data_5D7L # _model_server_result.job_id aMuWLQC98TlVM-Do2540ZA _model_server_result.datetime_utc '2024-12-01 09:06:44' _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 5d7l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":600}' # _entry.id 5D7L # _exptl.entry_id 5D7L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 316.31 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol _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 100.15 _cell.angle_gamma 90 _cell.entry_id 5D7L _cell.length_a 89.28 _cell.length_b 222.432 _cell.length_c 98.979 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D7L _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 2 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 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I 1 1 C,F,J 2 1 D,E 3 1 G,H 4 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 ? 5 I N N ? 5 J 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 disulf ? disulf1 A SG CYS 201 A CYS 200 1_555 A SG CYS 257 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 G SG CYS 132 G CYS 132 1_555 G SG CYS 182 G CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 G SG CYS 157 G CYS 157 1_555 H SG CYS 170 H CYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? covale ? covale1 A NZ LYS 44 A LYS 43 1_555 I C7 2LJ . A 2LJ 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.268 ? covale ? covale2 C NZ LYS 44 C LYS 43 1_555 J C7 2LJ . C 2LJ 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? # _chem_comp.formula 'C12 H20 N4 O6' _chem_comp.formula_weight 316.31 _chem_comp.id 2LJ _chem_comp.mon_nstd_flag . _chem_comp.name 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil # 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' 2LJ sing 1 n n C5' C4' 2LJ sing 2 n n O4' C4' 2LJ sing 3 n n C4' C3' 2LJ sing 4 n n O2' C2' 2LJ sing 5 n n C3' C2' 2LJ sing 6 n n C3' O3' 2LJ sing 7 n n C2' C1' 2LJ sing 8 n n C1' N8 2LJ sing 9 n n N8 C8A 2LJ sing 10 n n C8A N1 2LJ sing 11 n n C8A C4A 2LJ doub 12 n n N1 C2 2LJ sing 13 n n N5 C4A 2LJ sing 14 n n N5 C6 2LJ doub 15 n n C4A C4 2LJ sing 16 n n C8 C7 2LJ sing 17 n n C2 O2 2LJ doub 18 n n C2 N3 2LJ sing 19 n n C7 C6 2LJ sing 20 n n N3 C4 2LJ sing 21 n n C4 O4 2LJ doub 22 n n C6 H1 2LJ sing 23 n n C7 H2 2LJ sing 24 n n C7 H3 2LJ sing 25 n n C8 H4 2LJ sing 26 n n C8 H5 2LJ sing 27 n n C8 H6 2LJ sing 28 n n N3 H7 2LJ sing 29 n n N8 H9 2LJ sing 30 n n C1' H10 2LJ sing 31 n n C1' H11 2LJ sing 32 n n C2' H12 2LJ sing 33 n n O2' H13 2LJ sing 34 n n C3' H14 2LJ sing 35 n n O3' H15 2LJ sing 36 n n C4' H16 2LJ sing 37 n n O4' H17 2LJ sing 38 n n C5' H18 2LJ sing 39 n n C5' H19 2LJ sing 40 n n O5' H20 2LJ sing 41 n n N1 H8 2LJ sing 42 n n # _atom_sites.entry_id 5D7L _atom_sites.fract_transf_matrix[1][1] 0.011201 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002005 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004496 _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] 0.010264 _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 I 5 2LJ A 1 600 600 2LJ 2LJ . J 5 2LJ C 1 600 600 2LJ 2LJ . # 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 2LJ . . . J 5 120.016 -16.676 18.505 1 72.55 ? C4 2LJ 600 C 1 HETATM 2 C C6 2LJ . . . J 5 120.069 -15.644 21.251 1 60.02 ? C6 2LJ 600 C 1 HETATM 3 C C7 2LJ . . . J 5 120.099 -15.129 22.614 1 58.29 ? C7 2LJ 600 C 1 HETATM 4 C C8 2LJ . . . J 5 121.11 -14.066 22.938 1 57.99 ? C8 2LJ 600 C 1 HETATM 5 N N1 2LJ . . . J 5 121.382 -14.906 16.779 1 82.19 ? N1 2LJ 600 C 1 HETATM 6 N N3 2LJ . . . J 5 120.312 -16.94 17.18 1 74.96 ? N3 2LJ 600 C 1 HETATM 7 N N5 2LJ . . . J 5 120.523 -14.914 20.296 1 65.63 ? N5 2LJ 600 C 1 HETATM 8 C C4A 2LJ . . . J 5 120.521 -15.379 18.982 1 72.86 ? C4A 2LJ 600 C 1 HETATM 9 O O4 2LJ . . . J 5 119.366 -17.496 19.155 1 68.61 ? O4 2LJ 600 C 1 HETATM 10 C C2 2LJ . . . J 5 120.978 -16.125 16.299 1 78.38 ? C2 2LJ 600 C 1 HETATM 11 O O2 2LJ . . . J 5 121.199 -16.469 15.141 1 76.87 ? O2 2LJ 600 C 1 HETATM 12 C C8A 2LJ . . . J 5 121.164 -14.508 18.064 1 78.02 ? C8A 2LJ 600 C 1 HETATM 13 N N8 2LJ . . . J 5 121.561 -13.286 18.427 1 78.19 ? N8 2LJ 600 C 1 HETATM 14 C C1' 2LJ . . . J 5 122.281 -12.263 17.68 1 78.66 ? C1' 2LJ 600 C 1 HETATM 15 C C2' 2LJ . . . J 5 121.459 -11.328 16.791 1 78.88 ? C2' 2LJ 600 C 1 HETATM 16 O O2' 2LJ . . . J 5 120.32 -10.802 17.474 1 78.43 ? O2' 2LJ 600 C 1 HETATM 17 C C3' 2LJ . . . J 5 121.026 -12.023 15.497 1 80.93 ? C3' 2LJ 600 C 1 HETATM 18 O O3' 2LJ . . . J 5 122.089 -12.855 15.045 1 82.39 ? O3' 2LJ 600 C 1 HETATM 19 C C4' 2LJ . . . J 5 120.614 -11.092 14.357 1 79.24 ? C4' 2LJ 600 C 1 HETATM 20 O O4' 2LJ . . . J 5 121.178 -9.792 14.543 1 78.73 ? O4' 2LJ 600 C 1 HETATM 21 C C5' 2LJ . . . J 5 119.101 -10.984 14.18 1 77.24 ? C5' 2LJ 600 C 1 HETATM 22 O O5' 2LJ . . . J 5 118.753 -10.569 12.863 1 75.18 ? O5' 2LJ 600 C 1 # _model_server_stats.io_time_ms 131 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #