data_7ZAY # _model_server_result.job_id IoK-WWO6sSsqBdldiWSCQg _model_server_result.datetime_utc '2025-02-26 08:22:22' _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 7zay # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 7ZAY # _exptl.entry_id 7ZAY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 404.161 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 7ZAY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZAY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 ? _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 # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . 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 3 n C NAG 1 C 1 NAG B 800 NAG 3 n C NAG 2 C 2 NAG B 801 NAG 3 n C BMA 3 C 3 BMA B 802 BMA # 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 73 A CYS 98 1_555 A SG CYS 78 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 84 A CYS 109 1_555 A SG CYS 127 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 273 A CYS 298 1_555 A SG CYS 287 A CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 309 A CYS 334 1_555 A SG CYS 330 A CYS 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 A SG CYS 627 A CYS 652 1_555 A SG CYS 679 A CYS 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 42 B CYS 85 1_555 B SG CYS 47 B CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 53 B CYS 96 1_555 B SG CYS 108 B CYS 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 243 B CYS 286 1_555 B SG CYS 257 B CYS 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 275 B CYS 318 1_555 B SG CYS 296 B CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf10 B SG CYS 583 B CYS 626 1_555 B SG CYS 633 B CYS 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 305 A ASN 330 1_555 D C1 NAG . A NAG 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B ND2 ASN 594 B ASN 637 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 N1 C2 UDP sing 410 n n N1 C6 UDP sing 411 n n N1 C1' UDP sing 412 n n C2 N3 UDP sing 413 n n C2 O2 UDP doub 414 n n N3 C4 UDP sing 415 n n N3 HN3 UDP sing 416 n n C4 C5 UDP sing 417 n n C4 O4 UDP doub 418 n n C5 C6 UDP doub 419 n n C5 H5 UDP sing 420 n n C6 H6 UDP sing 421 n n C1' C2' UDP sing 422 n n C1' O4' UDP sing 423 n n C1' H1' UDP sing 424 n n C2' O2' UDP sing 425 n n C2' C3' UDP sing 426 n n C2' H2' UDP sing 427 n n O2' HO2' UDP sing 428 n n C3' C4' UDP sing 429 n n C3' O3' UDP sing 430 n n C3' H3' UDP sing 431 n n C4' O4' UDP sing 432 n n C4' C5' UDP sing 433 n n C4' H4' UDP sing 434 n n O3' HO3' UDP sing 435 n n C5' O5' UDP sing 436 n n C5' "H5'1" UDP sing 437 n n C5' "H5'2" UDP sing 438 n n O5' PA UDP sing 439 n n PA O1A UDP doub 440 n n PA O2A UDP sing 441 n n PA O3A UDP sing 442 n n O2A HOA2 UDP sing 443 n n O3A PB UDP sing 444 n n PB O1B UDP doub 445 n n PB O2B UDP sing 446 n n PB O3B UDP sing 447 n n O2B HOB2 UDP sing 448 n n O3B HOB3 UDP sing 449 n n # _atom_sites.entry_id 7ZAY _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 NAG A 1 800 800 NAG NAG . E 5 UDP A 1 801 801 UDP UDP . # 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 UDP . . . E 5 112.256 136.399 115.323 1 85.78 ? N1 UDP 801 A 1 HETATM 2 C C2 UDP . . . E 5 113.031 137.002 114.351 1 84.91 ? C2 UDP 801 A 1 HETATM 3 N N3 UDP . . . E 5 112.546 138.197 113.88 1 87.12 ? N3 UDP 801 A 1 HETATM 4 C C4 UDP . . . E 5 111.386 138.833 114.276 1 86.84 ? C4 UDP 801 A 1 HETATM 5 C C5 UDP . . . E 5 110.639 138.146 115.284 1 85.62 ? C5 UDP 801 A 1 HETATM 6 C C6 UDP . . . E 5 111.087 136.974 115.766 1 85.21 ? C6 UDP 801 A 1 HETATM 7 O O2 UDP . . . E 5 114.074 136.516 113.936 1 83.83 ? O2 UDP 801 A 1 HETATM 8 O O4 UDP . . . E 5 111.073 139.916 113.758 1 87.75 ? O4 UDP 801 A 1 HETATM 9 C C1' UDP . . . E 5 112.722 135.115 115.869 1 89.04 ? C1' UDP 801 A 1 HETATM 10 C C2' UDP . . . E 5 113.983 135.238 116.72 1 87.86 ? C2' UDP 801 A 1 HETATM 11 O O2' UDP . . . E 5 115.141 135.135 115.9 1 84.98 ? O2' UDP 801 A 1 HETATM 12 C C3' UDP . . . E 5 113.83 134.035 117.65 1 91.43 ? C3' UDP 801 A 1 HETATM 13 C C4' UDP . . . E 5 112.32 133.981 117.881 1 89.46 ? C4' UDP 801 A 1 HETATM 14 O O4' UDP . . . E 5 111.717 134.601 116.721 1 91.97 ? O4' UDP 801 A 1 HETATM 15 O O3' UDP . . . E 5 114.296 132.833 117.046 1 92.91 ? O3' UDP 801 A 1 HETATM 16 C C5' UDP . . . E 5 111.836 134.67 119.132 1 83.46 ? C5' UDP 801 A 1 HETATM 17 O O5' UDP . . . E 5 110.659 135.442 118.814 1 83.7 ? O5' UDP 801 A 1 HETATM 18 P PA UDP . . . E 5 109.224 134.983 119.289 1 88.16 ? PA UDP 801 A 1 HETATM 19 O O1A UDP . . . E 5 108.364 134.555 118.103 1 87.17 ? O1A UDP 801 A 1 HETATM 20 O O2A UDP . . . E 5 108.69 136.06 120.156 1 83.08 ? O2A UDP 801 A 1 HETATM 21 O O3A UDP . . . E 5 109.487 133.674 120.141 1 89.72 ? O3A UDP 801 A 1 HETATM 22 P PB UDP . . . E 5 109.425 133.63 121.723 1 95.89 ? PB UDP 801 A 1 HETATM 23 O O1B UDP . . . E 5 109.79 132.179 122.042 1 87 ? O1B UDP 801 A 1 HETATM 24 O O2B UDP . . . E 5 110.567 134.556 122.139 1 85.98 ? O2B UDP 801 A 1 HETATM 25 O O3B UDP . . . E 5 108.089 134.047 122.244 1 88.9 ? O3B UDP 801 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #