data_6VZ1
#
_model_server_result.job_id            DZotFcU69r0e78qNUnorNw 
_model_server_result.datetime_utc      '2024-11-05 03:24:04' 
_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          6vz1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":503}' 
#
_entry.id    6VZ1 
#
_exptl.entry_id    6VZ1 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              1031.98 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)' 
_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            6VZ1 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VZ1 
_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 
_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
? 3 E N N 
? 3 H N N 
#
_chem_comp.formula           'C39 H68 N7 O17 P3 S' 
_chem_comp.formula_weight    1031.98 
_chem_comp.id                3VV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     oleoyl-CoA 
#
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
C03 C02 3VV sing 1 n n 
C03 C04 3VV sing 2 n n 
C01 C02 3VV sing 3 n n 
C04 C05 3VV sing 4 n n 
C05 C06 3VV sing 5 n n 
C07 C06 3VV sing 6 n n 
C07 C08 3VV sing 7 n n 
C08 C09 3VV sing 8 n n 
C09 C10 3VV doub 9 z n 
C11 C10 3VV sing 10 n n 
C11 C12 3VV sing 11 n n 
C12 C13 3VV sing 12 n n 
C13 C14 3VV sing 13 n n 
C14 C15 3VV sing 14 n n 
C15 C16 3VV sing 15 n n 
C16 C17 3VV sing 16 n n 
O19 C18 3VV doub 17 n n 
C17 C18 3VV sing 18 n n 
C18 S20 3VV sing 19 n n 
S20 C21 3VV sing 20 n n 
C21 C22 3VV sing 21 n n 
N23 C22 3VV sing 22 n n 
N23 C24 3VV sing 23 n n 
O25 C24 3VV doub 24 n n 
C65 N64 3VV doub 25 n y 
C65 N66 3VV sing 26 n y 
C24 C26 3VV sing 27 n n 
N64 C62 3VV sing 28 n y 
N66 C67 3VV doub 29 n y 
C62 N63 3VV sing 30 n n 
C62 C61 3VV doub 31 n y 
C34 C33 3VV sing 32 n n 
C67 C61 3VV sing 33 n y 
C67 N58 3VV sing 34 n y 
O48 C47 3VV sing 35 n n 
O48 C49 3VV sing 36 n n 
C26 C27 3VV sing 37 n n 
O56 P54 3VV doub 38 n n 
O30 C29 3VV doub 39 n n 
C61 N60 3VV sing 40 n y 
C47 C46 3VV sing 41 n n 
C47 C52 3VV sing 42 n n 
C49 N58 3VV sing 43 n n 
C49 C50 3VV sing 44 n n 
C27 N28 3VV sing 45 n n 
O32 C31 3VV sing 46 n n 
N58 C59 3VV sing 47 n y 
C29 N28 3VV sing 48 n n 
C29 C31 3VV sing 49 n n 
C46 O45 3VV sing 50 n n 
O53 P54 3VV sing 51 n n 
O53 C52 3VV sing 52 n n 
C33 C31 3VV sing 53 n n 
C33 C36 3VV sing 54 n n 
C33 C35 3VV sing 55 n n 
O55 P54 3VV sing 56 n n 
P54 O57 3VV sing 57 n n 
N60 C59 3VV doub 58 n y 
C52 C50 3VV sing 59 n n 
C36 O37 3VV sing 60 n n 
C50 O51 3VV sing 61 n n 
O45 P42 3VV sing 62 n n 
O41 P42 3VV sing 63 n n 
O41 P38 3VV sing 64 n n 
P42 O44 3VV doub 65 n n 
P42 O43 3VV sing 66 n n 
O37 P38 3VV sing 67 n n 
O40 P38 3VV doub 68 n n 
P38 O39 3VV sing 69 n n 
C10 H1 3VV sing 70 n n 
C13 H2 3VV sing 71 n n 
C13 H3 3VV sing 72 n n 
C15 H4 3VV sing 73 n n 
C15 H5 3VV sing 74 n n 
C17 H6 3VV sing 75 n n 
C17 H7 3VV sing 76 n n 
C21 H8 3VV sing 77 n n 
C21 H9 3VV sing 78 n n 
C22 H10 3VV sing 79 n n 
C22 H11 3VV sing 80 n n 
C26 H12 3VV sing 81 n n 
C26 H13 3VV sing 82 n n 
C01 H14 3VV sing 83 n n 
C01 H15 3VV sing 84 n n 
C01 H16 3VV sing 85 n n 
C02 H17 3VV sing 86 n n 
C02 H18 3VV sing 87 n n 
C03 H19 3VV sing 88 n n 
C03 H20 3VV sing 89 n n 
C04 H21 3VV sing 90 n n 
C04 H22 3VV sing 91 n n 
C05 H23 3VV sing 92 n n 
C05 H24 3VV sing 93 n n 
C06 H25 3VV sing 94 n n 
C06 H26 3VV sing 95 n n 
C07 H27 3VV sing 96 n n 
C07 H28 3VV sing 97 n n 
C08 H29 3VV sing 98 n n 
C08 H30 3VV sing 99 n n 
C09 H31 3VV sing 100 n n 
C11 H32 3VV sing 101 n n 
C11 H33 3VV sing 102 n n 
C12 H34 3VV sing 103 n n 
C12 H35 3VV sing 104 n n 
C14 H36 3VV sing 105 n n 
C14 H37 3VV sing 106 n n 
C16 H38 3VV sing 107 n n 
C16 H39 3VV sing 108 n n 
N23 H40 3VV sing 109 n n 
C27 H41 3VV sing 110 n n 
C27 H42 3VV sing 111 n n 
N28 H43 3VV sing 112 n n 
C31 H44 3VV sing 113 n n 
O32 H45 3VV sing 114 n n 
C34 H46 3VV sing 115 n n 
C34 H47 3VV sing 116 n n 
C34 H48 3VV sing 117 n n 
C35 H49 3VV sing 118 n n 
C35 H50 3VV sing 119 n n 
C35 H51 3VV sing 120 n n 
C36 H52 3VV sing 121 n n 
C36 H53 3VV sing 122 n n 
O39 H54 3VV sing 123 n n 
O43 H55 3VV sing 124 n n 
C46 H56 3VV sing 125 n n 
C46 H57 3VV sing 126 n n 
C47 H58 3VV sing 127 n n 
C49 H59 3VV sing 128 n n 
C50 H60 3VV sing 129 n n 
O51 H61 3VV sing 130 n n 
C52 H62 3VV sing 131 n n 
O55 H63 3VV sing 132 n n 
O57 H64 3VV sing 133 n n 
C59 H65 3VV sing 134 n n 
N63 H66 3VV sing 135 n n 
N63 H67 3VV sing 136 n n 
C65 H68 3VV sing 137 n n 
#
_atom_sites.entry_id                     6VZ1 
_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 6OU A 1 501 1 6OU PPE . 
D 2 6OU A 1 502 3 6OU PPE . 
E 3 3VV A 1 503 1 3VV 3VV . 
F 2 6OU B 1 501 2 6OU PPE . 
G 2 6OU B 1 502 4 6OU PPE . 
H 3 3VV B 1 503 2 3VV 3VV . 
