data_6JNL # _model_server_result.job_id jv03GY6XMNbYFRRi1CEQuQ _model_server_result.datetime_utc '2024-11-27 01:05:05' _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 6jnl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":101}' # _entry.id 6JNL # _exptl.entry_id 6JNL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 90 _cell.angle_gamma 90 _cell.entry_id 6JNL _cell.length_a 89.16 _cell.length_b 89.16 _cell.length_c 72.603 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JNL _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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 7 _struct_asym.id I _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 metalc ? metalc1 A SG CYS 9 A CYS 1268 1_555 D ZN ZN . A ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc2 A SG CYS 14 A CYS 1273 1_555 D ZN ZN . A ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc3 A NE2 HIS 27 A HIS 1286 1_555 D ZN ZN . A ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc4 A NE2 HIS 31 A HIS 1290 1_555 D ZN ZN . A ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc5 A SG CYS 39 A CYS 1298 1_555 F ZN ZN . A ZN 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc6 A O CYS 39 A CYS 1298 1_555 G MG MG . A MG 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc7 A O TRP 41 A TRP 1300 1_555 G MG MG . A MG 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc8 A SG CYS 44 A CYS 1303 1_555 F ZN ZN . A ZN 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc9 A O CYS 44 A CYS 1303 1_555 G MG MG . A MG 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc10 A NE2 HIS 57 A HIS 1316 1_555 F ZN ZN . A ZN 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc11 A NE2 HIS 61 A HIS 1320 1_555 F ZN ZN . A ZN 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc12 A SG CYS 69 A CYS 1328 1_555 E ZN ZN . A ZN 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc13 A SG CYS 74 A CYS 1333 1_555 E ZN ZN . A ZN 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc14 A NE2 HIS 87 A HIS 1346 1_555 E ZN ZN . A ZN 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc15 A ND1 HIS 93 A HIS 1352 1_555 E ZN ZN . A ZN 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? hydrog WATSON-CRICK hydrog1 B N3 DT 2 D DT 2 1_555 C N1 DA 11 C DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 DT 2 D DT 2 1_555 C N6 DA 11 C DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DC 3 D DC 3 1_555 C N1 DG 10 C DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N4 DC 3 D DC 3 1_555 C O6 DG 10 C DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O2 DC 3 D DC 3 1_555 C N2 DG 10 C DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 4 D DT 4 1_555 C N1 DA 9 C DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 4 D DT 4 1_555 C N6 DA 9 C DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 5 D DC 5 1_555 C N1 DG 8 C DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 5 D DC 5 1_555 C O6 DG 8 C DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 5 D DC 5 1_555 C N2 DG 8 C DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DT 6 D DT 6 1_555 C N1 DA 7 C DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O4 DT 6 D DT 6 1_555 C N6 DA 7 C DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 7 D DG 7 1_555 C N3 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 7 D DG 7 1_555 C O2 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 7 D DG 7 1_555 C N4 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DT 8 D DT 8 1_555 C N1 DA 5 C DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O4 DT 8 D DT 8 1_555 C N6 DA 5 C DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DT 9 D DT 9 1_555 C N1 DA 4 C DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O4 DT 9 D DT 9 1_555 C N6 DA 4 C DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N3 DT 10 D DT 10 1_555 C N1 DA 3 C DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O4 DT 10 D DT 10 1_555 C N6 DA 3 C DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DT 11 D DT 11 1_555 C N1 DA 2 C DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O4 DT 11 D DT 11 1_555 C N6 DA 2 C DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N1 DG 12 D DG 12 1_555 C N3 DC 1 C DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N2 DG 12 D DG 12 1_555 C O2 DC 1 C DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O6 DG 12 D DG 12 1_555 C N4 DC 1 C DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H14 N5 O6 P' _chem_comp.formula_weight 331.222 _chem_comp.id D5M _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 O5' C5' D5M sing 83 n n O5' P D5M sing 84 n n C5' C4' D5M sing 85 n n C5' "H5'1" D5M sing 86 n n C5' "H5'2" D5M sing 87 n n C4' O4' D5M sing 88 n n C4' C3' D5M sing 89 n n C4' H4' D5M sing 90 n n O4' C1' D5M sing 91 n n C3' O3' D5M sing 92 n n C3' C2' D5M sing 93 n n C3' H1 D5M sing 94 n n O3' H3' D5M sing 95 n n C2' C1' D5M sing 96 n n C2' "H2'1" D5M sing 97 n n C2' "H2'2" D5M sing 98 n n C1' N9 D5M sing 99 n n C1' H1' D5M sing 100 n n N9 C8 D5M sing 101 n y N9 C4 D5M sing 102 n y C8 N7 D5M doub 103 n y C8 H8 D5M sing 104 n n N7 C5 D5M sing 105 n y C5 C6 D5M sing 106 n y C5 C4 D5M doub 107 n y C6 N6 D5M sing 108 n n C6 N1 D5M doub 109 n y N6 HN61 D5M sing 110 n n N6 HN62 D5M sing 111 n n N1 C2 D5M sing 112 n y C2 N3 D5M doub 113 n y C2 H2 D5M sing 114 n n N3 C4 D5M sing 115 n y P O1P D5M doub 116 n n P O3P D5M sing 117 n n P O2P D5M sing 118 n n O3P H3P D5M sing 119 n n O2P H2P D5M sing 120 n n # _atom_sites.entry_id 6JNL _atom_sites.fract_transf_matrix[1][1] 0.011216 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011216 _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] 0.013774 _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 4 ZN A 1 1401 1 ZN ZN . E 4 ZN A 1 1402 2 ZN ZN . F 4 ZN A 1 1403 3 ZN ZN . G 5 MG A 1 1404 1 MG MG . H 6 GOL D 1 101 1 GOL GOL . I 7 D5M C 1 101 12 D5M DA . J 8 HOH A 1 1501 29 HOH HOH . J 8 HOH A 2 1502 33 HOH HOH . J 8 HOH A 3 1503 8 HOH HOH . J 8 HOH A 4 1504 1 HOH HOH . J 8 HOH A 5 1505 3 HOH HOH . J 8 HOH A 6 1506 30 HOH HOH . J 8 HOH A 7 1507 21 HOH HOH . J 8 HOH A 8 1508 14 HOH HOH . J 8 HOH A 9 1509 32 HOH HOH . K 8 HOH D 1 201 38 HOH HOH . K 8 HOH D 2 202 7 HOH HOH . K 8 HOH D 3 203 6 HOH HOH . K 8 HOH D 4 204 12 HOH HOH . K 8 HOH D 5 205 5 HOH HOH . K 8 HOH D 6 206 4 HOH HOH . K 8 HOH D 7 207 9 HOH HOH . K 8 HOH D 8 208 39 HOH HOH . L 8 HOH C 1 201 28 HOH HOH . L 8 HOH C 2 202 11 HOH HOH . L 8 HOH C 3 203 16 HOH HOH . L 8 HOH C 4 204 34 HOH HOH . L 8 HOH C 5 205 13 HOH HOH . L 8 HOH C 6 206 26 HOH HOH . L 8 HOH C 7 207 18 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 O5' D5M . . . I 7 32.889 -11.381 -16.365 1 67.94 ? O5' D5M 101 C 1 HETATM 2 C C5' D5M . . . I 7 33.02 -10.352 -15.36 1 62.37 ? C5' D5M 101 C 1 HETATM 3 C C4' D5M . . . I 7 34.426 -9.81 -15.405 1 62.24 ? C4' D5M 101 C 1 HETATM 4 O O4' D5M . . . I 7 35.308 -10.798 -14.841 1 56.98 ? O4' D5M 101 C 1 HETATM 5 C C3' D5M . . . I 7 34.95 -9.594 -16.824 1 59.88 ? C3' D5M 101 C 1 HETATM 6 O O3' D5M . . . I 7 34.887 -8.221 -17.15 1 64.54 ? O3' D5M 101 C 1 HETATM 7 C C2' D5M . . . I 7 36.406 -10.018 -16.762 1 57.18 ? C2' D5M 101 C 1 HETATM 8 C C1' D5M . . . I 7 36.59 -10.502 -15.342 1 62.2 ? C1' D5M 101 C 1 HETATM 9 N N9 D5M . . . I 7 37.397 -11.704 -15.242 1 58.74 ? N9 D5M 101 C 1 HETATM 10 C C8 D5M . . . I 7 37.36 -12.852 -15.989 1 52.74 ? C8 D5M 101 C 1 HETATM 11 N N7 D5M . . . I 7 38.244 -13.747 -15.623 1 61.9 ? N7 D5M 101 C 1 HETATM 12 C C5 D5M . . . I 7 38.93 -13.131 -14.585 1 51.85 ? C5 D5M 101 C 1 HETATM 13 C C6 D5M . . . I 7 40.01 -13.538 -13.797 1 53.24 ? C6 D5M 101 C 1 HETATM 14 N N6 D5M . . . I 7 40.62 -14.71 -13.937 1 54.12 ? N6 D5M 101 C 1 HETATM 15 N N1 D5M . . . I 7 40.459 -12.684 -12.848 1 62.53 ? N1 D5M 101 C 1 HETATM 16 C C2 D5M . . . I 7 39.877 -11.484 -12.742 1 54.68 ? C2 D5M 101 C 1 HETATM 17 N N3 D5M . . . I 7 38.83 -10.998 -13.409 1 58.54 ? N3 D5M 101 C 1 HETATM 18 C C4 D5M . . . I 7 38.415 -11.875 -14.339 1 51.78 ? C4 D5M 101 C 1 HETATM 19 P P D5M . . . I 7 31.606 -12.324 -16.422 1 70.39 ? P D5M 101 C 1 HETATM 20 O O1P D5M . . . I 7 30.475 -11.363 -16.321 1 86.56 ? O1P D5M 101 C 1 HETATM 21 O O2P D5M . . . I 7 31.645 -13.315 -17.545 1 67.36 ? O2P D5M 101 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 566 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #