data_7ZT2 # _model_server_result.job_id Juqc3kUbB5-kw2pq8dzcLw _model_server_result.datetime_utc '2024-11-07 08:39:44' _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 7zt2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 7ZT2 # _exptl.entry_id 7ZT2 _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 7ZT2 _cell.length_a 91.19 _cell.length_b 103.85 _cell.length_c 117.86 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZT2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,H,I,J,K _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? disulf ? disulf2 A SG CYS 201 A CYS 200 1_555 A SG CYS 257 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 26 B CYS 25 1_555 B SG CYS 81 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 C SG CYS 24 D CYS 24 1_555 C SG CYS 90 D CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf5 C SG CYS 134 D CYS 134 1_555 C SG CYS 184 D CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 C SG CYS 159 D CYS 159 1_555 D SG CYS 169 E CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 D SG CYS 23 E CYS 23 1_555 D SG CYS 91 E CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? disulf ? disulf8 D SG CYS 143 E CYS 143 1_555 D SG CYS 208 E CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? covale ? covale1 A NZ LYS 44 A LYS 43 1_555 E C7 2LJ . A 2LJ 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.254 ? # _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 7ZT2 _atom_sites.fract_transf_matrix[1][1] 0.010966 _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] 0.009629 _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] 0.008485 _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 1 301 301 2LJ 2LJ . F 6 EDO A 1 302 401 EDO EDO . G 6 EDO E 1 301 301 EDO EDO . H 7 HOH A 1 401 22 HOH HOH . H 7 HOH A 2 402 16 HOH HOH . H 7 HOH A 3 403 10 HOH HOH . H 7 HOH A 4 404 11 HOH HOH . H 7 HOH A 5 405 54 HOH HOH . H 7 HOH A 6 406 37 HOH HOH . H 7 HOH A 7 407 20 HOH HOH . H 7 HOH A 8 408 35 HOH HOH . H 7 HOH A 9 409 55 HOH HOH . H 7 HOH A 10 410 27 HOH HOH . H 7 HOH A 11 411 24 HOH HOH . H 7 HOH A 12 412 21 HOH HOH . H 7 HOH A 13 413 36 HOH HOH . H 7 HOH A 14 414 39 HOH HOH . I 7 HOH B 1 101 2 HOH HOH . I 7 HOH B 2 102 14 HOH HOH . I 7 HOH B 3 103 5 HOH HOH . I 7 HOH B 4 104 1 HOH HOH . I 7 HOH B 5 105 50 HOH HOH . I 7 HOH B 6 106 25 HOH HOH . I 7 HOH B 7 107 48 HOH HOH . J 7 HOH D 1 301 26 HOH HOH . J 7 HOH D 2 302 13 HOH HOH . J 7 HOH D 3 303 15 HOH HOH . J 7 HOH D 4 304 8 HOH HOH . J 7 HOH D 5 305 19 HOH HOH . J 7 HOH D 6 306 9 HOH HOH . J 7 HOH D 7 307 3 HOH HOH . J 7 HOH D 8 308 53 HOH HOH . J 7 HOH D 9 309 7 HOH HOH . J 7 HOH D 10 310 34 HOH HOH . J 7 HOH D 11 311 52 HOH HOH . K 7 HOH E 1 401 33 HOH HOH . K 7 HOH E 2 402 47 HOH HOH . K 7 HOH E 3 403 49 HOH HOH . K 7 HOH E 4 404 4 HOH HOH . K 7 HOH E 5 405 12 HOH HOH . K 7 HOH E 6 406 41 HOH HOH . K 7 HOH E 7 407 46 HOH HOH . K 7 HOH E 8 408 43 HOH HOH . K 7 HOH E 9 409 29 HOH HOH . K 7 HOH E 10 410 32 HOH HOH . K 7 HOH E 11 411 17 HOH HOH . K 7 HOH E 12 412 18 HOH HOH . K 7 HOH E 13 413 6 HOH HOH . K 7 HOH E 14 414 42 HOH HOH . K 7 HOH E 15 415 44 HOH HOH . K 7 HOH E 16 416 23 HOH HOH . K 7 HOH E 17 417 51 HOH HOH . K 7 HOH E 18 418 30 HOH HOH . K 7 HOH E 19 419 31 HOH HOH . K 7 HOH E 20 420 45 HOH HOH . K 7 HOH E 21 421 38 HOH HOH . K 7 HOH E 22 422 40 HOH HOH . K 7 HOH E 23 423 28 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 7.008 12.833 -9.557 1 69.13 ? C4 2LJ 301 A 1 HETATM 2 C C6 2LJ . . . E 5 6.454 9.964 -9.606 1 74.77 ? C6 2LJ 301 A 1 HETATM 3 C C7 2LJ . . . E 5 6.684 8.519 -9.928 1 79.76 ? C7 2LJ 301 A 1 HETATM 4 C C8 2LJ . . . E 5 7.723 7.807 -9.061 1 81.68 ? C8 2LJ 301 A 1 HETATM 5 N N1 2LJ . . . E 5 8.494 13.642 -7.354 1 67.91 ? N1 2LJ 301 A 1 HETATM 6 N N3 2LJ . . . E 5 7.393 14.136 -9.333 1 70.1 ? N3 2LJ 301 A 1 HETATM 7 N N5 2LJ . . . E 5 7.097 10.528 -8.598 1 72.24 ? N5 2LJ 301 A 1 HETATM 8 C C4A 2LJ . . . E 5 7.397 11.895 -8.559 1 69.8 ? C4A 2LJ 301 A 1 HETATM 9 O O4 2LJ . . . E 5 6.386 12.539 -10.564 1 69.21 ? O4 2LJ 301 A 1 HETATM 10 C C2 2LJ . . . E 5 8.126 14.587 -8.27 1 69.15 ? C2 2LJ 301 A 1 HETATM 11 O O2 2LJ . . . E 5 8.475 15.76 -8.171 1 70.23 ? O2 2LJ 301 A 1 HETATM 12 C C8A 2LJ . . . E 5 8.153 12.324 -7.463 1 68.58 ? C8A 2LJ 301 A 1 HETATM 13 N N8 2LJ . . . E 5 8.554 11.455 -6.471 1 69 ? N8 2LJ 301 A 1 HETATM 14 C C1' 2LJ . . . E 5 9.798 11.606 -5.734 1 68.81 ? C1' 2LJ 301 A 1 HETATM 15 C C2' 2LJ . . . E 5 9.624 12.019 -4.276 1 68.11 ? C2' 2LJ 301 A 1 HETATM 16 O O2' 2LJ . . . E 5 8.944 10.94 -3.626 1 69.82 ? O2' 2LJ 301 A 1 HETATM 17 C C3' 2LJ . . . E 5 8.908 13.381 -4.123 1 65.7 ? C3' 2LJ 301 A 1 HETATM 18 O O3' 2LJ . . . E 5 9.612 14.3 -4.931 1 64.46 ? O3' 2LJ 301 A 1 HETATM 19 C C4' 2LJ . . . E 5 8.837 14.028 -2.735 1 64.5 ? C4' 2LJ 301 A 1 HETATM 20 O O4' 2LJ . . . E 5 8.329 15.362 -2.863 1 61.98 ? O4' 2LJ 301 A 1 HETATM 21 C C5' 2LJ . . . E 5 10.198 14.048 -2.059 1 65.29 ? C5' 2LJ 301 A 1 HETATM 22 O O5' 2LJ . . . E 5 10.234 14.902 -0.919 1 64.57 ? O5' 2LJ 301 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #