data_6VP0
#
_model_server_result.job_id            U4KGqG8XJRm5yPYj62S4Tg 
_model_server_result.datetime_utc      '2024-12-21 18:56:10' 
_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          6vp0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":605}' 
#
_entry.id    6VP0 
#
_exptl.entry_id    6VP0 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              1031.98 
_entity.id                          4 
_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            6VP0 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VP0 
_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 
_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
? 4 G N N 
? 4 M 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                     6VP0 
_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 POV C 1 601 601 POV POV . 
D 3 P5S C 1 602 1201 P5S P5S . 
E 3 P5S C 1 603 1801 P5S P5S . 
F 2 POV C 1 604 1701 POV POV . 
G 4 3VV C 1 605 1701 3VV 3VV . 
H 5 AV0 C 1 606 1901 AV0 AV0 . 
I 2 POV E 1 601 601 POV POV . 
J 3 P5S E 1 602 1201 P5S P5S . 
K 3 P5S E 1 603 1801 P5S P5S . 
L 2 POV E 1 604 1701 POV POV . 
M 4 3VV E 1 605 1701 3VV 3VV . 
N 5 AV0 E 1 606 1901 AV0 AV0 . 
#
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 . . . G 4 110.084 126.278 113.286 1 77.23 ? C10 3VV 605 C 1 
HETATM 2 C C13 3VV . . . G 4 108.611 129.261 111.911 1 77.23 ? C13 3VV 605 C 1 
HETATM 3 C C15 3VV . . . G 4 107.311 131.136 113.024 1 77.23 ? C15 3VV 605 C 1 
HETATM 4 C C17 3VV . . . G 4 107.717 133.549 112.396 1 77.23 ? C17 3VV 605 C 1 
HETATM 5 C C21 3VV . . . G 4 109.987 136.853 111.323 1 77.23 ? C21 3VV 605 C 1 
HETATM 6 C C22 3VV . . . G 4 110.226 138.071 112.195 1 77.23 ? C22 3VV 605 C 1 
HETATM 7 C C24 3VV . . . G 4 109.014 138.032 114.32 1 77.23 ? C24 3VV 605 C 1 
HETATM 8 C C26 3VV . . . G 4 109.065 137.671 115.784 1 77.23 ? C26 3VV 605 C 1 
HETATM 9 P P38 3VV . . . G 4 106.28 136.156 123.945 1 77.23 ? P38 3VV 605 C 1 
HETATM 10 P P42 3VV . . . G 4 104.759 137.413 126.056 1 77.23 ? P42 3VV 605 C 1 
HETATM 11 P P54 3VV . . . G 4 99.891 134.514 126.893 1 77.23 ? P54 3VV 605 C 1 
HETATM 12 C C01 3VV . . . G 4 113.678 135.356 113.132 1 77.23 ? C01 3VV 605 C 1 
HETATM 13 C C02 3VV . . . G 4 114.523 134.277 112.498 1 77.23 ? C02 3VV 605 C 1 
HETATM 14 C C03 3VV . . . G 4 113.734 133.024 112.17 1 77.23 ? C03 3VV 605 C 1 
HETATM 15 C C04 3VV . . . G 4 114.577 131.89 111.604 1 77.23 ? C04 3VV 605 C 1 
HETATM 16 C C05 3VV . . . G 4 113.798 130.608 111.356 1 77.23 ? C05 3VV 605 C 1 
HETATM 17 C C06 3VV . . . G 4 113.055 130.101 112.582 1 77.23 ? C06 3VV 605 C 1 
HETATM 18 C C07 3VV . . . G 4 112.392 128.745 112.396 1 77.23 ? C07 3VV 605 C 1 
HETATM 19 C C08 3VV . . . G 4 111.636 128.242 113.627 1 77.23 ? C08 3VV 605 C 1 
HETATM 20 C C09 3VV . . . G 4 111.273 126.793 113.523 1 77.23 ? C09 3VV 605 C 1 
HETATM 21 C C11 3VV . . . G 4 108.808 127.022 113.077 1 77.23 ? C11 3VV 605 C 1 
HETATM 22 C C12 3VV . . . G 4 108.74 127.758 111.746 1 77.23 ? C12 3VV 605 C 1 
HETATM 23 C C14 3VV . . . G 4 107.315 129.689 112.576 1 77.23 ? C14 3VV 605 C 1 
HETATM 24 C C16 3VV . . . G 4 107.868 132.093 111.988 1 77.23 ? C16 3VV 605 C 1 
HETATM 25 C C18 3VV . . . G 4 108.75 134.399 111.709 1 77.23 ? C18 3VV 605 C 1 
HETATM 26 O O19 3VV . . . G 4 109.754 133.954 111.218 1 77.23 ? O19 3VV 605 C 1 
HETATM 27 S S20 3VV . . . G 4 108.374 136.118 111.73 1 77.23 ? S20 3VV 605 C 1 
HETATM 28 N N23 3VV . . . G 4 110.112 137.772 113.616 1 77.23 ? N23 3VV 605 C 1 
HETATM 29 O O25 3VV . . . G 4 108.008 138.528 113.821 1 77.23 ? O25 3VV 605 C 1 
HETATM 30 C C27 3VV . . . G 4 108.399 136.341 116.061 1 77.23 ? C27 3VV 605 C 1 
HETATM 31 N N28 3VV . . . G 4 108.244 136.086 117.487 1 77.23 ? N28 3VV 605 C 1 
HETATM 32 C C29 3VV . . . G 4 109.271 135.79 118.284 1 77.23 ? C29 3VV 605 C 1 
HETATM 33 O O30 3VV . . . G 4 110.436 135.798 117.897 1 77.23 ? O30 3VV 605 C 1 
HETATM 34 C C31 3VV . . . G 4 108.936 135.403 119.721 1 77.23 ? C31 3VV 605 C 1 
HETATM 35 O O32 3VV . . . G 4 108.561 134.037 119.788 1 77.23 ? O32 3VV 605 C 1 
HETATM 36 C C33 3VV . . . G 4 107.933 136.281 120.513 1 77.23 ? C33 3VV 605 C 1 
HETATM 37 C C34 3VV . . . G 4 108.232 137.762 120.262 1 77.23 ? C34 3VV 605 C 1 
HETATM 38 C C35 3VV . . . G 4 106.498 135.961 120.081 1 77.23 ? C35 3VV 605 C 1 
HETATM 39 C C36 3VV . . . G 4 108.059 136.005 122.006 1 77.23 ? C36 3VV 605 C 1 
HETATM 40 O O37 3VV . . . G 4 107.111 136.797 122.734 1 77.23 ? O37 3VV 605 C 1 
HETATM 41 O O39 3VV . . . G 4 107.271 135.334 124.751 1 77.23 ? O39 3VV 605 C 1 
HETATM 42 O O40 3VV . . . G 4 105.108 135.406 123.453 1 77.23 ? O40 3VV 605 C 1 
HETATM 43 O O41 3VV . . . G 4 105.825 137.362 124.876 1 77.23 ? O41 3VV 605 C 1 
HETATM 44 O O43 3VV . . . G 4 105.308 138.355 127.12 1 77.23 ? O43 3VV 605 C 1 
HETATM 45 O O44 3VV . . . G 4 103.408 137.738 125.559 1 77.23 ? O44 3VV 605 C 1 
HETATM 46 O O45 3VV . . . G 4 104.799 135.951 126.671 1 77.23 ? O45 3VV 605 C 1 
HETATM 47 C C46 3VV . . . G 4 104.744 135.644 128.079 1 77.23 ? C46 3VV 605 C 1 
HETATM 48 C C47 3VV . . . G 4 103.532 134.787 128.337 1 77.23 ? C47 3VV 605 C 1 
HETATM 49 O O48 3VV . . . G 4 103.459 134.459 129.743 1 77.23 ? O48 3VV 605 C 1 
HETATM 50 C C49 3VV . . . G 4 102.268 134.99 130.294 1 77.23 ? C49 3VV 605 C 1 
HETATM 51 C C50 3VV . . . G 4 101.811 136.09 129.338 1 77.23 ? C50 3VV 605 C 1 
HETATM 52 O O51 3VV . . . G 4 100.407 136.293 129.434 1 77.23 ? O51 3VV 605 C 1 
HETATM 53 C C52 3VV . . . G 4 102.195 135.449 128.01 1 77.23 ? C52 3VV 605 C 1 
HETATM 54 O O53 3VV . . . G 4 101.298 134.367 127.679 1 77.23 ? O53 3VV 605 C 1 
HETATM 55 O O55 3VV . . . G 4 99.325 133.096 126.761 1 77.23 ? O55 3VV 605 C 1 
HETATM 56 O O56 3VV . . . G 4 98.984 135.426 127.643 1 77.23 ? O56 3VV 605 C 1 
HETATM 57 O O57 3VV . . . G 4 100.233 135.026 125.49 1 77.23 ? O57 3VV 605 C 1 
HETATM 58 N N58 3VV . . . G 4 102.533 135.446 131.655 1 77.23 ? N58 3VV 605 C 1 
HETATM 59 C C59 3VV . . . G 4 101.591 135.766 132.597 1 77.23 ? C59 3VV 605 C 1 
HETATM 60 N N60 3VV . . . G 4 102.091 136.145 133.748 1 77.23 ? N60 3VV 605 C 1 
HETATM 61 C C61 3VV . . . G 4 103.462 136.069 133.551 1 77.23 ? C61 3VV 605 C 1 
HETATM 62 C C62 3VV . . . G 4 104.557 136.338 134.394 1 77.23 ? C62 3VV 605 C 1 
HETATM 63 N N63 3VV . . . G 4 104.439 136.765 135.655 1 77.23 ? N63 3VV 605 C 1 
HETATM 64 N N64 3VV . . . G 4 105.796 136.155 133.889 1 77.23 ? N64 3VV 605 C 1 
HETATM 65 C C65 3VV . . . G 4 105.921 135.734 132.628 1 77.23 ? C65 3VV 605 C 1 
HETATM 66 N N66 3VV . . . G 4 104.964 135.453 131.741 1 77.23 ? N66 3VV 605 C 1 
HETATM 67 C C67 3VV . . . G 4 103.749 135.64 132.266 1 77.23 ? C67 3VV 605 C 1 
#
_model_server_stats.io_time_ms              54 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           67 
#