data_6DW7
#
_model_server_result.job_id            1T2WuRyPIOr1ZxJH9Syf8Q 
_model_server_result.datetime_utc      '2024-11-24 15:51:19' 
_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          6dw7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":702}' 
#
_entry.id    6DW7 
#
_exptl.entry_id    6DW7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          113.67 
_cell.angle_gamma         90 
_cell.entry_id            6DW7 
_cell.length_a            84.546 
_cell.length_b            146.372 
_cell.length_c            98.929 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DW7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z 
_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
? 2 E N N 
? 2 M N N 
? 2 N N N 
? 2 U 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
metalc ? metalc1 A O THR 38 A THR 114 1_555 J NA NA . A NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? 
metalc ? metalc2 A OD2 ASP 235 A ASP 311 1_555 I NA NA . A NA 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? 
metalc ? metalc3 E O1G DTP . A DTP 701 1_555 K MG MG . B MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc4 E O1B DTP . A DTP 701 1_555 K MG MG . B MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc5 F MG MG . A MG 702 1_555 G O1A GTP . A GTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc6 F MG MG . A MG 702 1_555 G O1B GTP . A GTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
metalc ? metalc7 F MG MG . A MG 702 1_555 G O1G GTP . A GTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc8 F MG MG . A MG 702 1_555 M O1B DTP . B DTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc9 F MG MG . A MG 702 1_555 M O3G DTP . B DTP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc10 I NA NA . A NA 705 1_555 W O HOH . A HOH 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? 
metalc ? metalc11 J NA NA . A NA 706 1_555 W O HOH . A HOH 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc12 K MG MG . B MG 701 1_555 L O2B GTP . B GTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc13 K MG MG . B MG 701 1_555 L O2A GTP . B GTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc14 K MG MG . B MG 701 1_555 L O2G GTP . B GTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.65 sing 
metalc ? metalc15 C O GLN 434 C GLN 510 1_555 S NA NA . C NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
metalc ? metalc16 C O LYS 436 C LYS 512 1_555 S NA NA . C NA 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? 
metalc ? metalc17 N O3G DTP . C DTP 701 1_555 O MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc18 N O2B DTP . C DTP 701 1_555 O MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc19 O MG MG . C MG 702 1_555 T O1G GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? 
metalc ? metalc20 O MG MG . C MG 702 1_555 T O1B GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? 
metalc ? metalc21 O MG MG . C MG 702 1_555 T O3A GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc22 P MG MG . C MG 703 1_555 Q O2A GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc23 P MG MG . C MG 703 1_555 Q O2B GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? 
metalc ? metalc24 P MG MG . C MG 703 1_555 Q O2G GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.689 sing 
metalc ? metalc25 P MG MG . C MG 703 1_555 U O1G DTP . D DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc26 P MG MG . C MG 703 1_555 U O2B DTP . D DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
#
_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                     6DW7 
_atom_sites.fract_transf_matrix[1][1]    0.011828 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005186 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006832 
_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]    0.011037 
_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 A 1 701 800 DTP DTP . 
F 3 MG A 1 702 850 MG MG . 
G 4 GTP A 1 703 900 GTP GTP . 
H 5 GLY A 1 704 2 GLY GLY . 
I 6 NA A 1 705 2 NA NA . 
J 6 NA A 1 706 3 NA NA . 
K 3 MG B 1 701 850 MG MG . 
L 4 GTP B 1 702 900 GTP GTP . 
M 2 DTP B 1 703 800 DTP DTP . 
N 2 DTP C 1 701 800 DTP DTP . 
O 3 MG C 1 702 850 MG MG . 
P 3 MG C 1 703 850 MG MG . 
Q 4 GTP C 1 704 900 GTP GTP . 
R 5 GLY C 1 705 1 GLY GLY . 
S 6 NA C 1 706 1 NA NA . 
T 4 GTP D 1 701 900 GTP GTP . 
U 2 DTP D 1 702 800 DTP DTP . 
V 7 PO4 D 1 703 1 PO4 PO4 . 
W 8 HOH A 1 801 29 HOH HOH . 
W 8 HOH A 2 802 35 HOH HOH . 
W 8 HOH A 3 803 22 HOH HOH . 
W 8 HOH A 4 804 21 HOH HOH . 
W 8 HOH A 5 805 19 HOH HOH . 
W 8 HOH A 6 806 53 HOH HOH . 
W 8 HOH A 7 807 20 HOH HOH . 
W 8 HOH A 8 808 31 HOH HOH . 
W 8 HOH A 9 809 56 HOH HOH . 
W 8 HOH A 10 810 7 HOH HOH . 
W 8 HOH A 11 811 54 HOH HOH . 
W 8 HOH A 12 812 55 HOH HOH . 
W 8 HOH A 13 813 3 HOH HOH . 
W 8 HOH A 14 814 52 HOH HOH . 
X 8 HOH B 1 801 14 HOH HOH . 
X 8 HOH B 2 802 9 HOH HOH . 
X 8 HOH B 3 803 38 HOH HOH . 
X 8 HOH B 4 804 2 HOH HOH . 
X 8 HOH B 5 805 8 HOH HOH . 
X 8 HOH B 6 806 15 HOH HOH . 
X 8 HOH B 7 807 30 HOH HOH . 
X 8 HOH B 8 808 28 HOH HOH . 
X 8 HOH B 9 809 37 HOH HOH . 
X 8 HOH B 10 810 25 HOH HOH . 
X 8 HOH B 11 811 42 HOH HOH . 
X 8 HOH B 12 812 12 HOH HOH . 
X 8 HOH B 13 813 57 HOH HOH . 
X 8 HOH B 14 814 1 HOH HOH . 
X 8 HOH B 15 815 48 HOH HOH . 
X 8 HOH B 16 816 44 HOH HOH . 
X 8 HOH B 17 817 46 HOH HOH . 
X 8 HOH B 18 818 16 HOH HOH . 
Y 8 HOH C 1 801 4 HOH HOH . 
Y 8 HOH C 2 802 43 HOH HOH . 
Y 8 HOH C 3 803 18 HOH HOH . 
Y 8 HOH C 4 804 34 HOH HOH . 
Y 8 HOH C 5 805 32 HOH HOH . 
Y 8 HOH C 6 806 11 HOH HOH . 
Y 8 HOH C 7 807 13 HOH HOH . 
Y 8 HOH C 8 808 50 HOH HOH . 
Y 8 HOH C 9 809 17 HOH HOH . 
Y 8 HOH C 10 810 26 HOH HOH . 
Y 8 HOH C 11 811 24 HOH HOH . 
Y 8 HOH C 12 812 45 HOH HOH . 
Y 8 HOH C 13 813 49 HOH HOH . 
Z 8 HOH D 1 801 39 HOH HOH . 
Z 8 HOH D 2 802 40 HOH HOH . 
Z 8 HOH D 3 803 36 HOH HOH . 
Z 8 HOH D 4 804 51 HOH HOH . 
Z 8 HOH D 5 805 33 HOH HOH . 
Z 8 HOH D 6 806 27 HOH HOH . 
Z 8 HOH D 7 807 58 HOH HOH . 
Z 8 HOH D 8 808 60 HOH HOH . 
Z 8 HOH D 9 809 47 HOH HOH . 
Z 8 HOH D 10 810 41 HOH HOH . 
Z 8 HOH D 11 811 59 HOH HOH . 
#
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 . . . U 2 35.761 -23.96 -23.82 1 44.95 ? PG DTP 702 D 1 
HETATM 2 O O1G DTP . . . U 2 35.309 -24.893 -24.925 1 41.87 ? O1G DTP 702 D 1 
HETATM 3 O O2G DTP . . . U 2 37.221 -23.502 -23.758 1 45.13 ? O2G DTP 702 D 1 
HETATM 4 O O3G DTP . . . U 2 35.208 -24.41 -22.542 1 40.77 ? O3G DTP 702 D 1 
HETATM 5 P PB DTP . . . U 2 34.032 -22.065 -25.16 1 42.5 ? PB DTP 702 D 1 
HETATM 6 O O1B DTP . . . U 2 34.704 -20.996 -25.955 1 40.28 ? O1B DTP 702 D 1 
HETATM 7 O O2B DTP . . . U 2 33.393 -23.225 -25.896 1 51.48 ? O2B DTP 702 D 1 
HETATM 8 O O3B DTP . . . U 2 35.051 -22.525 -24.013 1 46.32 ? O3B DTP 702 D 1 
HETATM 9 P PA DTP . . . U 2 33.047 -20.073 -23.292 1 37.02 ? PA DTP 702 D 1 
HETATM 10 O O1A DTP . . . U 2 34.122 -19.119 -23.735 1 35.33 ? O1A DTP 702 D 1 
HETATM 11 O O2A DTP . . . U 2 32.924 -20.663 -21.922 1 35.02 ? O2A DTP 702 D 1 
HETATM 12 O O3A DTP . . . U 2 32.908 -21.405 -24.226 1 44.21 ? O3A DTP 702 D 1 
HETATM 13 O O5' DTP . . . U 2 31.627 -19.4 -23.682 1 36.91 ? O5' DTP 702 D 1 
HETATM 14 C C5' DTP . . . U 2 30.388 -20.006 -23.286 1 31.2 ? C5' DTP 702 D 1 
HETATM 15 C C4' DTP . . . U 2 29.296 -18.972 -23.487 1 31.3 ? C4' DTP 702 D 1 
HETATM 16 O O4' DTP . . . U 2 29.55 -17.899 -22.587 1 32.59 ? O4' DTP 702 D 1 
HETATM 17 C C3' DTP . . . U 2 29.351 -18.338 -24.863 1 31.81 ? C3' DTP 702 D 1 
HETATM 18 O O3' DTP . . . U 2 28.013 -18.131 -25.226 1 31.52 ? O3' DTP 702 D 1 
HETATM 19 C C2' DTP . . . U 2 29.937 -16.955 -24.732 1 30.14 ? C2' DTP 702 D 1 
HETATM 20 C C1' DTP . . . U 2 29.711 -16.656 -23.267 1 32.97 ? C1' DTP 702 D 1 
HETATM 21 N N9 DTP . . . U 2 30.832 -16.07 -22.529 1 35.18 ? N9 DTP 702 D 1 
HETATM 22 C C8 DTP . . . U 2 32.151 -16.284 -22.731 1 37.52 ? C8 DTP 702 D 1 
HETATM 23 N N7 DTP . . . U 2 32.887 -15.606 -21.817 1 37.47 ? N7 DTP 702 D 1 
HETATM 24 C C5 DTP . . . U 2 32.01 -14.965 -21.043 1 34.3 ? C5 DTP 702 D 1 
HETATM 25 C C6 DTP . . . U 2 32.142 -14.117 -19.88 1 34.5 ? C6 DTP 702 D 1 
HETATM 26 N N6 DTP . . . U 2 33.379 -13.839 -19.431 1 37.82 ? N6 DTP 702 D 1 
HETATM 27 N N1 DTP . . . U 2 31.01 -13.676 -19.311 1 35.39 ? N1 DTP 702 D 1 
HETATM 28 C C2 DTP . . . U 2 29.776 -14.001 -19.79 1 36.03 ? C2 DTP 702 D 1 
HETATM 29 N N3 DTP . . . U 2 29.575 -14.783 -20.867 1 34.8 ? N3 DTP 702 D 1 
HETATM 30 C C4 DTP . . . U 2 30.656 -15.278 -21.502 1 33.8 ? C4 DTP 702 D 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           30 
#