data_5JVL # _model_server_result.job_id A5T9kn4lNqTlKOvzJy7ZDQ _model_server_result.datetime_utc '2025-08-31 07:19:08' _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 5jvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":901}' # _entry.id 5JVL # _exptl.entry_id 5JVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 569.093 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-Bromo-2'-deoxyadenosine 5'-[beta,gamma-imide]triphosphoric acid" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 106.22 _cell.angle_beta 101.81 _cell.angle_gamma 98.32 _cell.entry_id 5JVL _cell.length_a 69.98 _cell.length_b 108.45 _cell.length_c 152.76 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # 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,D,E,F,G,H,O,P,Q,R 1 1 B,C,I,J,K,L,M,N 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 ? 2 E N N ? 2 K N N ? 2 O 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 OE1 GLU 324 A GLU 324 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc2 A OE1 GLN 336 A GLN 336 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc3 A OE1 GLU 748 A GLU 748 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc4 A OE2 GLU 748 A GLU 748 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc5 A OD2 ASP 772 A ASP 772 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc6 E O3G 6NQ . A 6NQ 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc7 E O2B 6NQ . A 6NQ 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? metalc ? metalc8 E O3A 6NQ . A 6NQ 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc9 G O2' PEP . A PEP 903 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc10 G O2 PEP . A PEP 903 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc11 G O3P PEP . A PEP 903 1_555 H MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc12 B OE1 GLU 748 B GLU 748 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc13 B OD2 ASP 772 B ASP 772 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc14 I O1 PEP . B PEP 901 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc15 I O2 PEP . B PEP 901 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc16 I O1P PEP . B PEP 901 1_555 J MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc17 C OE1 GLU 324 C GLU 324 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc18 C OE1 GLU 748 C GLU 748 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc19 C OD2 ASP 772 C ASP 772 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc20 K O3G 6NQ . C 6NQ 901 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc21 K O2B 6NQ . C 6NQ 901 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc22 K O3A 6NQ . C 6NQ 901 1_555 L MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc23 M O2' PEP . C PEP 903 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc24 M O2 PEP . C PEP 903 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc25 M O3P PEP . C PEP 903 1_555 N MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc26 D OE1 GLU 324 D GLU 324 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc27 D OE1 GLN 336 D GLN 336 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc28 D OE1 GLU 748 D GLU 748 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc29 D OD2 ASP 772 D ASP 772 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc30 O O2G 6NQ . D 6NQ 901 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc31 O O1B 6NQ . D 6NQ 901 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc32 O O3A 6NQ . D 6NQ 901 1_555 P MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc33 Q O1 PEP . D PEP 903 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc34 Q O2 PEP . D PEP 903 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc35 Q O1P PEP . D PEP 903 1_555 R MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _chem_comp.formula 'C10 H16 Br N6 O11 P3' _chem_comp.formula_weight 569.093 _chem_comp.id 6NQ _chem_comp.mon_nstd_flag . _chem_comp.name "2'-Bromo-2'-deoxyadenosine 5'-[beta,gamma-imide]triphosphoric acid" _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 O3' C3' 6NQ sing 1 n n BR C2' 6NQ sing 2 n n C3' C2' 6NQ sing 3 n n C3' C4' 6NQ sing 4 n n C2' C1' 6NQ sing 5 n n C4' O4' 6NQ sing 6 n n C4' C5' 6NQ sing 7 n n O2B PB 6NQ doub 8 n n C1' O4' 6NQ sing 9 n n C1' N9 6NQ sing 10 n n N3 C2 6NQ doub 11 n y N3 C4 6NQ sing 12 n y C2 N1 6NQ sing 13 n y C5' O5' 6NQ sing 14 n n N9 C4 6NQ sing 15 n y N9 C8 6NQ sing 16 n y C4 C5 6NQ doub 17 n y O3G PG 6NQ doub 18 n n O3A PB 6NQ sing 19 n n O3A PA 6NQ sing 20 n n PB O1B 6NQ sing 21 n n PB N3B 6NQ sing 22 n n O5' PA 6NQ sing 23 n n N1 C6 6NQ doub 24 n y O2G PG 6NQ sing 25 n n PA O2A 6NQ doub 26 n n PA O1A 6NQ sing 27 n n PG N3B 6NQ sing 28 n n PG O1G 6NQ sing 29 n n C8 N7 6NQ doub 30 n y C5 C6 6NQ sing 31 n y C5 N7 6NQ sing 32 n y C6 N6 6NQ sing 33 n n C8 H1 6NQ sing 34 n n O1G H2 6NQ sing 35 n n O2G H3 6NQ sing 36 n n O1B H4 6NQ sing 37 n n N3B H5 6NQ sing 38 n n O1A H6 6NQ sing 39 n n C5' H7 6NQ sing 40 n n C5' H8 6NQ sing 41 n n C4' H9 6NQ sing 42 n n C3' H10 6NQ sing 43 n n O3' H11 6NQ sing 44 n n C2' H12 6NQ sing 45 n n C1' H13 6NQ sing 46 n n N6 H14 6NQ sing 47 n n N6 H15 6NQ sing 48 n n C2 H16 6NQ sing 49 n n # _atom_sites.entry_id 5JVL _atom_sites.fract_transf_matrix[1][1] 0.01429 _atom_sites.fract_transf_matrix[1][2] 0.002089 _atom_sites.fract_transf_matrix[1][3] 0.003855 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009319 _atom_sites.fract_transf_matrix[2][3] 0.003137 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007057 _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 6NQ A 1 901 875 6NQ DRG . F 3 MG A 1 902 876 MG MG . G 4 PEP A 1 903 877 PEP PEP . H 3 MG A 1 904 878 MG MG . I 4 PEP B 1 901 877 PEP PEP . J 3 MG B 1 902 878 MG MG . K 2 6NQ C 1 901 875 6NQ DRG . L 3 MG C 1 902 876 MG MG . M 4 PEP C 1 903 877 PEP PEP . N 3 MG C 1 904 878 MG MG . O 2 6NQ D 1 901 875 6NQ DRG . P 3 MG D 1 902 876 MG MG . Q 4 PEP D 1 903 877 PEP PEP . R 3 MG D 1 904 878 MG MG . # 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 C C4 6NQ . . . O 2 17.93 -77.708 -14.318 1 24.05 ? C4 6NQ 901 D 1 HETATM 2 C C5 6NQ . . . O 2 19.148 -77.977 -14.921 1 24.49 ? C5 6NQ 901 D 1 HETATM 3 C C6 6NQ . . . O 2 19.794 -79.175 -14.541 1 24.05 ? C6 6NQ 901 D 1 HETATM 4 C C8 6NQ . . . O 2 18.48 -76.132 -15.711 1 24.68 ? C8 6NQ 901 D 1 HETATM 5 N N1 6NQ . . . O 2 19.193 -79.944 -13.607 1 21.64 ? N1 6NQ 901 D 1 HETATM 6 N N3 6NQ . . . O 2 17.316 -78.448 -13.383 1 23.68 ? N3 6NQ 901 D 1 HETATM 7 P PG 6NQ . . . O 2 17.05 -67.755 -17.973 1 27.57 ? PG 6NQ 901 D 1 HETATM 8 O O1G 6NQ . . . O 2 16.155 -66.537 -17.902 1 29.78 ? O1G 6NQ 901 D 1 HETATM 9 O O2G 6NQ . . . O 2 17.179 -68.13 -16.511 1 38.23 ? O2G 6NQ 901 D 1 HETATM 10 O O3G 6NQ . . . O 2 18.49 -67.585 -18.439 1 23.05 ? O3G 6NQ 901 D 1 HETATM 11 P PB 6NQ . . . O 2 15.249 -69.888 -17.72 1 30.75 ? PB 6NQ 901 D 1 HETATM 12 O O1B 6NQ . . . O 2 14.48 -68.958 -16.846 1 34.36 ? O1B 6NQ 901 D 1 HETATM 13 O O2B 6NQ . . . O 2 14.157 -70.708 -18.421 1 30.96 ? O2B 6NQ 901 D 1 HETATM 14 N N3B 6NQ . . . O 2 16.123 -68.89 -18.794 1 28.12 ? N3B 6NQ 901 D 1 HETATM 15 P PA 6NQ . . . O 2 17.16 -71.989 -17.383 1 27.93 ? PA 6NQ 901 D 1 HETATM 16 O O1A 6NQ . . . O 2 18.596 -71.857 -17.188 1 25.28 ? O1A 6NQ 901 D 1 HETATM 17 O O2A 6NQ . . . O 2 16.721 -72.068 -18.806 1 30.91 ? O2A 6NQ 901 D 1 HETATM 18 O O3A 6NQ . . . O 2 16.356 -70.738 -16.726 1 28.77 ? O3A 6NQ 901 D 1 HETATM 19 O O5' 6NQ . . . O 2 16.502 -73.354 -16.955 1 29.25 ? O5' 6NQ 901 D 1 HETATM 20 C C5' 6NQ . . . O 2 15.072 -73.511 -16.814 1 29.38 ? C5' 6NQ 901 D 1 HETATM 21 C C4' 6NQ . . . O 2 14.853 -74.319 -15.547 1 30.02 ? C4' 6NQ 901 D 1 HETATM 22 O O4' 6NQ . . . O 2 15.569 -75.569 -15.634 1 27.49 ? O4' 6NQ 901 D 1 HETATM 23 C C3' 6NQ . . . O 2 15.322 -73.612 -14.276 1 31.44 ? C3' 6NQ 901 D 1 HETATM 24 O O3' 6NQ . . . O 2 14.26 -73.662 -13.331 1 33.07 ? O3' 6NQ 901 D 1 HETATM 25 C C2' 6NQ . . . O 2 16.563 -74.425 -13.844 1 32.18 ? C2' 6NQ 901 D 1 HETATM 26 BR BR 6NQ . . . O 2 16.778 -74.619 -11.849 1 63.12 ? BR 6NQ 901 D 1 HETATM 27 C C1' 6NQ . . . O 2 16.291 -75.819 -14.475 1 28.7 ? C1' 6NQ 901 D 1 HETATM 28 N N9 6NQ . . . O 2 17.504 -76.525 -14.85 1 23.97 ? N9 6NQ 901 D 1 HETATM 29 N N7 6NQ . . . O 2 19.498 -76.957 -15.787 1 23.55 ? N7 6NQ 901 D 1 HETATM 30 N N6 6NQ . . . O 2 20.974 -79.574 -15.029 1 24.71 ? N6 6NQ 901 D 1 HETATM 31 C C2 6NQ . . . O 2 18.02 -79.547 -13.104 1 22.39 ? C2 6NQ 901 D 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 400 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #