
_cell.length_c            240.085 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y8P 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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 
_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' 11_455 -x+y-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -120.904 0 120.0425 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             G 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
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
metalc ? metalc1 A O SER 33 A SER 20 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
metalc ? metalc2 A O PHE 35 A PHE 22 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? 
metalc ? metalc3 A OD1 ASN 72 A ASN 59 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? 
metalc ? metalc4 A OD1 ASN 264 A ASN 251 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc5 A O LEU 313 A LEU 300 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc6 A O ASN 315 A ASN 302 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.019 ? 
metalc ? metalc7 A O TYR 318 A TYR 305 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.077 ? 
metalc ? metalc8 A O GLY 338 A GLY 325 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? 
metalc ? metalc9 A O PHE 385 A PHE 372 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
metalc ? metalc10 C MG MG . A MG 501 1_555 F O2B ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? 
metalc ? metalc11 C MG MG . A MG 501 1_555 F O1G ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc12 C MG MG . A MG 501 1_555 F O2A ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc13 C MG MG . A MG 501 1_555 H O HOH . A HOH 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc14 E K K . A K 503 1_555 F O1A ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? 
#
_chem_comp.formula           'C8 H16 O2 S2' 
_chem_comp.formula_weight    208.341 
_chem_comp.id                RED 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIHYDROLIPOIC ACID' 
_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 O1 RED doub 326 n n 
C1 OXT RED sing 327 n n 
C1 C2 RED sing 328 n n 
OXT HO RED sing 329 n n 
C2 C3 RED sing 330 n n 
C2 H22 RED sing 331 n n 
C2 H21 RED sing 332 n n 
C3 C4 RED sing 333 n n 
C3 H32 RED sing 334 n n 
C3 H31 RED sing 335 n n 
C4 C5 RED sing 336 n n 
C4 H42 RED sing 337 n n 
C4 H41 RED sing 338 n n 
C5 C6 RED sing 339 n n 
C5 H52 RED sing 340 n n 
C5 H51 RED sing 341 n n 
C6 C7 RED sing 342 n n 
C6 S6 RED sing 343 n n 
C6 H6 RED sing 344 n n 
C7 C8 RED sing 345 n n 
C7 H72 RED sing 346 n n 
C7 H71 RED sing 347 n n 
C8 S8 RED sing 348 n n 
C8 H82 RED sing 349 n n 
C8 H81 RED sing 350 n n 
S8 H8S RED sing 351 n n 
S6 H6S RED sing 352 n n 
#
_atom_sites.entry_id                     1Y8P 
_atom_sites.fract_transf_matrix[1][1]    0.008271 
_atom_sites.fract_transf_matrix[1][2]    0.004775 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009551 
_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]    0.004165 
_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
C 3 MG A 1 501 1 MG MG . 
D 4 K A 1 502 2 K K . 
E 4 K A 1 503 3 K K . 
F 5 ATP A 1 504 1 ATP ATP . 
G 6 RED B 1 373 173 RED LPA . 
H 7 HOH A 1 505 1 HOH WAT . 
H 7 HOH A 2 506 2 HOH WAT . 
H 7 HOH A 3 507 3 HOH WAT . 
H 7 HOH A 4 508 4 HOH WAT . 
H 7 HOH A 5 509 5 HOH WAT . 
H 7 HOH A 6 510 7 HOH WAT . 
H 7 HOH A 7 511 8 HOH WAT . 
H 7 HOH A 8 512 10 HOH WAT . 
H 7 HOH A 9 513 11 HOH WAT . 
H 7 HOH A 10 514 12 HOH WAT . 
H 7 HOH A 11 515 13 HOH WAT . 
H 7 HOH A 12 516 14 HOH WAT . 
H 7 HOH A 13 517 15 HOH WAT . 
H 7 HOH A 14 518 16 HOH WAT . 
H 7 HOH A 15 519 17 HOH WAT . 
H 7 HOH A 16 520 18 HOH WAT . 
