data_3KE1
#
_model_server_result.job_id            87kL8ziAxvNxACueyvB28w 
_model_server_result.datetime_utc      '2024-10-19 08:24:22' 
_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          3ke1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":164}' 
#
_entry.id    3KE1 
#
_exptl.entry_id    3KE1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.326 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine" 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          95.42 
_cell.angle_gamma         90 
_cell.entry_id            3KE1 
_cell.length_a            117.083 
_cell.length_b            66.964 
_cell.length_c            59.166 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KE1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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 E N N 
? 3 H 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 A OD2 ASP 31 A ASP 10 1_555 D ZN ZN . A ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.864 ? 
metalc ? metalc2 A NE2 HIS 33 A HIS 12 1_555 D ZN ZN . A ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc3 A ND1 HIS 65 A HIS 44 1_555 D ZN ZN . A ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc4 D ZN ZN . A ZN 163 1_555 E N10 829 . A 829 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc5 F K K . A K 165 1_555 K O HOH . A HOH 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? 
metalc ? metalc6 F K K . A K 165 1_555 L O HOH . B HOH 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? 
metalc ? metalc7 F K K . A K 165 1_555 M O HOH . C HOH 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? 
metalc ? metalc8 B OD2 ASP 31 B ASP 10 1_555 G ZN ZN . B ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc9 B NE2 HIS 33 B HIS 12 1_555 G ZN ZN . B ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc10 B ND1 HIS 65 B HIS 44 1_555 G ZN ZN . B ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc11 G ZN ZN . B ZN 163 1_555 H N10 829 . B 829 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc12 C OD2 ASP 31 C ASP 10 1_555 I ZN ZN . C ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc13 C NE2 HIS 33 C HIS 12 1_555 I ZN ZN . C ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc14 C ND1 HIS 65 C HIS 44 1_555 I ZN ZN . C ZN 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc15 I ZN ZN . C ZN 163 1_555 J N10 829 . C 829 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
#
_chem_comp.formula           'C15 H17 N5 O5' 
_chem_comp.formula_weight    347.326 
_chem_comp.id                829 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine" 
_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
C6 N1 829 sing 1 n n 
N1 C1' 829 sing 2 n n 
N1 C2 829 sing 3 n n 
N3 C2 829 sing 4 n n 
C2 O2 829 doub 5 n n 
C4 N3 829 doub 6 n n 
C5 C4 829 sing 7 n n 
N4 C4 829 sing 8 n n 
N4 HN4 829 sing 9 n n 
N4 HN4A 829 sing 10 n n 
C5 C6 829 doub 11 n n 
C5 H5 829 sing 12 n n 
C6 H6 829 sing 13 n n 
O15 C07 829 doub 14 n n 
C13 C07 829 sing 15 n n 
C07 N5' 829 sing 16 n n 
C09 C08 829 doub 17 n y 
C13 C08 829 sing 18 n y 
C08 H08 829 sing 19 n n 
N10 C09 829 sing 20 n y 
C09 H09 829 sing 21 n n 
C2' C1' 829 sing 22 n n 
C1' O4' 829 sing 23 n n 
C1' H1' 829 sing 24 n n 
C11 N10 829 doub 25 n y 
C11 C12 829 sing 26 n y 
C11 H11 829 sing 27 n n 
C12 C13 829 doub 28 n y 
C12 H12 829 sing 29 n n 
C3' C2' 829 sing 30 n n 
C2' O2' 829 sing 31 n n 
C2' H2' 829 sing 32 n n 
O2' HO2' 829 sing 33 n n 
O3' C3' 829 sing 34 n n 
C3' C4' 829 sing 35 n n 
C3' H3' 829 sing 36 n n 
O3' HO3' 829 sing 37 n n 
C5' C4' 829 sing 38 n n 
C4' O4' 829 sing 39 n n 
C4' H4' 829 sing 40 n n 
N5' C5' 829 sing 41 n n 
C5' H5' 829 sing 42 n n 
C5' "H5'A" 829 sing 43 n n 
N5' HN5' 829 sing 44 n n 
#
_atom_sites.entry_id                     3KE1 
_atom_sites.fract_transf_matrix[1][1]    0.008541 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00081 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014933 
_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]    0.016977 
_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
D 2 ZN A 1 163 163 ZN ZN . 
