data_9CTO
#
_model_server_result.job_id            WpkWOpNs05Vaq1NohGUI8A 
_model_server_result.datetime_utc      '2025-03-05 22:48:34' 
_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          9cto 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":2302}' 
#
_entry.id    9CTO 
#
_exptl.entry_id    9CTO 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              400.385 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate' 
_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            9CTO 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9CTO 
_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_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
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
covale ? covale1 A C ALA 186 A ALA 186 1_555 A N SCY 187 A SCY 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 A C SCY 187 A SCY 187 1_555 A N SER 188 A SER 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale3 A OG SER 2241 A SER 2241 1_555 D P24 6VG . A 6VG 2302 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.605 ? 
covale ? covale4 B C ALA 186 B ALA 186 1_555 B N SCY 187 B SCY 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale5 B C SCY 187 B SCY 187 1_555 B N SER 188 B SER 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale6 B OG SER 2241 B SER 2241 1_555 F P24 6VG . B 6VG 2302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? 
#
_chem_comp.formula           'C13 H25 N2 O8 P S' 
_chem_comp.formula_weight    400.385 
_chem_comp.id                6VG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate' 
_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
C2 C1 6VG sing 1 n n 
C1 O1 6VG doub 2 n n 
C1 S1 6VG sing 3 n n 
S1 C43 6VG sing 4 n n 
C43 C42 6VG sing 5 n n 
O40 C39 6VG doub 6 n n 
C42 N41 6VG sing 7 n n 
C39 N41 6VG sing 8 n n 
C39 C38 6VG sing 9 n n 
C38 C37 6VG sing 10 n n 
C37 N36 6VG sing 11 n n 
N36 C34 6VG sing 12 n n 
O33 C32 6VG sing 13 n n 
C34 C32 6VG sing 14 n n 
C34 O35 6VG doub 15 n n 
C32 C29 6VG sing 16 n n 
C31 C29 6VG sing 17 n n 
C29 C30 6VG sing 18 n n 
C29 C28 6VG sing 19 n n 
C28 O27 6VG sing 20 n n 
O27 P24 6VG sing 21 n n 
O23 P24 6VG doub 22 n n 
P24 O26 6VG sing 23 n n 
P24 O2 6VG sing 24 n n 
O26 H1 6VG sing 25 n n 
C28 H2 6VG sing 26 n n 
C28 H3 6VG sing 27 n n 
C30 H4 6VG sing 28 n n 
C30 H5 6VG sing 29 n n 
C30 H6 6VG sing 30 n n 
C31 H7 6VG sing 31 n n 
C31 H8 6VG sing 32 n n 
C31 H9 6VG sing 33 n n 
C32 H10 6VG sing 34 n n 
O33 H11 6VG sing 35 n n 
N36 H12 6VG sing 36 n n 
C37 H13 6VG sing 37 n n 
C37 H14 6VG sing 38 n n 
C38 H15 6VG sing 39 n n 
C38 H16 6VG sing 40 n n 
N41 H17 6VG sing 41 n n 
C42 H18 6VG sing 42 n n 
C42 H19 6VG sing 43 n n 
C43 H20 6VG sing 44 n n 
C43 H21 6VG sing 45 n n 
C2 H22 6VG sing 46 n n 
C2 H23 6VG sing 47 n n 
C2 H24 6VG sing 48 n n 
O2 H25 6VG sing 49 n n 
#
_atom_sites.entry_id                     9CTO 
_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
C 2 NDP A 1 2301 2301 NDP NDP . 
D 3 6VG A 1 2302 2241 6VG 4HH . 
E 2 NDP B 1 2301 2301 NDP NDP . 
F 3 6VG B 1 2302 2241 6VG 4HH . 
#
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 P P24 6VG . . . F 3 155.17 144.443 130.796 1 144.05 ? P24 6VG 2302 B 1 
HETATM 2 O O26 6VG . . . F 3 156.102 143.354 130.339 1 122.95 ? O26 6VG 2302 B 1 
HETATM 3 O O23 6VG . . . F 3 154.153 144.168 131.869 1 142.48 ? O23 6VG 2302 B 1 
HETATM 4 O O27 6VG . . . F 3 156.056 145.707 131.237 1 128.07 ? O27 6VG 2302 B 1 
HETATM 5 C C28 6VG . . . F 3 156.79 145.693 132.492 1 119.73 ? C28 6VG 2302 B 1 
HETATM 6 C C29 6VG . . . F 3 157.732 146.893 132.486 1 117.48 ? C29 6VG 2302 B 1 
HETATM 7 C C30 6VG . . . F 3 158.74 146.698 131.35 1 111.76 ? C30 6VG 2302 B 1 
HETATM 8 C C31 6VG . . . F 3 156.917 148.158 132.199 1 117.71 ? C31 6VG 2302 B 1 
HETATM 9 C C32 6VG . . . F 3 158.472 147.049 133.823 1 116.76 ? C32 6VG 2302 B 1 
HETATM 10 O O33 6VG . . . F 3 158.533 145.806 134.509 1 114.7 ? O33 6VG 2302 B 1 
HETATM 11 C C34 6VG . . . F 3 159.873 147.611 133.641 1 113.57 ? C34 6VG 2302 B 1 
HETATM 12 O O35 6VG . . . F 3 160.853 146.902 133.863 1 103.8 ? O35 6VG 2302 B 1 
HETATM 13 N N36 6VG . . . F 3 159.97 148.87 133.238 1 112.66 ? N36 6VG 2302 B 1 
HETATM 14 C C37 6VG . . . F 3 161.225 149.503 132.85 1 110.19 ? C37 6VG 2302 B 1 
HETATM 15 C C38 6VG . . . F 3 162.172 149.732 134.007 1 102.33 ? C38 6VG 2302 B 1 
HETATM 16 C C39 6VG . . . F 3 163.078 150.904 133.691 1 105.67 ? C39 6VG 2302 B 1 
HETATM 17 O O40 6VG . . . F 3 162.913 151.988 134.244 1 106.36 ? O40 6VG 2302 B 1 
HETATM 18 N N41 6VG . . . F 3 164.05 150.715 132.791 1 105.57 ? N41 6VG 2302 B 1 
HETATM 19 C C42 6VG . . . F 3 164.817 151.808 132.21 1 98.61 ? C42 6VG 2302 B 1 
HETATM 20 C C43 6VG . . . F 3 166.144 152.039 132.89 1 93.56 ? C43 6VG 2302 B 1 
HETATM 21 S S1 6VG . . . F 3 167.417 150.81 132.505 1 122.19 ? S1 6VG 2302 B 1 
HETATM 22 C C1 6VG . . . F 3 167.868 150.88 130.861 1 113.89 ? C1 6VG 2302 B 1 
HETATM 23 O O1 6VG . . . F 3 166.899 150.997 130.191 1 115.62 ? O1 6VG 2302 B 1 
HETATM 24 C C2 6VG . . . F 3 169.105 150.213 130.261 1 95.17 ? C2 6VG 2302 B 1 
HETATM 25 H H2 6VG . . . F 3 157.303 144.864 132.576 1 118.46 ? H2 6VG 2302 B 1 
HETATM 26 H H3 6VG . . . F 3 156.172 145.756 133.248 1 121.33 ? H3 6VG 2302 B 1 
HETATM 27 H H4 6VG . . . F 3 159.24 147.519 131.206 1 111.48 ? H4 6VG 2302 B 1 
HETATM 28 H H5 6VG . . . F 3 159.355 145.979 131.576 1 109.32 ? H5 6VG 2302 B 1 
HETATM 29 H H6 6VG . . . F 3 158.265 146.47 130.531 1 114.51 ? H6 6VG 2302 B 1 
HETATM 30 H H7 6VG . . . F 3 156.426 148.046 131.367 1 121.36 ? H7 6VG 2302 B 1 
HETATM 31 H H8 6VG . . . F 3 156.288 148.311 132.925 1 115.34 ? H8 6VG 2302 B 1 
HETATM 32 H H9 6VG . . . F 3 157.513 148.921 132.121 1 113.71 ? H9 6VG 2302 B 1 
HETATM 33 H H10 6VG . . . F 3 157.956 147.684 134.376 1 110.74 ? H10 6VG 2302 B 1 
HETATM 34 H H11 6VG . . . F 3 158.965 145.25 134.044 1 110.31 ? H11 6VG 2302 B 1 
HETATM 35 H H12 6VG . . . F 3 159.248 149.354 133.219 1 108.7 ? H12 6VG 2302 B 1 
HETATM 36 H H13 6VG . . . F 3 161.025 150.367 132.434 1 107.35 ? H13 6VG 2302 B 1 
HETATM 37 H H14 6VG . . . F 3 161.669 148.943 132.182 1 105.24 ? H14 6VG 2302 B 1 
HETATM 38 H H15 6VG . . . F 3 161.665 149.923 134.816 1 99.8 ? H15 6VG 2302 B 1 
HETATM 39 H H16 6VG . . . F 3 162.71 148.936 134.162 1 96.77 ? H16 6VG 2302 B 1 
HETATM 40 H H17 6VG . . . F 3 164.235 149.896 132.553 1 98.85 ? H17 6VG 2302 B 1 
HETATM 41 H H18 6VG . . . F 3 164.971 151.619 131.261 1 98.07 ? H18 6VG 2302 B 1 
HETATM 42 H H19 6VG . . . F 3 164.288 152.631 132.269 1 98.23 ? H19 6VG 2302 B 1 
HETATM 43 H H20 6VG . . . F 3 166.477 152.914 132.632 1 91.29 ? H20 6VG 2302 B 1 
HETATM 44 H H21 6VG . . . F 3 166.003 152.042 133.851 1 93.12 ? H21 6VG 2302 B 1 
HETATM 45 H H22 6VG . . . F 3 169.8 150.153 130.935 1 92.96 ? H22 6VG 2302 B 1 
HETATM 46 H H23 6VG . . . F 3 168.873 149.322 129.955 1 91.24 ? H23 6VG 2302 B 1 
HETATM 47 H H24 6VG . . . F 3 169.425 150.738 129.511 1 91 ? H24 6VG 2302 B 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    85 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           47 
#