data_2Z3M # _model_server_result.job_id KNrTtctbj6DDv2TB9VDFCQ _model_server_result.datetime_utc '2024-11-07 19:08:16' _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 2z3m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 2Z3M # _exptl.entry_id 2Z3M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _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 90 _cell.angle_gamma 90 _cell.entry_id 2Z3M _cell.length_a 116.681 _cell.length_b 127.682 _cell.length_c 38.354 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Z3M _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 C N N ? 2 F 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 covale ? covale1 C O3' 3D1 . A 3D1 301 1_555 D C PHE . A PHE 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? covale ? covale2 F O3' 3D1 . B 3D1 401 1_555 G C PHE . B PHE 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? # _chem_comp.formula 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 3D1 _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-DEOXYADENOSINE" # 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' 3D1 sing 1 n n O5' H5' 3D1 sing 2 n n C5' C4' 3D1 sing 3 n n C5' "H5'1" 3D1 sing 4 n n C5' "H5'2" 3D1 sing 5 n n C4' O4' 3D1 sing 6 n n C4' C3' 3D1 sing 7 n n C4' H4' 3D1 sing 8 n n O4' C1' 3D1 sing 9 n n C1' N9 3D1 sing 10 n n C1' C2' 3D1 sing 11 n n C1' H1' 3D1 sing 12 n n N9 C4 3D1 sing 13 n y N9 C8 3D1 sing 14 n y C4 N3 3D1 doub 15 n y C4 C5 3D1 sing 16 n y N3 C2 3D1 sing 17 n y C2 N1 3D1 doub 18 n y C2 H2 3D1 sing 19 n n N1 C6 3D1 sing 20 n y C6 N6 3D1 sing 21 n n C6 C5 3D1 doub 22 n y N6 HN61 3D1 sing 23 n n N6 HN62 3D1 sing 24 n n C5 N7 3D1 sing 25 n y N7 C8 3D1 doub 26 n y C8 H8 3D1 sing 27 n n C2' C3' 3D1 sing 28 n n C2' "H2'1" 3D1 sing 29 n n C2' "H2'2" 3D1 sing 30 n n C3' O3' 3D1 sing 31 n n C3' H3' 3D1 sing 32 n n O3' H1 3D1 sing 33 n n # _atom_sites.entry_id 2Z3M _atom_sites.fract_transf_matrix[1][1] 0.00857 _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] 0.007832 _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] 0.026073 _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 C 2 3D1 A 1 301 301 3D1 ADE . D 3 PHE A 1 302 302 PHE PHE . E 4 TAR A 1 501 501 TAR TAR . F 2 3D1 B 1 401 401 3D1 ADE . G 3 PHE B 1 402 402 PHE PHE . H 4 TAR B 1 502 502 TAR TAR . I 5 HOH A 1 502 1002 HOH HOH . I 5 HOH A 2 503 1003 HOH HOH . I 5 HOH A 3 504 1008 HOH HOH . I 5 HOH A 4 505 1010 HOH HOH . I 5 HOH A 5 506 1011 HOH HOH . I 5 HOH A 6 507 1015 HOH HOH . I 5 HOH A 7 508 1016 HOH HOH . I 5 HOH A 8 509 1021 HOH HOH . I 5 HOH A 9 510 1023 HOH HOH . I 5 HOH A 10 511 1024 HOH HOH . I 5 HOH A 11 512 1025 HOH HOH . I 5 HOH A 12 513 1026 HOH HOH . I 5 HOH A 13 514 1027 HOH HOH . I 5 HOH A 14 515 1029 HOH HOH . I 5 HOH A 15 516 1030 HOH HOH . I 5 HOH A 16 517 1031 HOH HOH . J 5 HOH B 1 503 1001 HOH HOH . J 5 HOH B 2 504 1004 HOH HOH . J 5 HOH B 3 505 1005 HOH HOH . J 5 HOH B 4 506 1006 HOH HOH . J 5 HOH B 5 507 1007 HOH HOH . J 5 HOH B 6 508 1009 HOH HOH . J 5 HOH B 7 509 1012 HOH HOH . J 5 HOH B 8 510 1013 HOH HOH . J 5 HOH B 9 511 1014 HOH HOH . J 5 HOH B 10 512 1017 HOH HOH . J 5 HOH B 11 513 1018 HOH HOH . J 5 HOH B 12 514 1019 HOH HOH . J 5 HOH B 13 515 1020 HOH HOH . J 5 HOH B 14 516 1022 HOH HOH . J 5 HOH B 15 517 1028 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' 3D1 . . . F 2 9.755 18.902 22.49 1 86.85 ? O5' 3D1 401 B 1 HETATM 2 C C5' 3D1 . . . F 2 10.909 18.07 22.612 1 88.79 ? C5' 3D1 401 B 1 HETATM 3 C C4' 3D1 . . . F 2 12.136 18.844 22.194 1 89.63 ? C4' 3D1 401 B 1 HETATM 4 O O4' 3D1 . . . F 2 13.303 18.342 22.877 1 91.79 ? O4' 3D1 401 B 1 HETATM 5 C C1' 3D1 . . . F 2 14.451 18.547 22.052 1 91.77 ? C1' 3D1 401 B 1 HETATM 6 N N9 3D1 . . . F 2 15.132 17.266 21.885 1 93.28 ? N9 3D1 401 B 1 HETATM 7 C C4 3D1 . . . F 2 16.428 17.12 21.459 1 94.59 ? C4 3D1 401 B 1 HETATM 8 N N3 3D1 . . . F 2 17.282 18.098 21.112 1 95.7 ? N3 3D1 401 B 1 HETATM 9 C C2 3D1 . . . F 2 18.458 17.587 20.756 1 96.07 ? C2 3D1 401 B 1 HETATM 10 N N1 3D1 . . . F 2 18.849 16.305 20.717 1 96.17 ? N1 3D1 401 B 1 HETATM 11 C C6 3D1 . . . F 2 17.967 15.346 21.078 1 95.49 ? C6 3D1 401 B 1 HETATM 12 N N6 3D1 . . . F 2 18.365 14.07 21.05 1 96.17 ? N6 3D1 401 B 1 HETATM 13 C C5 3D1 . . . F 2 16.678 15.759 21.467 1 94.8 ? C5 3D1 401 B 1 HETATM 14 N N7 3D1 . . . F 2 15.553 15.056 21.877 1 93.71 ? N7 3D1 401 B 1 HETATM 15 C C8 3D1 . . . F 2 14.665 15.994 22.111 1 93.78 ? C8 3D1 401 B 1 HETATM 16 C C2' 3D1 . . . F 2 13.962 19.144 20.741 1 90.28 ? C2' 3D1 401 B 1 HETATM 17 C C3' 3D1 . . . F 2 12.498 18.747 20.721 1 89.21 ? C3' 3D1 401 B 1 HETATM 18 O O3' 3D1 . . . F 2 11.74 19.635 19.964 1 86.54 ? O3' 3D1 401 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #