data_6KKT
#
_model_server_result.job_id            yjrmKxqiWokyAupAmh-OCw 
_model_server_result.datetime_utc      '2024-10-15 11:29:36' 
_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          6kkt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":2000}' 
#
_entry.id    6KKT 
#
_exptl.entry_id    6KKT 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              516.752 
_entity.id                          6 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            "2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol" 
_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            6KKT 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6KKT 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 6 N N N 
? 6 R N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
2 oligosaccharide 
3 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 ? 3 2 1 GLC BGC 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 C NAG 1 C 1 NAG A 1102 NAG 
2 n C NAG 2 C 2 NAG A 1101 NAG 
2 n D NAG 1 D 1 NAG A 1104 NAG 
2 n D NAG 2 D 2 NAG A 1103 NAG 
3 n E BGC 1 E 1 BGC A 1109 BGC 
3 n E GLC 2 E 2 GLC A 1110 GLC 
3 n F BGC 1 F 1 BGC A 1112 BGC 
3 n F GLC 2 F 2 GLC A 1113 GLC 
2 n G NAG 1 G 1 NAG B 1102 NAG 
2 n G NAG 2 G 2 NAG B 1101 NAG 
2 n H NAG 1 H 1 NAG B 1104 NAG 
2 n H NAG 2 H 2 NAG B 1103 NAG 
3 n I BGC 1 I 1 BGC B 1108 BGC 
3 n I GLC 2 I 2 GLC B 1109 GLC 
3 n J BGC 1 J 1 BGC B 1110 BGC 
3 n J GLC 2 J 2 GLC B 1111 GLC 
#
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 163 A CYS 163 1_555 A SG CYS 626 A CYS 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 308 A CYS 308 1_555 A SG CYS 323 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf3 A SG CYS 343 A CYS 343 1_555 A SG CYS 353 A CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf4 B SG CYS 163 B CYS 163 1_555 B SG CYS 626 B CYS 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 B SG CYS 308 B CYS 308 1_555 B SG CYS 323 B CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf6 B SG CYS 343 B CYS 343 1_555 B SG CYS 353 B CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
covale ? covale1 A ND2 ASN 312 A ASN 312 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? 
covale ? covale2 A ND2 ASN 361 A ASN 361 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? 
covale ? covale3 N O52 DU0 . A DU0 2000 1_555 E C1 BGC . E BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? 
covale ? covale4 N O28 DU0 . A DU0 2000 1_555 I C1 BGC . I BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? 
covale ? covale5 B ND2 ASN 312 B ASN 312 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? 
covale ? covale6 B ND2 ASN 361 B ASN 361 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale7 R O52 DU0 . B DU0 2000 1_555 F C1 BGC . F BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? 
covale ? covale8 R O28 DU0 . B DU0 2000 1_555 J C1 BGC . J BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? 
covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale11 E O4 BGC . E BGC 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? 
covale ? covale12 F O4 BGC . F BGC 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? 
covale ? covale13 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale14 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? 
covale ? covale15 I O4 BGC . I BGC 1 1_555 I C1 GLC . I GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? 
covale ? covale16 J O4 BGC . J BGC 1 1_555 J C1 GLC . J GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? 
metalc ? metalc1 A O ASN 131 A ASN 131 1_555 L K K . A K 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? 
metalc ? metalc2 A O ILE 132 A ILE 132 1_555 L K K . A K 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? 
metalc ? metalc3 A O PRO 429 A PRO 429 1_555 L K K . A K 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? 
metalc ? metalc4 A O THR 432 A THR 432 1_555 L K K . A K 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? 
metalc ? metalc5 B O ASN 131 B ASN 131 1_555 P K K . B K 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? 
metalc ? metalc6 B O ILE 132 B ILE 132 1_555 P K K . B K 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? 
metalc ? metalc7 B O PRO 429 B PRO 429 1_555 P K K . B K 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.089 ? 
metalc ? metalc8 B O THR 432 B THR 432 1_555 P K K . B K 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
#
_chem_comp.formula           'C32 H52 O5' 
_chem_comp.formula_weight    516.752 
_chem_comp.id                DU0 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     6KKT 
_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
K 4 CL A 1 1101 1105 CL CL . 
L 5 K A 1 1102 1106 K K . 
M 4 CL A 1 1103 1107 CL CL . 
N 6 DU0 A 1 2000 1108 DU0 DU0 . 
O 4 CL B 1 1101 1105 CL CL . 
P 5 K B 1 1102 1106 K K . 
Q 4 CL B 1 1103 1107 CL CL . 
R 6 DU0 B 1 2000 1111 DU0 DU0 . 
#
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 C13 DU0 . . . R 6 110.671 120.072 101.496 1 30 ? C13 DU0 2000 B 1 
HETATM 2 C C15 DU0 . . . R 6 107.931 120.062 104.106 1 30 ? C15 DU0 2000 B 1 
HETATM 3 C C17 DU0 . . . R 6 110.296 117.694 109.968 1 30 ? C17 DU0 2000 B 1 
HETATM 4 C C20 DU0 . . . R 6 111.049 117.08 112.669 1 30 ? C20 DU0 2000 B 1 
HETATM 5 C C21 DU0 . . . R 6 111.363 117.039 114.151 1 30 ? C21 DU0 2000 B 1 
HETATM 6 C C22 DU0 . . . R 6 110.831 115.76 114.789 1 30 ? C22 DU0 2000 B 1 
HETATM 7 C C24 DU0 . . . R 6 112.173 114.98 116.54 1 30 ? C24 DU0 2000 B 1 
HETATM 8 C C26 DU0 . . . R 6 111.61 116.177 118.741 1 30 ? C26 DU0 2000 B 1 
HETATM 9 C C01 DU0 . . . R 6 107.885 118.918 108.349 1 30 ? C01 DU0 2000 B 1 
HETATM 10 C C02 DU0 . . . R 6 108.581 117.584 108.026 1 30 ? C02 DU0 2000 B 1 
HETATM 11 C C03 DU0 . . . R 6 110.058 117.522 108.466 1 30 ? C03 DU0 2000 B 1 
HETATM 12 C C04 DU0 . . . R 6 110.749 118.491 107.508 1 30 ? C04 DU0 2000 B 1 
HETATM 13 C C05 DU0 . . . R 6 110.067 118.108 106.196 1 30 ? C05 DU0 2000 B 1 
HETATM 14 C C06 DU0 . . . R 6 108.769 117.361 106.511 1 30 ? C06 DU0 2000 B 1 
HETATM 15 C C07 DU0 . . . R 6 107.77 117.952 105.507 1 30 ? C07 DU0 2000 B 1 
HETATM 16 C C08 DU0 . . . R 6 106.89 116.905 104.815 1 30 ? C08 DU0 2000 B 1 
HETATM 17 C C09 DU0 . . . R 6 108.649 118.811 104.6 1 30 ? C09 DU0 2000 B 1 
HETATM 18 C C11 DU0 . . . R 6 109 118.354 102.25 1 30 ? C11 DU0 2000 B 1 
HETATM 19 C C12 DU0 . . . R 6 109.214 119.827 101.911 1 30 ? C12 DU0 2000 B 1 
HETATM 20 C C14 DU0 . . . R 6 108.781 120.773 103.046 1 30 ? C14 DU0 2000 B 1 
HETATM 21 C C18 DU0 . . . R 6 111.778 117.49 110.303 1 30 ? C18 DU0 2000 B 1 
HETATM 22 C C19 DU0 . . . R 6 112.008 117.38 111.78 1 30 ? C19 DU0 2000 B 1 
HETATM 23 C C25 DU0 . . . R 6 112.305 114.999 118.062 1 30 ? C25 DU0 2000 B 1 
HETATM 24 C C27 DU0 . . . R 6 112.378 116.892 119.944 1 30 ? C27 DU0 2000 B 1 
HETATM 25 C C51 DU0 . . . R 6 110.068 115.861 118.932 1 30 ? C51 DU0 2000 B 1 
HETATM 26 C C75 DU0 . . . R 6 109.334 115.659 114.522 1 30 ? C75 DU0 2000 B 1 
HETATM 27 C C76 DU0 . . . R 6 109.065 115.654 113.014 1 30 ? C76 DU0 2000 B 1 
HETATM 28 C C77 DU0 . . . R 6 109.591 116.902 112.28 1 30 ? C77 DU0 2000 B 1 
HETATM 29 C C78 DU0 . . . R 6 108.804 118.144 112.727 1 30 ? C78 DU0 2000 B 1 
HETATM 30 C C79 DU0 . . . R 6 109.447 116.679 110.753 1 30 ? C79 DU0 2000 B 1 
HETATM 31 C C80 DU0 . . . R 6 107.988 116.653 110.268 1 30 ? C80 DU0 2000 B 1 
HETATM 32 C C81 DU0 . . . R 6 107.86 116.448 108.751 1 30 ? C81 DU0 2000 B 1 
HETATM 33 O O10 DU0 . . . R 6 109.297 118.059 103.59 1 30 ? O10 DU0 2000 B 1 
HETATM 34 O O16 DU0 . . . R 6 109.693 119.218 105.447 1 30 ? O16 DU0 2000 B 1 
HETATM 35 O O23 DU0 . . . R 6 111.109 115.808 116.16 1 30 ? O23 DU0 2000 B 1 
HETATM 36 O O28 DU0 . . . R 6 112.112 116.302 121.207 1 30 ? O28 DU0 2000 B 1 
HETATM 37 O O52 DU0 . . . R 6 109.946 115.1 120.068 1 30 ? O52 DU0 2000 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           37 
#