#
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 C10 3VV . . . H 3 84.601 95.423 114.457 1 74.63 ? C10 3VV 503 B 1 
HETATM 2 C C13 3VV . . . H 3 82.962 95.932 111.447 1 74.63 ? C13 3VV 503 B 1 
HETATM 3 C C15 3VV . . . H 3 83.85 97.227 109.438 1 74.63 ? C15 3VV 503 B 1 
HETATM 4 C C17 3VV . . . H 3 82.332 98.153 107.651 1 74.63 ? C17 3VV 503 B 1 
HETATM 5 C C21 3VV . . . H 3 82.669 98.232 103.81 1 74.63 ? C21 3VV 503 B 1 
HETATM 6 C C22 3VV . . . H 3 82.236 99.294 102.826 1 74.63 ? C22 3VV 503 B 1 
HETATM 7 C C24 3VV . . . H 3 82.099 99.797 100.503 1 74.63 ? C24 3VV 503 B 1 
HETATM 8 C C26 3VV . . . H 3 82.703 99.828 99.14 1 74.63 ? C26 3VV 503 B 1 
HETATM 9 P P38 3VV . . . H 3 82.279 104.937 91.418 1 74.63 ? P38 3VV 503 B 1 
HETATM 10 P P42 3VV . . . H 3 80.354 106.019 89.735 1 74.63 ? P42 3VV 503 B 1 
HETATM 11 P P54 3VV . . . H 3 81.65 102.074 84.919 1 74.63 ? P54 3VV 503 B 1 
HETATM 12 C C01 3VV . . . H 3 86.026 93.123 123.607 1 74.63 ? C01 3VV 503 B 1 
HETATM 13 C C02 3VV . . . H 3 85.041 92.915 122.537 1 74.63 ? C02 3VV 503 B 1 
HETATM 14 C C03 3VV . . . H 3 85.631 93.056 121.204 1 74.63 ? C03 3VV 503 B 1 
HETATM 15 C C04 3VV . . . H 3 84.987 92.16 120.205 1 74.63 ? C04 3VV 503 B 1 
HETATM 16 C C05 3VV . . . H 3 85.183 92.558 118.77 1 74.63 ? C05 3VV 503 B 1 
HETATM 17 C C06 3VV . . . H 3 84.017 93.285 118.186 1 74.63 ? C06 3VV 503 B 1 
HETATM 18 C C07 3VV . . . H 3 83.733 92.914 116.774 1 74.63 ? C07 3VV 503 B 1 
HETATM 19 C C08 3VV . . . H 3 83.14 94.032 115.969 1 74.63 ? C08 3VV 503 B 1 
HETATM 20 C C09 3VV . . . H 3 84.094 95.122 115.636 1 74.63 ? C09 3VV 503 B 1 
HETATM 21 C C11 3VV . . . H 3 84.38 94.723 113.155 1 74.63 ? C11 3VV 503 B 1 
HETATM 22 C C12 3VV . . . H 3 84.334 95.601 111.92 1 74.63 ? C12 3VV 503 B 1 
HETATM 23 C C14 3VV . . . H 3 82.875 97.163 110.582 1 74.63 ? C14 3VV 503 B 1 
HETATM 24 C C16 3VV . . . H 3 83.599 98.367 108.47 1 74.63 ? C16 3VV 503 B 1 
HETATM 25 C C18 3VV . . . H 3 82.136 98.964 106.402 1 74.63 ? C18 3VV 503 B 1 
HETATM 26 O O19 3VV . . . H 3 82.449 100.095 106.291 1 74.63 ? O19 3VV 503 B 1 
HETATM 27 S S20 3VV . . . H 3 81.43 98.072 105.114 1 74.63 ? S20 3VV 503 B 1 
HETATM 28 N N23 3VV . . . H 3 82.722 99.139 101.466 1 74.63 ? N23 3VV 503 B 1 
HETATM 29 O O25 3VV . . . H 3 81.077 100.427 100.719 1 74.63 ? O25 3VV 503 B 1 
HETATM 30 C C27 3VV . . . H 3 82.25 101.067 98.452 1 74.63 ? C27 3VV 503 B 1 
HETATM 31 N N28 3VV . . . H 3 82.149 100.899 97.022 1 74.63 ? N28 3VV 503 B 1 
HETATM 32 C C29 3VV . . . H 3 81.814 101.916 96.264 1 74.63 ? C29 3VV 503 B 1 
HETATM 33 O O30 3VV . . . H 3 81.58 102.996 96.734 1 74.63 ? O30 3VV 503 B 1 
HETATM 34 C C31 3VV . . . H 3 81.71 101.671 94.781 1 74.63 ? C31 3VV 503 B 1 
HETATM 35 O O32 3VV . . . H 3 82.974 101.269 94.291 1 74.63 ? O32 3VV 503 B 1 
HETATM 36 C C33 3VV . . . H 3 81.001 102.668 93.83 1 74.63 ? C33 3VV 503 B 1 
HETATM 37 C C34 3VV . . . H 3 79.547 102.258 93.634 1 74.63 ? C34 3VV 503 B 1 
HETATM 38 C C35 3VV . . . H 3 81.043 104.094 94.359 1 74.63 ? C35 3VV 503 B 1 
HETATM 39 C C36 3VV . . . H 3 81.677 102.662 92.469 1 74.63 ? C36 3VV 503 B 1 
HETATM 40 O O37 3VV . . . H 3 81.313 103.832 91.747 1 74.63 ? O37 3VV 503 B 1 
HETATM 41 O O39 3VV . . . H 3 82.893 104.77 90.097 1 74.63 ? O39 3VV 503 B 1 
HETATM 42 O O40 3VV . . . H 3 83.119 105.464 92.489 1 74.63 ? O40 3VV 503 B 1 
HETATM 43 O O41 3VV . . . H 3 80.984 105.802 91.168 1 74.63 ? O41 3VV 503 B 1 
HETATM 44 O O43 3VV . . . H 3 79.018 105.359 89.695 1 74.63 ? O43 3VV 503 B 1 
HETATM 45 O O44 3VV . . . H 3 80.396 107.407 89.334 1 74.63 ? O44 3VV 503 B 1 
HETATM 46 O O45 3VV . . . H 3 81.227 105.238 88.74 1 74.63 ? O45 3VV 503 B 1 
HETATM 47 C C46 3VV . . . H 3 80.574 104.725 87.571 1 74.63 ? C46 3VV 503 B 1 
HETATM 48 C C47 3VV . . . H 3 81.024 105.436 86.322 1 74.63 ? C47 3VV 503 B 1 
HETATM 49 O O48 3VV . . . H 3 81.479 106.766 86.631 1 74.63 ? O48 3VV 503 B 1 
HETATM 50 C C49 3VV . . . H 3 82.357 107.214 85.617 1 74.63 ? C49 3VV 503 B 1 
HETATM 51 C C50 3VV . . . H 3 82.769 105.964 84.777 1 74.63 ? C50 3VV 503 B 1 
HETATM 52 O O51 3VV . . . H 3 82.282 105.953 83.438 1 74.63 ? O51 3VV 503 B 1 
HETATM 53 C C52 3VV . . . H 3 82.185 104.799 85.585 1 74.63 ? C52 3VV 503 B 1 
HETATM 54 O O53 3VV . . . H 3 81.663 103.747 84.734 1 74.63 ? O53 3VV 503 B 1 
HETATM 55 O O55 3VV . . . H 3 82.132 101.363 83.639 1 74.63 ? O55 3VV 503 B 1 
HETATM 56 O O56 3VV . . . H 3 82.56 101.793 86.043 1 74.63 ? O56 3VV 503 B 1 
HETATM 57 O O57 3VV . . . H 3 80.195 101.694 85.136 1 74.63 ? O57 3VV 503 B 1 
HETATM 58 N N58 3VV . . . H 3 83.459 107.937 86.272 1 74.63 ? N58 3VV 503 B 1 
HETATM 59 C C59 3VV . . . H 3 83.775 107.851 87.602 1 74.63 ? C59 3VV 503 B 1 
HETATM 60 N N60 3VV . . . H 3 84.929 108.39 87.915 1 74.63 ? N60 3VV 503 B 1 
HETATM 61 C C61 3VV . . . H 3 85.401 108.877 86.707 1 74.63 ? C61 3VV 503 B 1 
HETATM 62 C C62 3VV . . . H 3 86.609 109.499 86.343 1 74.63 ? C62 3VV 503 B 1 
HETATM 63 N N63 3VV . . . H 3 87.618 109.728 87.189 1 74.63 ? N63 3VV 503 B 1 
HETATM 64 N N64 3VV . . . H 3 86.758 109.869 85.054 1 74.63 ? N64 3VV 503 B 1 
HETATM 65 C C65 3VV . . . H 3 85.76 109.644 84.198 1 74.63 ? C65 3VV 503 B 1 
HETATM 66 N N66 3VV . . . H 3 84.593 109.038 84.42 1 74.63 ? N66 3VV 503 B 1 
HETATM 67 C C67 3VV . . . H 3 84.483 108.652 85.695 1 74.63 ? C67 3VV 503 B 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           67 
#