E 3 829 A 1 164 164 829 829 . 
F 4 K A 1 165 2 K K . 
G 2 ZN B 1 163 163 ZN ZN . 
H 3 829 B 1 164 164 829 829 . 
I 2 ZN C 1 163 163 ZN ZN . 
J 3 829 C 1 164 164 829 829 . 
K 5 HOH A 1 167 1 HOH HOH . 
K 5 HOH A 2 168 3 HOH HOH . 
K 5 HOH A 3 169 4 HOH HOH . 
K 5 HOH A 4 170 6 HOH HOH . 
K 5 HOH A 5 171 7 HOH HOH . 
K 5 HOH A 6 172 8 HOH HOH . 
K 5 HOH A 7 173 9 HOH HOH . 
K 5 HOH A 8 174 10 HOH HOH . 
K 5 HOH A 9 175 11 HOH HOH . 
K 5 HOH A 10 176 12 HOH HOH . 
K 5 HOH A 11 177 13 HOH HOH . 
K 5 HOH A 12 178 15 HOH HOH . 
K 5 HOH A 13 179 16 HOH HOH . 
K 5 HOH A 14 180 19 HOH HOH . 
K 5 HOH A 15 181 21 HOH HOH . 
K 5 HOH A 16 182 25 HOH HOH . 
K 5 HOH A 17 183 27 HOH HOH . 
K 5 HOH A 18 184 28 HOH HOH . 
K 5 HOH A 19 185 29 HOH HOH . 
K 5 HOH A 20 186 33 HOH HOH . 
K 5 HOH A 21 187 35 HOH HOH . 
K 5 HOH A 22 188 37 HOH HOH . 
K 5 HOH A 23 189 38 HOH HOH . 
K 5 HOH A 24 190 40 HOH HOH . 
K 5 HOH A 25 191 43 HOH HOH . 
K 5 HOH A 26 192 44 HOH HOH . 
K 5 HOH A 27 193 45 HOH HOH . 
K 5 HOH A 28 194 48 HOH HOH . 
K 5 HOH A 29 195 49 HOH HOH . 
K 5 HOH A 30 196 50 HOH HOH . 
K 5 HOH A 31 197 51 HOH HOH . 
K 5 HOH A 32 198 52 HOH HOH . 
K 5 HOH A 33 199 53 HOH HOH . 
K 5 HOH A 34 200 54 HOH HOH . 
K 5 HOH A 35 201 55 HOH HOH . 
K 5 HOH A 36 202 56 HOH HOH . 
K 5 HOH A 37 203 57 HOH HOH . 
K 5 HOH A 38 204 58 HOH HOH . 
K 5 HOH A 39 205 60 HOH HOH . 
K 5 HOH A 40 206 64 HOH HOH . 
K 5 HOH A 41 207 94 HOH HOH . 
K 5 HOH A 42 208 96 HOH HOH . 
K 5 HOH A 43 209 99 HOH HOH . 
K 5 HOH A 44 210 100 HOH HOH . 
K 5 HOH A 45 211 106 HOH HOH . 
K 5 HOH A 46 212 108 HOH HOH . 
K 5 HOH A 47 213 109 HOH HOH . 
K 5 HOH A 48 214 112 HOH HOH . 
K 5 HOH A 49 215 114 HOH HOH . 
K 5 HOH A 50 216 119 HOH HOH . 
K 5 HOH A 51 217 123 HOH HOH . 
K 5 HOH A 52 218 124 HOH HOH . 
K 5 HOH A 53 219 127 HOH HOH . 
K 5 HOH A 54 220 129 HOH HOH . 
K 5 HOH A 55 221 130 HOH HOH . 
K 5 HOH A 56 222 131 HOH HOH . 
K 5 HOH A 57 223 133 HOH HOH . 
L 5 HOH B 1 165 17 HOH HOH . 
L 5 HOH B 2 166 18 HOH HOH . 
L 5 HOH B 3 167 20 HOH HOH . 
L 5 HOH B 4 168 22 HOH HOH . 
L 5 HOH B 5 169 23 HOH HOH . 
L 5 HOH B 6 170 30 HOH HOH . 
L 5 HOH B 7 171 41 HOH HOH . 
L 5 HOH B 8 172 46 HOH HOH . 
L 5 HOH B 9 173 61 HOH HOH . 
L 5 HOH B 10 174 62 HOH HOH . 
L 5 HOH B 11 175 66 HOH HOH . 
L 5 HOH B 12 176 68 HOH HOH . 
L 5 HOH B 13 177 69 HOH HOH . 
L 5 HOH B 14 178 71 HOH HOH . 
L 5 HOH B 15 179 72 HOH HOH . 
L 5 HOH B 16 180 74 HOH HOH . 
L 5 HOH B 17 181 75 HOH HOH . 
L 5 HOH B 18 182 76 HOH HOH . 
L 5 HOH B 19 183 77 HOH HOH . 
L 5 HOH B 20 184 78 HOH HOH . 
L 5 HOH B 21 185 79 HOH HOH . 
L 5 HOH B 22 186 80 HOH HOH . 
L 5 HOH B 23 187 82 HOH HOH . 
L 5 HOH B 24 188 86 HOH HOH . 
L 5 HOH B 25 189 105 HOH HOH . 
L 5 HOH B 26 190 107 HOH HOH . 
L 5 HOH B 27 191 110 HOH HOH . 
L 5 HOH B 28 192 111 HOH HOH . 
L 5 HOH B 29 193 113 HOH HOH . 
L 5 HOH B 30 194 115 HOH HOH . 
L 5 HOH B 31 195 116 HOH HOH . 
L 5 HOH B 32 196 120 HOH HOH . 
L 5 HOH B 33 197 121 HOH HOH . 
L 5 HOH B 34 198 122 HOH HOH . 
L 5 HOH B 35 199 125 HOH HOH . 
L 5 HOH B 36 200 126 HOH HOH . 
L 5 HOH B 37 201 132 HOH HOH . 
L 5 HOH B 38 202 134 HOH HOH . 
L 5 HOH B 39 203 2 HOH HOH . 
M 5 HOH C 1 165 5 HOH HOH . 
M 5 HOH C 2 166 14 HOH HOH . 
M 5 HOH C 3 167 24 HOH HOH . 
M 5 HOH C 4 168 26 HOH HOH . 
M 5 HOH C 5 169 31 HOH HOH . 
M 5 HOH C 6 170 32 HOH HOH . 
M 5 HOH C 7 171 34 HOH HOH . 
M 5 HOH C 8 172 36 HOH HOH . 
M 5 HOH C 9 173 39 HOH HOH . 
M 5 HOH C 10 174 42 HOH HOH . 
M 5 HOH C 11 175 47 HOH HOH . 
M 5 HOH C 12 176 59 HOH HOH . 
M 5 HOH C 13 177 63 HOH HOH . 
M 5 HOH C 14 178 65 HOH HOH . 
M 5 HOH C 15 179 67 HOH HOH . 
M 5 HOH C 16 180 70 HOH HOH . 
M 5 HOH C 17 181 73 HOH HOH . 
M 5 HOH C 18 182 81 HOH HOH . 
M 5 HOH C 19 183 83 HOH HOH . 
M 5 HOH C 20 184 84 HOH HOH . 
M 5 HOH C 21 185 85 HOH HOH . 
M 5 HOH C 22 186 87 HOH HOH . 
M 5 HOH C 23 187 88 HOH HOH . 
M 5 HOH C 24 188 89 HOH HOH . 
M 5 HOH C 25 189 90 HOH HOH . 
M 5 HOH C 26 190 91 HOH HOH . 
M 5 HOH C 27 191 92 HOH HOH . 
M 5 HOH C 28 192 93 HOH HOH . 
M 5 HOH C 29 193 95 HOH HOH . 
M 5 HOH C 30 194 97 HOH HOH . 
M 5 HOH C 31 195 98 HOH HOH . 
M 5 HOH C 32 196 101 HOH HOH . 
M 5 HOH C 33 197 102 HOH HOH . 
M 5 HOH C 34 198 103 HOH HOH . 
M 5 HOH C 35 199 104 HOH HOH . 
M 5 HOH C 36 200 117 HOH HOH . 
M 5 HOH C 37 201 118 HOH HOH . 
M 5 HOH C 38 202 128 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 829 . . . H 3 38.07 -38.136 -21.641 1 31.96 ? N1 829 164 B 1 
HETATM 2 C C2 829 . . . H 3 39.138 -38.363 -20.816 1 31.55 ? C2 829 164 B 1 
HETATM 3 O O2 829 . . . H 3 39.983 -39.245 -21.058 1 31.29 ? O2 829 164 B 1 
HETATM 4 N N3 829 . . . H 3 39.335 -37.638 -19.67 1 30.52 ? N3 829 164 B 1 
HETATM 5 C C4 829 . . . H 3 38.476 -36.655 -19.297 1 28.73 ? C4 829 164 B 1 
HETATM 6 N N4 829 . . . H 3 38.677 -35.949 -18.159 1 25.26 ? N4 829 164 B 1 
HETATM 7 C C5 829 . . . H 3 37.385 -36.392 -20.115 1 28.16 ? C5 829 164 B 1 
HETATM 8 C C6 829 . . . H 3 37.224 -37.14 -21.284 1 30.72 ? C6 829 164 B 1 
HETATM 9 C C07 829 . . . H 3 34.427 -35.469 -24.528 1 47.32 ? C07 829 164 B 1 
HETATM 10 C C08 829 . . . H 3 32.758 -35.751 -26.427 1 50.89 ? C08 829 164 B 1 
HETATM 11 C C09 829 . . . H 3 31.66 -35.272 -27.16 1 51.86 ? C09 829 164 B 1 
HETATM 12 C C1' 829 . . . H 3 37.851 -38.878 -22.929 1 33.87 ? C1' 829 164 B 1 
HETATM 13 N N10 829 . . . H 3 31.093 -34.087 -26.85 1 51.61 ? N10 829 164 B 1 
HETATM 14 C C11 829 . . . H 3 31.551 -33.329 -25.829 1 50.98 ? C11 829 164 B 1 
HETATM 15 C C12 829 . . . H 3 32.639 -33.764 -25.064 1 50.64 ? C12 829 164 B 1 
HETATM 16 C C13 829 . . . H 3 33.263 -34.987 -25.367 1 49.66 ? C13 829 164 B 1 
HETATM 17 O O15 829 . . . H 3 34.272 -35.494 -23.318 1 45.78 ? O15 829 164 B 1 
HETATM 18 C C2' 829 . . . H 3 36.586 -39.76 -23.039 1 34.91 ? C2' 829 164 B 1 
HETATM 19 O O2' 829 . . . H 3 36.837 -40.936 -23.851 1 30.41 ? O2' 829 164 B 1 
HETATM 20 C C3' 829 . . . H 3 35.604 -38.86 -23.792 1 37.07 ? C3' 829 164 B 1 
HETATM 21 O O3' 829 . . . H 3 34.513 -39.545 -24.436 1 38.03 ? O3' 829 164 B 1 
HETATM 22 C C4' 829 . . . H 3 36.541 -38.228 -24.803 1 38.86 ? C4' 829 164 B 1 
HETATM 23 O O4' 829 . . . H 3 37.728 -37.923 -24.02 1 36.32 ? O4' 829 164 B 1 
HETATM 24 C C5' 829 . . . H 3 35.867 -37.139 -25.673 1 42.64 ? C5' 829 164 B 1 
HETATM 25 N N5' 829 . . . H 3 35.596 -35.839 -25.067 1 46.41 ? N5' 829 164 B 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#