data_6MYX
#
_model_server_result.job_id            OrxDpl6JnKS7d0RF9Db9dA 
_model_server_result.datetime_utc      '2025-03-03 16:52:09' 
_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          6myx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":1002}' 
#
_entry.id    6MYX 
#
_exptl.entry_id    6MYX 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              491.182 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dodecameric 12 'representative helical assembly' 1 
? tetrameric 4 'helical asymmetric unit' 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L 1 (1-3) 
A,B,C,D,E,F,G,H,I,J,K,L 2 1 
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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 'helical symmetry operation' ? ? 0.152649 0.98828 -0.000239 -0.98828 0.152648 -0.0012 -0.00115 0.000419 0.999999 -16.902699 221.104032 -73.740949 
3 'helical symmetry operation' ? ? 0.156897 -0.987614 0.001206 0.987608 0.1569 0.003617 -0.003761 0.000624 0.999993 220.36768 -18.007797 74.051516 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
#
_chem_comp.formula           'C10 H16 N5 O12 P3' 
_chem_comp.formula_weight    491.182 
_chem_comp.id                DTP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" 
_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
PG O1G DTP doub 83 n n 
PG O2G DTP sing 84 n n 
PG O3G DTP sing 85 n n 
PG O3B DTP sing 86 n n 
O2G HOG2 DTP sing 87 n n 
O3G HOG3 DTP sing 88 n n 
PB O1B DTP doub 89 n n 
PB O2B DTP sing 90 n n 
PB O3B DTP sing 91 n n 
PB O3A DTP sing 92 n n 
O2B HOB2 DTP sing 93 n n 
PA O1A DTP doub 94 n n 
PA O2A DTP sing 95 n n 
PA O3A DTP sing 96 n n 
PA O5' DTP sing 97 n n 
O2A HOA2 DTP sing 98 n n 
O5' C5' DTP sing 99 n n 
C5' C4' DTP sing 100 n n 
C5' "H5'1" DTP sing 101 n n 
C5' "H5'2" DTP sing 102 n n 
C4' O4' DTP sing 103 n n 
C4' C3' DTP sing 104 n n 
C4' H4' DTP sing 105 n n 
O4' C1' DTP sing 106 n n 
C3' O3' DTP sing 107 n n 
C3' C2' DTP sing 108 n n 
C3' H3' DTP sing 109 n n 
O3' HO3' DTP sing 110 n n 
C2' C1' DTP sing 111 n n 
C2' "H2'1" DTP sing 112 n n 
C2' "H2'2" DTP sing 113 n n 
C1' N9 DTP sing 114 n n 
C1' H1' DTP sing 115 n n 
N9 C8 DTP sing 116 n y 
N9 C4 DTP sing 117 n y 
C8 N7 DTP doub 118 n y 
C8 H8 DTP sing 119 n n 
N7 C5 DTP sing 120 n y 
C5 C6 DTP sing 121 n y 
C5 C4 DTP doub 122 n y 
C6 N6 DTP sing 123 n n 
C6 N1 DTP doub 124 n y 
N6 HN61 DTP sing 125 n n 
N6 HN62 DTP sing 126 n n 
N1 C2 DTP sing 127 n y 
C2 N3 DTP doub 128 n y 
C2 H2 DTP sing 129 n n 
N3 C4 DTP sing 130 n y 
#
_atom_sites.entry_id                     6MYX 
_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
E 2 DTP C 1 1001 1001 DTP DTP . 
F 2 DTP C 1 1002 1003 DTP DTP . 
G 2 DTP D 1 1001 1001 DTP DTP . 
H 2 DTP D 1 1002 1003 DTP DTP . 
I 2 DTP I 1 1001 1001 DTP DTP . 
J 2 DTP I 1 1002 1003 DTP DTP . 
K 2 DTP J 1 1001 1001 DTP DTP . 
L 2 DTP J 1 1002 1003 DTP DTP . 
#
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 PG DTP . . . H 2 69.879 86.294 161.754 0.95 132.2 ? PG DTP 1002 D 1 
HETATM 2 O O1G DTP . . . H 2 70.337 84.886 161.479 0.95 132.2 ? O1G DTP 1002 D 1 
HETATM 3 O O2G DTP . . . H 2 70.93 87.034 162.542 0.95 132.2 ? O2G DTP 1002 D 1 
HETATM 4 O O3G DTP . . . H 2 68.587 86.274 162.527 0.95 132.2 ? O3G DTP 1002 D 1 
HETATM 5 P PB DTP . . . H 2 69.351 88.644 160.107 0.95 132.2 ? PB DTP 1002 D 1 
HETATM 6 O O1B DTP . . . H 2 68.134 88.801 159.233 0.95 132.2 ? O1B DTP 1002 D 1 
HETATM 7 O O2B DTP . . . H 2 69.139 89.32 161.437 0.95 132.2 ? O2B DTP 1002 D 1 
HETATM 8 O O3B DTP . . . H 2 69.644 87.056 160.378 0.95 132.2 ? O3B DTP 1002 D 1 
HETATM 9 P PA DTP . . . H 2 72.268 89.017 159.598 0.95 132.2 ? PA DTP 1002 D 1 
HETATM 10 O O1A DTP . . . H 2 72.972 89.182 158.276 0.95 132.2 ? O1A DTP 1002 D 1 
HETATM 11 O O2A DTP . . . H 2 72.469 87.615 160.112 0.95 132.2 ? O2A DTP 1002 D 1 
HETATM 12 O O3A DTP . . . H 2 70.667 89.311 159.39 0.95 132.2 ? O3A DTP 1002 D 1 
HETATM 13 O O5' DTP . . . H 2 72.872 90.09 160.691 0.95 132.2 ? O5' DTP 1002 D 1 
HETATM 14 C C5' DTP . . . H 2 73.923 90.924 160.295 0.95 132.2 ? C5' DTP 1002 D 1 
HETATM 15 C C4' DTP . . . H 2 73.55 92.387 160.428 0.95 132.2 ? C4' DTP 1002 D 1 
HETATM 16 O O4' DTP . . . H 2 74.094 93.17 159.333 0.95 132.2 ? O4' DTP 1002 D 1 
HETATM 17 C C3' DTP . . . H 2 72.047 92.585 160.311 0.95 132.2 ? C3' DTP 1002 D 1 
HETATM 18 O O3' DTP . . . H 2 71.706 93.865 160.834 0.95 132.2 ? O3' DTP 1002 D 1 
HETATM 19 C C2' DTP . . . H 2 71.848 92.561 158.78 0.95 132.2 ? C2' DTP 1002 D 1 
HETATM 20 C C1' DTP . . . H 2 73.194 93.087 158.23 0.95 132.2 ? C1' DTP 1002 D 1 
HETATM 21 N N9 DTP . . . H 2 73.837 92.277 157.182 0.95 132.2 ? N9 DTP 1002 D 1 
HETATM 22 C C8 DTP . . . H 2 74.791 91.335 156.948 0.95 132.2 ? C8 DTP 1002 D 1 
HETATM 23 N N7 DTP . . . H 2 74.836 91.057 155.646 0.95 132.2 ? N7 DTP 1002 D 1 
HETATM 24 C C5 DTP . . . H 2 73.921 91.816 155.042 0.95 132.2 ? C5 DTP 1002 D 1 
HETATM 25 C C6 DTP . . . H 2 73.559 91.943 153.723 0.95 132.2 ? C6 DTP 1002 D 1 
HETATM 26 N N6 DTP . . . H 2 74.151 91.184 152.801 0.95 132.2 ? N6 DTP 1002 D 1 
HETATM 27 N N1 DTP . . . H 2 72.596 92.779 153.368 0.95 132.2 ? N1 DTP 1002 D 1 
HETATM 28 C C2 DTP . . . H 2 72.033 93.492 154.358 0.95 132.2 ? C2 DTP 1002 D 1 
HETATM 29 N N3 DTP . . . H 2 72.316 93.46 155.638 0.95 132.2 ? N3 DTP 1002 D 1 
HETATM 30 C C4 DTP . . . H 2 73.284 92.601 156.011 0.95 132.2 ? C4 DTP 1002 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           30 
#