data_3AGO
#
_model_server_result.job_id            vVpPlJYhK6EqAb48EI70iA 
_model_server_result.datetime_utc      '2024-10-14 18:30:54' 
_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          3ago 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":115}' 
#
_entry.id    3AGO 
#
_exptl.entry_id    3AGO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          108.98 
_cell.angle_gamma         90 
_cell.entry_id            3AGO 
_cell.length_a            34.586 
_cell.length_b            39.425 
_cell.length_c            31.646 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3AGO 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 A SG CYS 1 A CYS 1 1_555 A SG CYS 54 A CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
disulf ? disulf2 A SG CYS 9 A CYS 9 1_555 A SG CYS 113 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf3 A SG CYS 55 A CYS 55 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc1 A OD1 ASP 29 A ASP 29 1_555 C CA CA . A CA 116 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc2 A OD1 ASP 29 A ASP 29 1_555 C CA CA . A CA 116 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.578 ? 
metalc ? metalc3 A O ALA 31 A ALA 31 1_555 C CA CA . A CA 116 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc4 A O ALA 31 A ALA 31 1_555 C CA CA . A CA 116 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.534 ? 
metalc ? metalc5 A OD1 ASN 32 A ASN 32 1_555 C CA CA . A CA 116 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.67 ? 
metalc ? metalc6 A O TYR 39 A TYR 39 1_555 C CA CA . A CA 116 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.854 ? 
metalc ? metalc7 A OD1 ASP 45 A ASP 45 1_555 D CA CA . A CA 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc8 A O ILE 51 A ILE 51 1_555 D CA CA . A CA 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc9 C CA CA . A CA 116 1_555 F O HOH . A HOH 198 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.182 ? 
metalc ? metalc10 D CA CA . A CA 117 1_555 F O HOH . A HOH 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc11 D CA CA . A CA 117 1_555 F O HOH . A HOH 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc12 D CA CA . A CA 117 1_555 F O HOH . A HOH 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? 
metalc ? metalc13 D CA CA . A CA 117 1_555 F O HOH . A HOH 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
#
_chem_comp.formula           'C10 H14 N5 O7 P' 
_chem_comp.formula_weight    347.221 
_chem_comp.id                3AM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "3'-AMP" 
#
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
O1P P 3AM doub 1 n n 
P O2P 3AM sing 2 n n 
P O3P 3AM sing 3 n n 
P O3' 3AM sing 4 n n 
O2' C2' 3AM sing 5 n n 
C2' C3' 3AM sing 6 n n 
C2' C1' 3AM sing 7 n n 
C3' O3' 3AM sing 8 n n 
C3' C4' 3AM sing 9 n n 
C1' O4' 3AM sing 10 n n 
C1' N9 3AM sing 11 n n 
O4' C4' 3AM sing 12 n n 
C4' C5' 3AM sing 13 n n 
C5' O5' 3AM sing 14 n n 
N9 C8 3AM sing 15 n y 
N9 C4 3AM sing 16 n y 
C8 N7 3AM doub 17 n y 
N7 C5 3AM sing 18 n y 
C5 C6 3AM doub 19 n y 
C5 C4 3AM sing 20 n y 
C6 N6 3AM sing 21 n n 
C6 N1 3AM sing 22 n y 
C4 N3 3AM doub 23 n y 
N3 C2 3AM sing 24 n y 
C2 N1 3AM doub 25 n y 
O2P HO2P 3AM sing 26 n n 
O3P HO3P 3AM sing 27 n n 
O2' HO2' 3AM sing 28 n n 
C2' H2' 3AM sing 29 n n 
C3' H3' 3AM sing 30 n n 
C1' H1' 3AM sing 31 n n 
C4' H4' 3AM sing 32 n n 
C5' H5' 3AM sing 33 n n 
C5' "H5'A" 3AM sing 34 n n 
O5' HO5' 3AM sing 35 n n 
C8 H8 3AM sing 36 n n 
N6 HN6 3AM sing 37 n n 
N6 HN6A 3AM sing 38 n n 
C2 H2 3AM sing 39 n n 
#
_atom_sites.entry_id                     3AGO 
_atom_sites.fract_transf_matrix[1][1]    0.028913 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.009944 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.025365 
_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]    0.033416 
_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
B 2 3AM A 1 115 115 3AM 3AM . 
C 3 CA A 1 116 116 CA CA . 
D 3 CA A 1 117 117 CA CA . 
E 4 CL A 1 118 118 CL CL . 
F 5 HOH A 1 119 119 HOH HOH . 
F 5 HOH A 2 120 120 HOH HOH . 
F 5 HOH A 3 121 121 HOH HOH . 
F 5 HOH A 4 122 122 HOH HOH . 
F 5 HOH A 5 123 123 HOH HOH . 
F 5 HOH A 6 124 124 HOH HOH . 
F 5 HOH A 7 125 125 HOH HOH . 
F 5 HOH A 8 126 126 HOH HOH . 
F 5 HOH A 9 127 127 HOH HOH . 
F 5 HOH A 10 128 128 HOH HOH . 
F 5 HOH A 11 129 129 HOH HOH . 
F 5 HOH A 12 130 130 HOH HOH . 
F 5 HOH A 13 131 131 HOH HOH . 
F 5 HOH A 14 132 132 HOH HOH . 
F 5 HOH A 15 133 133 HOH HOH . 
F 5 HOH A 16 134 134 HOH HOH . 
F 5 HOH A 17 135 135 HOH HOH . 
F 5 HOH A 18 138 138 HOH HOH . 
F 5 HOH A 19 139 139 HOH HOH . 
F 5 HOH A 20 140 140 HOH HOH . 
F 5 HOH A 21 141 141 HOH HOH . 
F 5 HOH A 22 142 142 HOH HOH . 
F 5 HOH A 23 143 143 HOH HOH . 
F 5 HOH A 24 144 144 HOH HOH . 
F 5 HOH A 25 145 145 HOH HOH . 
F 5 HOH A 26 146 146 HOH HOH . 
F 5 HOH A 27 147 147 HOH HOH . 
F 5 HOH A 28 148 148 HOH HOH . 
F 5 HOH A 29 149 149 HOH HOH . 
F 5 HOH A 30 150 150 HOH HOH . 
F 5 HOH A 31 151 151 HOH HOH . 
F 5 HOH A 32 152 152 HOH HOH . 
F 5 HOH A 33 153 153 HOH HOH . 
F 5 HOH A 34 154 154 HOH HOH . 
F 5 HOH A 35 155 155 HOH HOH . 
F 5 HOH A 36 156 156 HOH HOH . 
F 5 HOH A 37 157 157 HOH HOH . 
F 5 HOH A 38 158 158 HOH HOH . 
F 5 HOH A 39 159 159 HOH HOH . 
F 5 HOH A 40 160 160 HOH HOH . 
F 5 HOH A 41 161 161 HOH HOH . 
F 5 HOH A 42 162 162 HOH HOH . 
F 5 HOH A 43 163 163 HOH HOH . 
F 5 HOH A 44 164 164 HOH HOH . 
F 5 HOH A 45 165 165 HOH HOH . 
F 5 HOH A 46 166 166 HOH HOH . 
F 5 HOH A 47 167 167 HOH HOH . 
F 5 HOH A 48 168 168 HOH HOH . 
F 5 HOH A 49 169 169 HOH HOH . 
F 5 HOH A 50 170 170 HOH HOH . 
F 5 HOH A 51 171 171 HOH HOH . 
F 5 HOH A 52 172 172 HOH HOH . 
F 5 HOH A 53 173 173 HOH HOH . 
F 5 HOH A 54 174 174 HOH HOH . 
F 5 HOH A 55 175 175 HOH HOH . 
F 5 HOH A 56 176 176 HOH HOH . 
F 5 HOH A 57 177 177 HOH HOH . 
F 5 HOH A 58 178 178 HOH HOH . 
F 5 HOH A 59 179 179 HOH HOH . 
F 5 HOH A 60 180 180 HOH HOH . 
F 5 HOH A 61 181 181 HOH HOH . 
F 5 HOH A 62 182 182 HOH HOH . 
F 5 HOH A 63 183 183 HOH HOH . 
F 5 HOH A 64 184 184 HOH HOH . 
F 5 HOH A 65 185 185 HOH HOH . 
F 5 HOH A 66 186 186 HOH HOH . 
F 5 HOH A 67 187 187 HOH HOH . 
F 5 HOH A 68 188 188 HOH HOH . 
F 5 HOH A 69 189 189 HOH HOH . 
F 5 HOH A 70 190 190 HOH HOH . 
F 5 HOH A 71 191 191 HOH HOH . 
F 5 HOH A 72 192 192 HOH HOH . 
F 5 HOH A 73 193 193 HOH HOH . 
F 5 HOH A 74 194 194 HOH HOH . 
F 5 HOH A 75 195 195 HOH HOH . 
F 5 HOH A 76 196 196 HOH HOH . 
F 5 HOH A 77 197 197 HOH HOH . 
F 5 HOH A 78 198 198 HOH HOH . 
F 5 HOH A 79 199 199 HOH HOH . 
F 5 HOH A 80 200 200 HOH HOH . 
F 5 HOH A 81 201 201 HOH HOH . 
F 5 HOH A 82 202 202 HOH HOH . 
F 5 HOH A 83 203 203 HOH HOH . 
F 5 HOH A 84 204 204 HOH HOH . 
F 5 HOH A 85 205 205 HOH HOH . 
F 5 HOH A 86 206 206 HOH HOH . 
F 5 HOH A 87 207 207 HOH HOH . 
F 5 HOH A 88 208 208 HOH HOH . 
F 5 HOH A 89 209 209 HOH HOH . 
F 5 HOH A 90 210 210 HOH HOH . 
F 5 HOH A 91 211 211 HOH HOH . 
F 5 HOH A 92 212 212 HOH HOH . 
F 5 HOH A 93 213 213 HOH HOH . 
F 5 HOH A 94 214 214 HOH HOH . 
F 5 HOH A 95 215 215 HOH HOH . 
F 5 HOH A 96 216 216 HOH HOH . 
F 5 HOH A 97 217 217 HOH HOH . 
F 5 HOH A 98 219 219 HOH HOH . 
F 5 HOH A 99 220 220 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 O O1P 3AM . . . B 2 6.444 8.894 2.184 1 10.06 ? O1P 3AM 115 A 1 
HETATM 2 P P 3AM . . . B 2 7.301 8.246 0.973 1 8.99 ? P 3AM 115 A 1 
HETATM 3 O O2P 3AM . . . B 2 6.435 8.375 -0.231 1 8.47 ? O2P 3AM 115 A 1 
HETATM 4 O O3P 3AM . . . B 2 7.669 6.951 1.449 1 13.82 ? O3P 3AM 115 A 1 
HETATM 5 O O2' 3AM . . . B 2 10.778 9.995 0.214 1 7.05 ? O2' 3AM 115 A 1 
HETATM 6 C C2' 3AM . . . B 2 10.628 9.57 1.573 1 6.24 ? C2' 3AM 115 A 1 
HETATM 7 C C3' 3AM . . . B 2 9.184 9.75 1.997 1 5.96 ? C3' 3AM 115 A 1 
HETATM 8 O O3' 3AM . . . B 2 8.321 9.417 0.925 1 8.38 ? O3' 3AM 115 A 1 
HETATM 9 C C1' 3AM . . . B 2 11.311 10.568 2.461 1 5.4 ? C1' 3AM 115 A 1 
HETATM 10 O O4' 3AM . . . B 2 10.368 11.568 2.866 1 5.39 ? O4' 3AM 115 A 1 
HETATM 11 C C4' 3AM . . . B 2 9.091 11.241 2.323 1 5.36 ? C4' 3AM 115 A 1 
HETATM 12 C C5' 3AM . . . B 2 8.065 11.607 3.349 1 6.1 ? C5' 3AM 115 A 1 
HETATM 13 O O5' 3AM . A . B 2 7.82 12.986 3.5 0.5 8.52 ? O5' 3AM 115 A 1 
HETATM 14 O O5' 3AM . B . B 2 6.809 11.588 2.765 0.5 6.71 ? O5' 3AM 115 A 1 
HETATM 15 N N9 3AM . . . B 2 11.935 9.988 3.685 1 5.19 ? N9 3AM 115 A 1 
HETATM 16 C C8 3AM . . . B 2 13.224 9.54 3.712 1 5.48 ? C8 3AM 115 A 1 
HETATM 17 N N7 3AM . . . B 2 13.603 9.128 4.898 1 5.56 ? N7 3AM 115 A 1 
HETATM 18 C C5 3AM . . . B 2 12.518 9.282 5.676 1 5.43 ? C5 3AM 115 A 1 
HETATM 19 C C6 3AM . . . B 2 12.292 9.083 7.076 1 5.14 ? C6 3AM 115 A 1 
HETATM 20 N N6 3AM . . . B 2 13.167 8.563 7.906 1 5.44 ? N6 3AM 115 A 1 
HETATM 21 C C4 3AM . . . B 2 11.429 9.851 4.912 1 5.37 ? C4 3AM 115 A 1 
HETATM 22 N N3 3AM . . . B 2 10.209 10.143 5.422 1 6.19 ? N3 3AM 115 A 1 
HETATM 23 C C2 3AM . . . B 2 10.087 9.905 6.721 1 6.41 ? C2 3AM 115 A 1 
HETATM 24 N N1 3AM . . . B 2 11.059 9.43 7.513 1 5.44 ? N1 3AM 115 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           401 
_model_server_stats.encode_time_ms          26 
_model_server_stats.element_count           24 
#