data_4TO1
#
_model_server_result.job_id            '_o3563KJNIAwdnunVeIGKA' 
_model_server_result.datetime_utc      '2024-11-07 01:36:58' 
_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":"S","auth_seq_id":703}' 
#
_entry.id    4TO1 
#
_exptl.entry_id    4TO1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.157 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_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
? 2 E N N 
? 2 I N N 
? 2 K N N 
? 2 O N N 
? 2 R N N 
? 2 S 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           'C9 H16 N3 O13 P3' 
_chem_comp.formula_weight    467.157 
_chem_comp.id                DCP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYCYTIDINE-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
N1 C2 DCP sing 83 n n 
N1 C6 DCP sing 84 n n 
N1 C1' DCP sing 85 n n 
C2 N3 DCP sing 86 n n 
C2 O2 DCP doub 87 n n 
N3 C4 DCP doub 88 n n 
C4 C5 DCP sing 89 n n 
C4 N4 DCP sing 90 n n 
C5 C6 DCP doub 91 n n 
C5 H5 DCP sing 92 n n 
C6 H6 DCP sing 93 n n 
N4 HN41 DCP sing 94 n n 
N4 HN42 DCP sing 95 n n 
C1' C2' DCP sing 96 n n 
C1' O4' DCP sing 97 n n 
C1' H1' DCP sing 98 n n 
C2' C3' DCP sing 99 n n 
C2' "H2'1" DCP sing 100 n n 
C2' "H2'2" DCP sing 101 n n 
C3' C4' DCP sing 102 n n 
C3' O3' DCP sing 103 n n 
C3' H3' DCP sing 104 n n 
C4' O4' DCP sing 105 n n 
C4' C5' DCP sing 106 n n 
C4' H4' DCP sing 107 n n 
O3' HO3' DCP sing 108 n n 
C5' O5' DCP sing 109 n n 
C5' "H5'1" DCP sing 110 n n 
C5' "H5'2" DCP sing 111 n n 
O5' PA DCP sing 112 n n 
PA O1A DCP doub 113 n n 
PA O2A DCP sing 114 n n 
PA O3A DCP sing 115 n n 
O2A HOA2 DCP sing 116 n n 
O3A PB DCP sing 117 n n 
PB O1B DCP doub 118 n n 
PB O2B DCP sing 119 n n 
PB O3B DCP sing 120 n n 
O2B HOB2 DCP sing 121 n n 
O3B PG DCP sing 122 n n 
PG O1G DCP doub 123 n n 
PG O2G DCP sing 124 n n 
PG O3G DCP sing 125 n n 
O2G HOG2 DCP sing 126 n n 
O3G HOG3 DCP sing 127 n n 
#
_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 N N1 DCP . . . S 2 -5.381 -16.155 123.171 1 37.23 ? N1 DCP 703 D 1 
HETATM 2 C C2 DCP . . . S 2 -5.658 -15.057 123.992 1 39.04 ? C2 DCP 703 D 1 
HETATM 3 N N3 DCP . . . S 2 -4.648 -14.466 124.701 1 38.64 ? N3 DCP 703 D 1 
HETATM 4 C C4 DCP . . . S 2 -3.39 -14.949 124.607 1 34.57 ? C4 DCP 703 D 1 
HETATM 5 C C5 DCP . . . S 2 -3.108 -16.012 123.792 1 34.81 ? C5 DCP 703 D 1 
HETATM 6 C C6 DCP . . . S 2 -4.125 -16.612 123.076 1 37.69 ? C6 DCP 703 D 1 
HETATM 7 O O2 DCP . . . S 2 -6.837 -14.656 124.043 1 39.14 ? O2 DCP 703 D 1 
HETATM 8 N N4 DCP . . . S 2 -2.374 -14.393 125.283 1 34.06 ? N4 DCP 703 D 1 
HETATM 9 C C1' DCP . . . S 2 -6.457 -16.798 122.43 1 36.73 ? C1' DCP 703 D 1 
HETATM 10 C C2' DCP . . . S 2 -6.432 -16.338 120.988 1 38.65 ? C2' DCP 703 D 1 
HETATM 11 C C3' DCP . . . S 2 -6.798 -17.573 120.205 1 36.95 ? C3' DCP 703 D 1 
HETATM 12 C C4' DCP . . . S 2 -6.422 -18.733 121.095 1 37.24 ? C4' DCP 703 D 1 
HETATM 13 O O4' DCP . . . S 2 -6.29 -18.214 122.407 1 36.1 ? O4' DCP 703 D 1 
HETATM 14 O O3' DCP . . . S 2 -8.208 -17.587 119.931 1 32.7 ? O3' DCP 703 D 1 
HETATM 15 C C5' DCP . . . S 2 -5.131 -19.404 120.679 1 40.5 ? C5' DCP 703 D 1 
HETATM 16 O O5' DCP . . . S 2 -4.672 -20.228 121.752 1 48.18 ? O5' DCP 703 D 1 
HETATM 17 P PA DCP . . . S 2 -5.219 -21.726 121.955 1 56.07 ? PA DCP 703 D 1 
HETATM 18 O O1A DCP . . . S 2 -5.166 -22.071 123.408 1 54.37 ? O1A DCP 703 D 1 
HETATM 19 O O2A DCP . . . S 2 -6.515 -21.861 121.198 1 58.29 ? O2A DCP 703 D 1 
HETATM 20 O O3A DCP . . . S 2 -4.128 -22.673 121.224 1 57.29 ? O3A DCP 703 D 1 
HETATM 21 P PB DCP . . . S 2 -2.534 -22.432 121.332 1 58.24 ? PB DCP 703 D 1 
HETATM 22 O O1B DCP . . . S 2 -1.811 -23.617 120.697 1 55.26 ? O1B DCP 703 D 1 
HETATM 23 O O2B DCP . . . S 2 -2.244 -22.057 122.766 1 57.55 ? O2B DCP 703 D 1 
HETATM 24 O O3B DCP . . . S 2 -2.292 -21.102 120.439 1 55.15 ? O3B DCP 703 D 1 
HETATM 25 P PG DCP . . . S 2 -1.263 -21.092 119.211 1 50.3 ? PG DCP 703 D 1 
HETATM 26 O O1G DCP . . . S 2 -1.503 -19.818 118.461 1 49.39 ? O1G DCP 703 D 1 
HETATM 27 O O2G DCP . . . S 2 0.089 -21.128 119.891 1 64.63 ? O2G DCP 703 D 1 
HETATM 28 O O3G DCP . . . S 2 -1.576 -22.345 118.462 1 56.48 ? O3G DCP 703 D 1 
#
_model_server_stats.io_time_ms              39 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#