data_1LDQ
#
_model_server_result.job_id            3VKLVApCrubPNrzJUO6-3w 
_model_server_result.datetime_utc      '2024-11-28 09:44:44' 
_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          1ldq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    1LDQ 
#
_exptl.entry_id    1LDQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              258.337 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            HOMOBIOTIN 
_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         90 
_cell.entry_id            1LDQ 
_cell.length_a            71.758 
_cell.length_b            79.836 
_cell.length_c            42.906 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1LDQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 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 
_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' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 79.836 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F N 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
disulf ? disulf1 A SG CYS 4 A CYS 4 1_555 A SG CYS 83 A CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf2 B SG CYS 4 B CYS 204 1_555 B SG CYS 83 B CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
covale ? covale1 A ND2 ASN 17 A ASN 17 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale2 B ND2 ASN 17 B ASN 217 1_555 E C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
#
_chem_comp.formula           'C11 H18 N2 O3 S' 
_chem_comp.formula_weight    258.337 
_chem_comp.id                SHM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              HOMOBIOTIN 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '6-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-4-YL)-HEXANOIC ACID' 
#
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 SHM sing 320 n n 
C1 N5 SHM sing 321 n n 
C1 C8 SHM sing 322 n n 
C1 H11 SHM sing 323 n n 
C2 N3 SHM sing 324 n n 
C2 C6 SHM sing 325 n n 
C2 H12 SHM sing 326 n n 
N3 C4 SHM sing 327 n n 
N3 HN3 SHM sing 328 n n 
C4 N5 SHM sing 329 n n 
C4 O17 SHM doub 330 n n 
N5 HN5 SHM sing 331 n n 
C6 S7 SHM sing 332 n n 
C6 C9 SHM sing 333 n n 
C6 H6 SHM sing 334 n n 
S7 C8 SHM sing 335 n n 
C8 H81 SHM sing 336 n n 
C8 H82 SHM sing 337 n n 
C9 C10 SHM sing 338 n n 
C9 H11A SHM sing 339 n n 
C9 H21 SHM sing 340 n n 
C10 C11 SHM sing 341 n n 
C10 H12A SHM sing 342 n n 
C10 H22 SHM sing 343 n n 
C11 C12 SHM sing 344 n n 
C11 H13 SHM sing 345 n n 
C11 H23 SHM sing 346 n n 
C12 C13 SHM sing 347 n n 
C12 H14 SHM sing 348 n n 
C12 H24 SHM sing 349 n n 
C13 C14 SHM sing 350 n n 
C13 H15 SHM sing 351 n n 
C13 H25 SHM sing 352 n n 
C14 O15 SHM doub 353 n n 
C14 O16 SHM sing 354 n n 
O16 H16 SHM sing 355 n n 
#
_atom_sites.entry_id                     1LDQ 
_atom_sites.fract_transf_matrix[1][1]    0.013936 
_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]    0.012526 
_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]    0.023307 
_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 2 NAG A 1 401 401 NAG NAG . 
D 3 SHM A 1 402 1 SHM SHM . 
E 2 NAG B 1 402 402 NAG NAG . 
F 3 SHM B 1 2 2 SHM SHM . 
G 4 HOH A 1 500 500 HOH WAT . 
G 4 HOH A 2 501 501 HOH WAT . 
G 4 HOH A 3 502 502 HOH WAT . 
G 4 HOH A 4 504 504 HOH WAT . 
G 4 HOH A 5 507 507 HOH WAT . 
G 4 HOH A 6 510 510 HOH WAT . 
H 4 HOH B 1 503 503 HOH WAT . 
H 4 HOH B 2 505 505 HOH WAT . 
H 4 HOH B 3 506 506 HOH WAT . 
H 4 HOH B 4 508 508 HOH WAT . 
H 4 HOH B 5 509 509 HOH WAT . 
H 4 HOH B 6 511 511 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 SHM . . . D 3 -0.212 29.113 22.141 1 62.88 ? C1 SHM 402 A 1 
HETATM 2 C C2 SHM . . . D 3 -0.384 28.652 23.606 1 63.66 ? C2 SHM 402 A 1 
HETATM 3 N N3 SHM . . . D 3 -0.323 27.188 23.482 1 65.1 ? N3 SHM 402 A 1 
HETATM 4 C C4 SHM . . . D 3 -0.143 26.816 22.178 1 65.22 ? C4 SHM 402 A 1 
HETATM 5 N N5 SHM . . . D 3 -0.073 27.897 21.359 1 62.94 ? N5 SHM 402 A 1 
HETATM 6 C C6 SHM . . . D 3 -1.769 29.243 24.177 1 63.48 ? C6 SHM 402 A 1 
HETATM 7 S S7 SHM . . . D 3 -2.769 29.429 22.653 1 62.22 ? S7 SHM 402 A 1 
HETATM 8 C C8 SHM . . . D 3 -1.383 29.989 21.612 1 62.31 ? C8 SHM 402 A 1 
HETATM 9 C C9 SHM . . . D 3 -2.43 28.405 25.363 1 62.71 ? C9 SHM 402 A 1 
HETATM 10 C C10 SHM . . . D 3 -3.764 28.936 25.978 1 61.96 ? C10 SHM 402 A 1 
HETATM 11 C C11 SHM . . . D 3 -3.539 30.267 26.709 1 62.22 ? C11 SHM 402 A 1 
HETATM 12 C C12 SHM . . . D 3 -4.056 30.229 28.146 1 61.05 ? C12 SHM 402 A 1 
HETATM 13 C C13 SHM . . . D 3 -3.753 31.605 28.808 1 63.32 ? C13 SHM 402 A 1 
HETATM 14 C C14 SHM . . . D 3 -2.266 31.71 29.252 1 65.82 ? C14 SHM 402 A 1 
HETATM 15 O O15 SHM . . . D 3 -1.485 32.756 28.809 1 65.22 ? O15 SHM 402 A 1 
HETATM 16 O O16 SHM . . . D 3 -1.738 30.861 30.006 1 66.39 ? O16 SHM 402 A 1 
HETATM 17 O O17 SHM . . . D 3 -0.054 25.628 21.791 1 64.61 ? O17 SHM 402 A 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           17 
#