data_4U4F # _model_server_result.job_id 4bNYdj8I7uNnawBbw41iww _model_server_result.datetime_utc '2024-10-19 10:25:39' _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 4u4f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":903}' # _entry.id 4U4F # _exptl.entry_id 4U4F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.162 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine _entity.pdbx_number_of_molecules 4 _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 4U4F _cell.length_a 141.374 _cell.length_b 166.575 _cell.length_c 566.604 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U4F _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 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,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 I N N ? 3 J N N ? 3 L N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n E NAG 1 E 1 NAG A 834 NAG 2 n E NAG 2 E 2 NAG A 835 NAG 2 n F NAG 1 F 1 NAG B 834 NAG 2 n F NAG 2 F 2 NAG B 835 NAG 2 n G NAG 1 G 1 NAG C 834 NAG 2 n G NAG 2 G 2 NAG C 835 NAG # 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 54 A CYS 63 1_555 A SG CYS 306 A CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 709 A CYS 718 1_555 A SG CYS 764 A CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 B SG CYS 54 B CYS 63 1_555 B SG CYS 306 B CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 709 B CYS 718 1_555 B SG CYS 764 B CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 54 C CYS 63 1_555 C SG CYS 306 C CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 709 C CYS 718 1_555 C SG CYS 764 C CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 D SG CYS 54 D CYS 63 1_555 D SG CYS 306 D CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 D SG CYS 709 D CYS 718 1_555 D SG CYS 764 D CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 346 A ASN 355 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale2 B ND2 ASN 346 B ASN 355 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale3 C ND2 ASN 346 C ASN 355 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale4 D ND2 ASN 346 D ASN 355 1_555 K C1 NAG . D NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _chem_comp.formula 'C7 H8 N4 O6' _chem_comp.formula_weight 244.162 _chem_comp.id NWD _chem_comp.mon_nstd_flag n _chem_comp.name 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms nitrowillardiine # 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 N1 C2 NWD sing 265 n n N1 C6 NWD sing 266 n n N1 C7 NWD sing 267 n n O1 N2 NWD doub 268 n n C2 O2 NWD doub 269 n n C2 N3 NWD sing 270 n n N2 O3 NWD sing 271 n n N2 C5 NWD sing 272 n n N3 C4 NWD sing 273 n n N3 HN3 NWD sing 274 n n C4 O4 NWD doub 275 n n C4 C5 NWD sing 276 n n C5 C6 NWD doub 277 n n C6 H6 NWD sing 278 n n C7 C8 NWD sing 279 n n C7 H7 NWD sing 280 n n C7 H7A NWD sing 281 n n C8 N8 NWD sing 282 n n C8 C9 NWD sing 283 n n C8 H8 NWD sing 284 n n N8 HN8 NWD sing 285 n n N8 HN8A NWD sing 286 n n C9 O91 NWD doub 287 n n C9 O92 NWD sing 288 n n O92 H81 NWD sing 289 n n # _atom_sites.entry_id 4U4F _atom_sites.fract_transf_matrix[1][1] 0.007073 _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] 0.006003 _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] 0.001765 _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 H 3 NWD A 1 903 901 NWD NWD . I 3 NWD B 1 903 901 NWD NWD . J 3 NWD C 1 903 901 NWD NWD . K 4 NAG D 1 901 834 NAG NAG . L 3 NWD D 1 902 901 NWD NWD . # 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 N N1 NWD . . . I 3 134.617 214.943 72.635 1 119.36 ? N1 NWD 903 B 1 HETATM 2 O O1 NWD . . . I 3 136.015 211.574 74.919 1 119.36 ? O1 NWD 903 B 1 HETATM 3 C C2 NWD . . . I 3 133.604 215.709 73.28 1 119.36 ? C2 NWD 903 B 1 HETATM 4 N N2 NWD . . . I 3 134.838 211.785 74.633 1 119.36 ? N2 NWD 903 B 1 HETATM 5 O O2 NWD . . . I 3 133.275 216.814 72.879 1 119.36 ? O2 NWD 903 B 1 HETATM 6 N N3 NWD . . . I 3 133.007 215.105 74.401 1 119.36 ? N3 NWD 903 B 1 HETATM 7 O O3 NWD . . . I 3 134.028 210.765 74.523 1 119.36 ? O3 NWD 903 B 1 HETATM 8 C C4 NWD . . . I 3 133.374 213.828 74.881 1 119.36 ? C4 NWD 903 B 1 HETATM 9 O O4 NWD . . . I 3 132.798 213.359 75.88 1 119.36 ? O4 NWD 903 B 1 HETATM 10 C C5 NWD . . . I 3 134.448 213.08 74.159 1 119.36 ? C5 NWD 903 B 1 HETATM 11 C C6 NWD . . . I 3 135.056 213.636 73.065 1 119.36 ? C6 NWD 903 B 1 HETATM 12 C C7 NWD . . . I 3 135.219 215.562 71.506 1 119.36 ? C7 NWD 903 B 1 HETATM 13 C C8 NWD . . . I 3 134.716 214.956 70.244 1 119.36 ? C8 NWD 903 B 1 HETATM 14 N N8 NWD . . . I 3 135.35 213.691 69.99 1 119.36 ? N8 NWD 903 B 1 HETATM 15 C C9 NWD . . . I 3 135.068 215.84 69.11 1 119.36 ? C9 NWD 903 B 1 HETATM 16 O O91 NWD . . . I 3 136.234 215.796 68.625 1 119.36 ? O91 NWD 903 B 1 HETATM 17 O O92 NWD . . . I 3 134.183 216.604 68.648 1 119.36 ? O92 NWD 903 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 17 #