data_2QRO # _model_server_result.job_id UhZQ63snd4dTqhbOuxiDGw _model_server_result.datetime_utc '2024-11-23 00:49:43' _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 2qro # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":503}' # _entry.id 2QRO # _exptl.entry_id 2QRO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 2QRO _cell.length_a 93.688 _cell.length_b 93.688 _cell.length_c 332.408 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QRO _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J 1 1 C,D,K,L,M,N,O,P 2 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 ? 4 G N N ? 4 J N N ? 4 M N N ? 4 P 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 OG SER 55 A SER 35 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A OE2 GLU 147 A GLU 127 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc3 E MG MG . A MG 401 1_555 F O1B UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc4 B OG SER 55 B SER 35 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc5 H MG MG . B MG 401 1_555 I O1B UDP . B UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc6 C OG SER 55 C SER 35 1_555 K MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc7 K MG MG . C MG 401 1_555 L O1B UDP . C UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc8 D OG SER 55 D SER 35 1_555 N MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc9 D OE2 GLU 147 D GLU 127 1_555 N MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc10 N MG MG . D MG 401 1_555 O O1B UDP . D UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? # _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 2QRO _atom_sites.fract_transf_matrix[1][1] 0.010674 _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] 0.010674 _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] 0.003008 _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 E 2 MG A 1 401 401 MG MG . F 3 UDP A 1 402 402 UDP UDP . G 4 D5M A 1 503 503 D5M D5M . H 2 MG B 1 401 401 MG MG . I 3 UDP B 1 402 402 UDP UDP . J 4 D5M B 1 503 503 D5M D5M . K 2 MG C 1 401 401 MG MG . L 3 UDP C 1 402 402 UDP UDP . M 4 D5M C 1 503 503 D5M D5M . N 2 MG D 1 401 401 MG MG . O 3 UDP D 1 402 402 UDP UDP . P 4 D5M D 1 503 503 D5M D5M . # 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 . . . J 4 31.21 76.246 11.776 1 75.4 ? O5' D5M 503 B 1 HETATM 2 C C5' D5M . . . J 4 31.316 77.414 11.027 1 75.4 ? C5' D5M 503 B 1 HETATM 3 C C4' D5M . . . J 4 31.782 78.477 11.94 1 75.4 ? C4' D5M 503 B 1 HETATM 4 O O4' D5M . . . J 4 33.079 78.145 12.483 1 75.4 ? O4' D5M 503 B 1 HETATM 5 C C3' D5M . . . J 4 31.92 79.785 11.181 1 75.4 ? C3' D5M 503 B 1 HETATM 6 O O3' D5M . . . J 4 31.55 80.862 12.044 1 75.4 ? O3' D5M 503 B 1 HETATM 7 C C2' D5M . . . J 4 33.397 79.838 10.77 1 75.4 ? C2' D5M 503 B 1 HETATM 8 C C1' D5M . . . J 4 34.055 78.798 11.676 1 75.4 ? C1' D5M 503 B 1 HETATM 9 N N9 D5M . . . J 4 34.85 77.839 10.917 1 75.4 ? N9 D5M 503 B 1 HETATM 10 C C8 D5M . . . J 4 34.641 76.492 10.779 1 75.4 ? C8 D5M 503 B 1 HETATM 11 N N7 D5M . . . J 4 35.582 75.971 10.042 1 75.4 ? N7 D5M 503 B 1 HETATM 12 C C5 D5M . . . J 4 36.44 76.943 9.667 1 75.4 ? C5 D5M 503 B 1 HETATM 13 C C6 D5M . . . J 4 37.607 76.99 8.908 1 75.4 ? C6 D5M 503 B 1 HETATM 14 N N6 D5M . . . J 4 38.125 75.843 8.345 1 75.4 ? N6 D5M 503 B 1 HETATM 15 N N1 D5M . . . J 4 38.213 78.179 8.745 1 75.4 ? N1 D5M 503 B 1 HETATM 16 C C2 D5M . . . J 4 37.734 79.307 9.281 1 75.4 ? C2 D5M 503 B 1 HETATM 17 N N3 D5M . . . J 4 36.64 79.302 10.005 1 75.4 ? N3 D5M 503 B 1 HETATM 18 C C4 D5M . . . J 4 35.973 78.16 10.221 1 75.4 ? C4 D5M 503 B 1 HETATM 19 P P D5M . . . J 4 30.732 75.165 10.732 1 75.4 ? P D5M 503 B 1 HETATM 20 O O1P D5M . . . J 4 31.782 75.028 9.69 1 75.4 ? O1P D5M 503 B 1 HETATM 21 O O3P D5M . . . J 4 29.34 75.629 10.033 1 75.4 ? O3P D5M 503 B 1 HETATM 22 O O2P D5M . . . J 4 30.549 73.759 11.522 1 75.4 ? O2P D5M 503 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #