data_2Z3M # _model_server_result.job_id N_dCzhhMsjWD2u6unXr0tw _model_server_result.datetime_utc '2025-02-17 11:36:51' _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":"C","auth_seq_id":301}' # _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 . . . C 2 39.26 54.386 13.768 1 77.55 ? O5' 3D1 301 A 1 HETATM 2 C C5' 3D1 . . . C 2 38.812 55.684 13.365 1 80.62 ? C5' 3D1 301 A 1 HETATM 3 C C4' 3D1 . . . C 2 37.311 55.661 13.211 1 80.63 ? C4' 3D1 301 A 1 HETATM 4 O O4' 3D1 . . . C 2 36.71 56.672 14.051 1 82.51 ? O4' 3D1 301 A 1 HETATM 5 C C1' 3D1 . . . C 2 35.507 57.137 13.432 1 82.82 ? C1' 3D1 301 A 1 HETATM 6 N N9 3D1 . . . C 2 35.613 58.582 13.247 1 85.39 ? N9 3D1 301 A 1 HETATM 7 C C4 3D1 . . . C 2 34.694 59.357 12.581 1 86.88 ? C4 3D1 301 A 1 HETATM 8 N N3 3D1 . . . C 2 33.565 58.944 11.978 1 87.35 ? N3 3D1 301 A 1 HETATM 9 C C2 3D1 . . . C 2 32.917 59.976 11.437 1 86.84 ? C2 3D1 301 A 1 HETATM 10 N N1 3D1 . . . C 2 33.241 61.275 11.437 1 86.62 ? N1 3D1 301 A 1 HETATM 11 C C6 3D1 . . . C 2 34.379 61.658 12.058 1 87.32 ? C6 3D1 301 A 1 HETATM 12 N N6 3D1 . . . C 2 34.695 62.957 12.073 1 88.2 ? N6 3D1 301 A 1 HETATM 13 C C5 3D1 . . . C 2 35.165 60.656 12.662 1 86.51 ? C5 3D1 301 A 1 HETATM 14 N N7 3D1 . . . C 2 36.369 60.698 13.354 1 85.65 ? N7 3D1 301 A 1 HETATM 15 C C8 3D1 . . . C 2 36.591 59.445 13.677 1 86.04 ? C8 3D1 301 A 1 HETATM 16 C C2' 3D1 . . . C 2 35.366 56.393 12.111 1 81.25 ? C2' 3D1 301 A 1 HETATM 17 C C3' 3D1 . . . C 2 36.798 55.994 11.821 1 80.5 ? C3' 3D1 301 A 1 HETATM 18 O O3' 3D1 . . . C 2 36.855 54.896 10.975 1 76.58 ? O3' 3D1 301 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 18 #