data_5JVN # _model_server_result.job_id eRVzIaOrWTLgr34OwYZP5Q _model_server_result.datetime_utc '2024-12-02 17:54:07' _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 5jvn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 5JVN # _exptl.entry_id 5JVN _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 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 120 _cell.entry_id 5JVN _cell.length_a 249.43 _cell.length_b 249.43 _cell.length_c 84.06 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JVN _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_674 x-y+1,-y+2,-z-1 1 0 0 0 -1 0 0 0 -1 0 432.025433 -84.06 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 OE1 GLU 749 A GLU 748 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc2 A OD2 ASP 773 A ASP 772 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc3 C O2' PEP . A PEP 902 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc4 C O2 PEP . A PEP 902 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc5 C O3P PEP . A PEP 902 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? # _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 5JVN _atom_sites.fract_transf_matrix[1][1] 0.004011 _atom_sites.fract_transf_matrix[1][2] 0.002316 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004631 _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] 0.011904 _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 B 2 6NQ A 1 901 875 6NQ DRG . C 3 PEP A 1 902 876 PEP PEP . D 4 MG A 1 903 1 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 . . . B 2 15.061 168.63 -69.587 0.87 109.41 ? C4 6NQ 901 A 1 HETATM 2 C C5 6NQ . . . B 2 13.681 168.583 -69.433 0.87 101.23 ? C5 6NQ 901 A 1 HETATM 3 C C6 6NQ . . . B 2 12.952 167.867 -70.397 0.87 92.93 ? C6 6NQ 901 A 1 HETATM 4 C C8 6NQ . . . B 2 14.41 169.752 -67.823 0.87 110.09 ? C8 6NQ 901 A 1 HETATM 5 N N1 6NQ . . . B 2 13.645 167.252 -71.387 0.87 92.21 ? N1 6NQ 901 A 1 HETATM 6 N N3 6NQ . . . B 2 15.778 168.044 -70.566 0.87 107.11 ? N3 6NQ 901 A 1 HETATM 7 P PG 6NQ . . . B 2 15.911 176.586 -62.781 0.87 155.22 ? PG 6NQ 901 A 1 HETATM 8 O O1G 6NQ . . . B 2 15.547 175.644 -61.646 0.87 151.85 ? O1G 6NQ 901 A 1 HETATM 9 O O2G 6NQ . . . B 2 16.217 177.963 -62.226 0.87 151.93 ? O2G 6NQ 901 A 1 HETATM 10 O O3G 6NQ . . . B 2 14.734 176.702 -63.728 0.87 156.16 ? O3G 6NQ 901 A 1 HETATM 11 P PB 6NQ . . . B 2 17.322 175.586 -65.284 0.87 149.78 ? PB 6NQ 901 A 1 HETATM 12 O O1B 6NQ . . . B 2 18.767 175.662 -65.762 0.87 146.98 ? O1B 6NQ 901 A 1 HETATM 13 O O2B 6NQ . . . B 2 16.48 176.605 -66.019 0.87 147.38 ? O2B 6NQ 901 A 1 HETATM 14 N N3B 6NQ . . . B 2 17.276 175.933 -63.6 0.87 155.22 ? N3B 6NQ 901 A 1 HETATM 15 P PA 6NQ . . . B 2 15.641 173.179 -64.902 0.87 131.77 ? PA 6NQ 901 A 1 HETATM 16 O O1A 6NQ . . . B 2 15.872 173.279 -63.378 0.87 126.77 ? O1A 6NQ 901 A 1 HETATM 17 O O2A 6NQ . . . B 2 14.275 173.504 -65.422 0.87 124.33 ? O2A 6NQ 901 A 1 HETATM 18 O O3A 6NQ . . . B 2 16.727 174.079 -65.645 0.87 138.22 ? O3A 6NQ 901 A 1 HETATM 19 O O5' 6NQ . . . B 2 16.097 171.737 -65.354 0.87 130.81 ? O5' 6NQ 901 A 1 HETATM 20 C C5' 6NQ . . . B 2 17.432 171.242 -65.087 0.87 135.55 ? C5' 6NQ 901 A 1 HETATM 21 C C4' 6NQ . . . B 2 18.052 170.626 -66.328 0.87 137.12 ? C4' 6NQ 901 A 1 HETATM 22 O O4' 6NQ . . . B 2 17.184 169.575 -66.846 0.87 136.11 ? O4' 6NQ 901 A 1 HETATM 23 C C3' 6NQ . . . B 2 18.281 171.595 -67.49 0.87 139.97 ? C3' 6NQ 901 A 1 HETATM 24 O O3' 6NQ . . . B 2 19.492 171.326 -68.191 0.87 140.54 ? O3' 6NQ 901 A 1 HETATM 25 C C2' 6NQ . . . B 2 17.031 171.31 -68.359 0.87 136.94 ? C2' 6NQ 901 A 1 HETATM 26 BR BR 6NQ . . . B 2 17.139 171.81 -70.254 0.87 141.21 ? BR 6NQ 901 A 1 HETATM 27 C C1' 6NQ . . . B 2 16.901 169.792 -68.227 0.87 131.43 ? C1' 6NQ 901 A 1 HETATM 28 N N9 6NQ . . . B 2 15.526 169.385 -68.529 0.87 116.59 ? N9 6NQ 901 A 1 HETATM 29 N N7 6NQ . . . B 2 13.285 169.29 -68.314 0.87 101.91 ? N7 6NQ 901 A 1 HETATM 30 N N6 6NQ . . . B 2 11.626 167.76 -70.37 0.87 87.13 ? N6 6NQ 901 A 1 HETATM 31 C C2 6NQ . . . B 2 14.98 167.374 -71.414 0.87 100.15 ? C2 6NQ 901 A 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #