data_6MWR # _model_server_result.job_id N1FpyQ-dRCM5MmWm93WLwA _model_server_result.datetime_utc '2024-12-12 13:55:07' _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 6mwr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":600}' # _entry.id 6MWR # _exptl.entry_id 6MWR _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 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 90 _cell.entry_id 6MWR _cell.length_a 88.39 _cell.length_b 88.39 _cell.length_c 257.15 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MWR _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 disulf ? disulf1 A SG CYS 99 A CYS 98 1_555 A SG CYS 162 A CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 201 A CYS 200 1_555 A SG CYS 257 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 C SG CYS 23 C CYS 23 1_555 C SG CYS 97 C CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 D SG CYS 23 D CYS 26 1_555 D SG CYS 91 D CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A NZ LYS 44 A LYS 43 1_555 E C7 2LJ . A 2LJ 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.193 doub covale ? covale2 D ND2 ASN 134 D ASN 137 1_555 F C1 NAG . D NAG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? # _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 6MWR _atom_sites.fract_transf_matrix[1][1] 0.011313 _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] 0.011313 _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] 0.003889 _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 5 2LJ A 1 600 600 2LJ 2LJ . F 6 NAG D 1 700 700 NAG NAG . G 7 HOH A 1 701 2 HOH HOH . G 7 HOH A 2 702 1 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 C C4 2LJ . . . E 5 9.157 14.141 37.68 1 47.44 ? C4 2LJ 600 A 1 HETATM 2 C C6 2LJ . . . E 5 7.755 11.559 37.33 1 52.48 ? C6 2LJ 600 A 1 HETATM 3 C C7 2LJ . . . E 5 7.107 10.252 37.184 1 55.63 ? C7 2LJ 600 A 1 HETATM 4 C C8 2LJ . . . E 5 5.677 10.201 36.72 1 55.35 ? C8 2LJ 600 A 1 HETATM 5 N N1 2LJ . . . E 5 8.152 16.03 35.833 1 45.21 ? N1 2LJ 600 A 1 HETATM 6 N N3 2LJ . . . E 5 9.533 15.473 37.631 1 45.5 ? N3 2LJ 600 A 1 HETATM 7 N N5 2LJ . . . E 5 7.53 12.517 36.503 1 50.39 ? N5 2LJ 600 A 1 HETATM 8 C C4A 2LJ . . . E 5 8.154 13.755 36.656 1 48.23 ? C4A 2LJ 600 A 1 HETATM 9 O O4 2LJ . . . E 5 9.643 13.407 38.54 1 48.72 ? O4 2LJ 600 A 1 HETATM 10 C C2 2LJ . . . E 5 9.077 16.433 36.763 1 44.65 ? C2 2LJ 600 A 1 HETATM 11 O O2 2LJ . . . E 5 9.448 17.6 36.838 1 44.17 ? O2 2LJ 600 A 1 HETATM 12 C C8A 2LJ . . . E 5 7.683 14.753 35.753 1 46.92 ? C8A 2LJ 600 A 1 HETATM 13 N N8 2LJ . . . E 5 6.698 14.493 34.893 1 47.74 ? N8 2LJ 600 A 1 HETATM 14 C C1' 2LJ . . . E 5 5.929 15.411 34.067 1 47.82 ? C1' 2LJ 600 A 1 HETATM 15 C C2' 2LJ . . . E 5 6.351 15.503 32.601 1 49.79 ? C2' 2LJ 600 A 1 HETATM 16 O O2' 2LJ . . . E 5 6.466 14.201 32.024 1 51.91 ? O2' 2LJ 600 A 1 HETATM 17 C C3' 2LJ . . . E 5 7.653 16.287 32.415 1 49.97 ? C3' 2LJ 600 A 1 HETATM 18 O O3' 2LJ . . . E 5 7.668 17.438 33.253 1 48.41 ? O3' 2LJ 600 A 1 HETATM 19 C C4' 2LJ . . . E 5 7.97 16.699 30.975 1 51.48 ? C4' 2LJ 600 A 1 HETATM 20 O O4' 2LJ . . . E 5 9.341 17.091 30.897 1 51.96 ? O4' 2LJ 600 A 1 HETATM 21 C C5' 2LJ . . . E 5 7.092 17.823 30.413 1 51.37 ? C5' 2LJ 600 A 1 HETATM 22 O O5' 2LJ . . . E 5 7.483 18.17 29.091 1 52.61 ? O5' 2LJ 600 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #