data_4TO1
#
_model_server_result.job_id            uNO7Kp3LjNOy7gSgtBYMPg 
_model_server_result.datetime_utc      '2024-11-07 01:38:10' 
_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          4to1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":702}' 
#
_entry.id    4TO1 
#
_exptl.entry_id    4TO1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              491.182 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" 
_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          115.79 
_cell.angle_gamma         90 
_cell.entry_id            4TO1 
_cell.length_a            86.204 
_cell.length_b            141.586 
_cell.length_c            98.187 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4TO1 
_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 
_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 F N N 
? 3 J 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 F O3G DTP . A DTP 702 1_555 G MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? 
metalc ? metalc2 F O1B DTP . A DTP 702 1_555 G MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc3 G MG MG . A MG 703 1_555 P O2B GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc4 G MG MG . A MG 703 1_555 P O1A GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc5 G MG MG . A MG 703 1_555 P O3G GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? 
metalc ? metalc6 G MG MG . A MG 703 1_555 W O HOH . C HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc7 H MG MG . A MG 704 1_555 U O HOH . A HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc8 H MG MG . A MG 704 1_555 J O1B DTP . B DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc9 H MG MG . A MG 704 1_555 J O2G DTP . B DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.725 ? 
metalc ? metalc10 H MG MG . A MG 704 1_555 T O1G GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.781 ? 
metalc ? metalc11 H MG MG . A MG 704 1_555 T O1B GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc12 H MG MG . A MG 704 1_555 T O2A GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc13 K O1B DCP . C DCP 701 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? 
metalc ? metalc14 K O2G DCP . C DCP 701 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? 
metalc ? metalc15 L MG MG . C MG 702 1_555 Q O3G GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? 
metalc ? metalc16 L MG MG . C MG 702 1_555 Q O2B GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? 
metalc ? metalc17 L MG MG . C MG 702 1_555 Q O1A GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc18 L MG MG . C MG 702 1_555 X O HOH . D HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc19 M MG MG . C MG 703 1_555 N O1G GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.835 ? 
metalc ? metalc20 M MG MG . C MG 703 1_555 N O1A GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc21 M MG MG . C MG 703 1_555 N O1B GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc22 M MG MG . C MG 703 1_555 W O HOH . C HOH 821 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc23 M MG MG . C MG 703 1_555 R O2G DCP . D DCP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? 
metalc ? metalc24 M MG MG . C MG 703 1_555 R O1B DCP . D DCP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? 
#
_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 128 n n 
PG O2G DTP sing 129 n n 
PG O3G DTP sing 130 n n 
PG O3B DTP sing 131 n n 
O2G HOG2 DTP sing 132 n n 
O3G HOG3 DTP sing 133 n n 
PB O1B DTP doub 134 n n 
PB O2B DTP sing 135 n n 
PB O3B DTP sing 136 n n 
PB O3A DTP sing 137 n n 
O2B HOB2 DTP sing 138 n n 
PA O1A DTP doub 139 n n 
PA O2A DTP sing 140 n n 
PA O3A DTP sing 141 n n 
PA O5' DTP sing 142 n n 
O2A HOA2 DTP sing 143 n n 
O5' C5' DTP sing 144 n n 
C5' C4' DTP sing 145 n n 
C5' "H5'1" DTP sing 146 n n 
C5' "H5'2" DTP sing 147 n n 
C4' O4' DTP sing 148 n n 
C4' C3' DTP sing 149 n n 
C4' H4' DTP sing 150 n n 
O4' C1' DTP sing 151 n n 
C3' O3' DTP sing 152 n n 
C3' C2' DTP sing 153 n n 
C3' H3' DTP sing 154 n n 
O3' HO3' DTP sing 155 n n 
C2' C1' DTP sing 156 n n 
C2' "H2'1" DTP sing 157 n n 
C2' "H2'2" DTP sing 158 n n 
C1' N9 DTP sing 159 n n 
C1' H1' DTP sing 160 n n 
N9 C8 DTP sing 161 n y 
N9 C4 DTP sing 162 n y 
C8 N7 DTP doub 163 n y 
C8 H8 DTP sing 164 n n 
N7 C5 DTP sing 165 n y 
C5 C6 DTP sing 166 n y 
C5 C4 DTP doub 167 n y 
C6 N6 DTP sing 168 n n 
C6 N1 DTP doub 169 n y 
N6 HN61 DTP sing 170 n n 
N6 HN62 DTP sing 171 n n 
N1 C2 DTP sing 172 n y 
C2 N3 DTP doub 173 n y 
C2 H2 DTP sing 174 n n 
N3 C4 DTP sing 175 n y 
#
_atom_sites.entry_id                     4TO1 
_atom_sites.fract_transf_matrix[1][1]    0.0116 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005605 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007063 
_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]    0.011311 
_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 DCP A 1 701 700 DCP DCP . 
F 3 DTP A 1 702 800 DTP DTP . 
G 4 MG A 1 703 850 MG MG . 
H 4 MG A 1 704 850 MG MG . 
I 2 DCP B 1 701 700 DCP DCP . 
J 3 DTP B 1 702 800 DTP DTP . 
K 2 DCP C 1 701 800 DCP DCP . 
L 4 MG C 1 702 850 MG MG . 
M 4 MG C 1 703 850 MG MG . 
N 5 GTP C 1 704 900 GTP GTP . 
O 2 DCP C 1 705 700 DCP DCP . 
P 5 GTP C 1 706 900 GTP GTP . 
Q 5 GTP D 1 701 900 GTP GTP . 
R 2 DCP D 1 702 800 DCP DCP . 
S 2 DCP D 1 703 700 DCP DCP . 
T 5 GTP D 1 704 900 GTP GTP . 
U 6 HOH A 1 801 11 HOH HOH . 
U 6 HOH A 2 802 18 HOH HOH . 
U 6 HOH A 3 803 22 HOH HOH . 
U 6 HOH A 4 804 31 HOH HOH . 
U 6 HOH A 5 805 32 HOH HOH . 
U 6 HOH A 6 806 44 HOH HOH . 
U 6 HOH A 7 807 46 HOH HOH . 
V 6 HOH B 1 801 15 HOH HOH . 
V 6 HOH B 2 802 34 HOH HOH . 
V 6 HOH B 3 803 38 HOH HOH . 
V 6 HOH B 4 804 48 HOH HOH . 
V 6 HOH B 5 805 51 HOH HOH . 
V 6 HOH B 6 806 52 HOH HOH . 
W 6 HOH C 1 801 25 HOH HOH . 
W 6 HOH C 2 802 1 HOH HOH . 
W 6 HOH C 3 803 3 HOH HOH . 
W 6 HOH C 4 804 4 HOH HOH . 
W 6 HOH C 5 805 9 HOH HOH . 
W 6 HOH C 6 806 10 HOH HOH . 
W 6 HOH C 7 807 12 HOH HOH . 
W 6 HOH C 8 808 14 HOH HOH . 
W 6 HOH C 9 809 17 HOH HOH . 
W 6 HOH C 10 810 19 HOH HOH . 
W 6 HOH C 11 811 20 HOH HOH . 
W 6 HOH C 12 812 21 HOH HOH . 
W 6 HOH C 13 813 27 HOH HOH . 
W 6 HOH C 14 814 33 HOH HOH . 
W 6 HOH C 15 815 47 HOH HOH . 
W 6 HOH C 16 816 49 HOH HOH . 
W 6 HOH C 17 817 50 HOH HOH . 
W 6 HOH C 18 818 53 HOH HOH . 
W 6 HOH C 19 819 54 HOH HOH . 
W 6 HOH C 20 820 58 HOH HOH . 
W 6 HOH C 21 821 59 HOH HOH . 
W 6 HOH C 22 822 60 HOH HOH . 
X 6 HOH D 1 801 55 HOH HOH . 
X 6 HOH D 2 802 56 HOH HOH . 
X 6 HOH D 3 803 57 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 . . . F 3 -33.489 9.441 91.301 1 23.14 ? PG DTP 702 A 1 
HETATM 2 O O1G DTP . . . F 3 -34.96 9.263 91.071 1 21.06 ? O1G DTP 702 A 1 
HETATM 3 O O2G DTP . . . F 3 -33.226 9.843 92.717 1 21.09 ? O2G DTP 702 A 1 
HETATM 4 O O3G DTP . . . F 3 -32.644 10.206 90.329 1 20.35 ? O3G DTP 702 A 1 
HETATM 5 P PB DTP . . . F 3 -31.687 7.299 90.599 1 19.55 ? PB DTP 702 A 1 
HETATM 6 O O1B DTP . . . F 3 -30.825 8.348 90 1 19.06 ? O1B DTP 702 A 1 
HETATM 7 O O2B DTP . . . F 3 -32.012 6.161 89.642 1 20.7 ? O2B DTP 702 A 1 
HETATM 8 O O3B DTP . . . F 3 -32.989 7.892 91.263 1 21.11 ? O3B DTP 702 A 1 
HETATM 9 P PA DTP . . . F 3 -31.113 5.428 92.673 1 18.25 ? PA DTP 702 A 1 
HETATM 10 O O1A DTP . . . F 3 -31.386 5.595 94.153 1 15.98 ? O1A DTP 702 A 1 
HETATM 11 O O2A DTP . . . F 3 -32.012 4.491 91.921 1 20.15 ? O2A DTP 702 A 1 
HETATM 12 O O3A DTP . . . F 3 -30.938 6.804 91.914 1 18.7 ? O3A DTP 702 A 1 
HETATM 13 O O5' DTP . . . F 3 -29.671 4.82 92.435 1 20.47 ? O5' DTP 702 A 1 
HETATM 14 C C5' DTP . . . F 3 -28.509 5.299 93.11 1 19.47 ? C5' DTP 702 A 1 
HETATM 15 C C4' DTP . . . F 3 -27.525 4.165 93.378 1 19.43 ? C4' DTP 702 A 1 
HETATM 16 O O4' DTP . . . F 3 -28.128 3.203 94.198 1 19.46 ? O4' DTP 702 A 1 
HETATM 17 C C3' DTP . . . F 3 -27.069 3.396 92.161 1 20.31 ? C3' DTP 702 A 1 
HETATM 18 O O3' DTP . . . F 3 -25.674 2.987 92.312 1 20.26 ? O3' DTP 702 A 1 
HETATM 19 C C2' DTP . . . F 3 -28.023 2.206 92.059 1 21.15 ? C2' DTP 702 A 1 
HETATM 20 C C1' DTP . . . F 3 -28.239 1.939 93.523 1 22.49 ? C1' DTP 702 A 1 
HETATM 21 N N9 DTP . . . F 3 -29.544 1.467 93.954 1 26.03 ? N9 DTP 702 A 1 
HETATM 22 C C8 DTP . . . F 3 -30.751 1.796 93.44 1 28.01 ? C8 DTP 702 A 1 
HETATM 23 N N7 DTP . . . F 3 -31.785 1.219 94.146 1 28.05 ? N7 DTP 702 A 1 
HETATM 24 C C5 DTP . . . F 3 -31.211 0.545 95.12 1 28.4 ? C5 DTP 702 A 1 
HETATM 25 C C6 DTP . . . F 3 -31.75 -0.239 96.186 1 36.96 ? C6 DTP 702 A 1 
HETATM 26 N N6 DTP . . . F 3 -33.119 -0.329 96.203 1 37.76 ? N6 DTP 702 A 1 
HETATM 27 N N1 DTP . . . F 3 -30.831 -0.842 97.047 1 42.9 ? N1 DTP 702 A 1 
HETATM 28 C C2 DTP . . . F 3 -29.477 -0.639 96.858 1 39.71 ? C2 DTP 702 A 1 
HETATM 29 N N3 DTP . . . F 3 -28.916 0.111 95.86 1 28.34 ? N3 DTP 702 A 1 
HETATM 30 C C4 DTP . . . F 3 -29.739 0.695 95.007 1 26.98 ? C4 DTP 702 A 1 
#
_model_server_stats.io_time_ms              64 
_model_server_stats.parse_time_ms           52 
_model_server_stats.create_model_time_ms    178 
_model_server_stats.query_time_ms           469 
_model_server_stats.encode_time_ms          51 
_model_server_stats.element_count           30 
#