H 7 HOH A 17 521 19 HOH WAT . 
H 7 HOH A 18 522 20 HOH WAT . 
H 7 HOH A 19 523 21 HOH WAT . 
H 7 HOH A 20 524 22 HOH WAT . 
H 7 HOH A 21 525 23 HOH WAT . 
H 7 HOH A 22 526 24 HOH WAT . 
H 7 HOH A 23 527 25 HOH WAT . 
H 7 HOH A 24 528 26 HOH WAT . 
H 7 HOH A 25 529 27 HOH WAT . 
H 7 HOH A 26 530 28 HOH WAT . 
H 7 HOH A 27 531 29 HOH WAT . 
H 7 HOH A 28 532 30 HOH WAT . 
H 7 HOH A 29 533 31 HOH WAT . 
H 7 HOH A 30 534 32 HOH WAT . 
H 7 HOH A 31 535 33 HOH WAT . 
H 7 HOH A 32 536 34 HOH WAT . 
H 7 HOH A 33 537 35 HOH WAT . 
H 7 HOH A 34 538 36 HOH WAT . 
H 7 HOH A 35 539 37 HOH WAT . 
H 7 HOH A 36 540 38 HOH WAT . 
H 7 HOH A 37 541 39 HOH WAT . 
H 7 HOH A 38 542 40 HOH WAT . 
H 7 HOH A 39 543 41 HOH WAT . 
H 7 HOH A 40 544 42 HOH WAT . 
H 7 HOH A 41 545 43 HOH WAT . 
H 7 HOH A 42 546 44 HOH WAT . 
H 7 HOH A 43 547 45 HOH WAT . 
H 7 HOH A 44 548 46 HOH WAT . 
H 7 HOH A 45 549 47 HOH WAT . 
H 7 HOH A 46 550 48 HOH WAT . 
H 7 HOH A 47 551 49 HOH WAT . 
H 7 HOH A 48 552 50 HOH WAT . 
H 7 HOH A 49 553 51 HOH WAT . 
H 7 HOH A 50 554 52 HOH WAT . 
H 7 HOH A 51 555 53 HOH WAT . 
H 7 HOH A 52 556 55 HOH WAT . 
H 7 HOH A 53 557 56 HOH WAT . 
I 7 HOH B 1 6 6 HOH WAT . 
I 7 HOH B 2 9 9 HOH WAT . 
I 7 HOH B 3 54 54 HOH WAT . 
#
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 RED . . . G 6 -79.567 0.846 85.148 1 54.9 ? C1 RED 373 B 1 
HETATM 2 O O1 RED . . . G 6 -79.584 -0.099 85.935 1 56.25 ? O1 RED 373 B 1 
HETATM 3 C C2 RED . . . G 6 -79.968 2.244 85.528 1 56.08 ? C2 RED 373 B 1 
HETATM 4 C C3 RED . . . G 6 -78.981 2.686 86.578 1 56.35 ? C3 RED 373 B 1 
HETATM 5 C C4 RED . . . G 6 -79.427 4.033 87.075 1 58.8 ? C4 RED 373 B 1 
HETATM 6 C C5 RED . . . G 6 -78.717 4.269 88.389 1 62.28 ? C5 RED 373 B 1 
HETATM 7 C C6 RED . . . G 6 -77.229 4.48 88.15 1 64.05 ? C6 RED 373 B 1 
HETATM 8 C C7 RED . . . G 6 -76.524 4.103 89.446 1 66.77 ? C7 RED 373 B 1 
HETATM 9 C C8 RED . . . G 6 -75.846 5.284 90.118 1 69.16 ? C8 RED 373 B 1 
HETATM 10 S S8 RED . . . G 6 -74.24 5.432 89.31 1 73.07 ? S8 RED 373 B 1 
HETATM 11 S S6 RED . . . G 6 -76.949 6.19 87.698 1 63.46 ? S6 RED 373 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           241 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           11 
#