data_7SCK # _model_server_result.job_id M1apiPo7RKz7RWf1UJrKkw _model_server_result.datetime_utc '2025-03-09 02:35:12' _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 7sck # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 7SCK # _exptl.entry_id 7SCK _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 2 _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 7SCK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7SCK _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,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 G N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 3 ? 4 2 1 BDP NDG C1 O1 . O4 HO4 . sing 4 ? 4 3 2 NDG BDP C1 O1 . O4 HO4 . sing 5 ? 4 4 3 BDP NDG 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 801 NAG 3 n C NAG 2 C 2 NAG B 802 NAG 3 n C BMA 3 C 3 BMA B 803 BMA 4 n D NDG 1 D 1 NDG B 1104 NDG 4 n D BDP 2 D 2 BDP B 1103 BDP 4 n D NDG 3 D 3 NDG B 1102 NDG 4 n D BDP 4 D 4 BDP B 1101 BDP # 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 72 A CYS 98 1_555 A SG CYS 77 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 83 A CYS 109 1_555 A SG CYS 126 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 272 A CYS 298 1_555 A SG CYS 286 A CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 308 A CYS 334 1_555 A SG CYS 329 A CYS 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 626 A CYS 652 1_555 A SG CYS 678 A CYS 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 41 B CYS 85 1_555 B SG CYS 46 B CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 52 B CYS 96 1_555 B SG CYS 107 B CYS 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 B SG CYS 274 B CYS 318 1_555 B SG CYS 295 B CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 582 B CYS 626 1_555 B SG CYS 632 B CYS 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 304 A ASN 330 1_555 F C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 B ND2 ASN 593 B ASN 637 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 D O4 NDG . D NDG 1 1_555 D C1 BDP . D BDP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 D O4 BDP . D BDP 2 1_555 D C1 NDG . D NDG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 D O4 NDG . D NDG 3 1_555 D C1 BDP . D BDP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 B OD2 ASP 496 B ASP 540 1_555 H MN MN . B MN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc2 G PA UDP . B UDP 901 1_555 H MN MN . B MN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc3 G O1A UDP . B UDP 901 1_555 H MN MN . B MN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc4 G O2A UDP . B UDP 901 1_555 H MN MN . B MN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.744 ? # _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 463 n n N1 C6 UDP sing 464 n n N1 C1' UDP sing 465 n n C2 N3 UDP sing 466 n n C2 O2 UDP doub 467 n n N3 C4 UDP sing 468 n n N3 HN3 UDP sing 469 n n C4 C5 UDP sing 470 n n C4 O4 UDP doub 471 n n C5 C6 UDP doub 472 n n C5 H5 UDP sing 473 n n C6 H6 UDP sing 474 n n C1' C2' UDP sing 475 n n C1' O4' UDP sing 476 n n C1' H1' UDP sing 477 n n C2' O2' UDP sing 478 n n C2' C3' UDP sing 479 n n C2' H2' UDP sing 480 n n O2' HO2' UDP sing 481 n n C3' C4' UDP sing 482 n n C3' O3' UDP sing 483 n n C3' H3' UDP sing 484 n n C4' O4' UDP sing 485 n n C4' C5' UDP sing 486 n n C4' H4' UDP sing 487 n n O3' HO3' UDP sing 488 n n C5' O5' UDP sing 489 n n C5' "H5'1" UDP sing 490 n n C5' "H5'2" UDP sing 491 n n O5' PA UDP sing 492 n n PA O1A UDP doub 493 n n PA O2A UDP sing 494 n n PA O3A UDP sing 495 n n O2A HOA2 UDP sing 496 n n O3A PB UDP sing 497 n n PB O1B UDP doub 498 n n PB O2B UDP sing 499 n n PB O3B UDP sing 500 n n O2B HOB2 UDP sing 501 n n O3B HOB3 UDP sing 502 n n # _atom_sites.entry_id 7SCK _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 E 5 UDP A 1 801 801 UDP UDP . F 6 NAG A 1 802 901 NAG NAG . G 5 UDP B 1 901 901 UDP UDP . H 7 MN B 1 902 1001 MN MN . # 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 5 131.979 121.916 105.1 1 59.34 ? N1 UDP 801 A 1 HETATM 2 C C2 UDP . . . E 5 132.012 122.476 103.84 1 59.34 ? C2 UDP 801 A 1 HETATM 3 N N3 UDP . . . E 5 133.105 122.14 103.085 1 59.34 ? N3 UDP 801 A 1 HETATM 4 C C4 UDP . . . E 5 134.148 121.317 103.46 1 59.34 ? C4 UDP 801 A 1 HETATM 5 C C5 UDP . . . E 5 134.041 120.779 104.779 1 59.34 ? C5 UDP 801 A 1 HETATM 6 C C6 UDP . . . E 5 132.981 121.086 105.542 1 59.34 ? C6 UDP 801 A 1 HETATM 7 O O2 UDP . . . E 5 131.135 123.216 103.418 1 59.34 ? O2 UDP 801 A 1 HETATM 8 O O4 UDP . . . E 5 135.077 121.104 102.666 1 59.34 ? O4 UDP 801 A 1 HETATM 9 C C1' UDP . . . E 5 130.831 122.236 105.959 1 59.34 ? C1' UDP 801 A 1 HETATM 10 C C2' UDP . . . E 5 129.737 121.178 105.921 1 59.34 ? C2' UDP 801 A 1 HETATM 11 O O2' UDP . . . E 5 128.841 121.45 104.85 1 59.34 ? O2' UDP 801 A 1 HETATM 12 C C3' UDP . . . E 5 129.076 121.389 107.282 1 59.34 ? C3' UDP 801 A 1 HETATM 13 C C4' UDP . . . E 5 130.255 121.77 108.176 1 59.34 ? C4' UDP 801 A 1 HETATM 14 O O4' UDP . . . E 5 131.278 122.285 107.295 1 59.34 ? O4' UDP 801 A 1 HETATM 15 O O3' UDP . . . E 5 128.119 122.441 107.237 1 59.34 ? O3' UDP 801 A 1 HETATM 16 C C5' UDP . . . E 5 130.831 120.654 109.008 1 59.34 ? C5' UDP 801 A 1 HETATM 17 O O5' UDP . . . E 5 132.192 120.45 108.583 1 59.34 ? O5' UDP 801 A 1 HETATM 18 P PA UDP . . . E 5 133.406 120.816 109.52 1 59.34 ? PA UDP 801 A 1 HETATM 19 O O1A UDP . . . E 5 133.742 122.235 109.259 1 59.34 ? O1A UDP 801 A 1 HETATM 20 O O2A UDP . . . E 5 134.533 119.8 109.379 1 59.34 ? O2A UDP 801 A 1 HETATM 21 O O3A UDP . . . E 5 132.843 120.649 110.982 1 59.34 ? O3A UDP 801 A 1 HETATM 22 P PB UDP . . . E 5 132.91 119.284 111.78 1 59.34 ? PB UDP 801 A 1 HETATM 23 O O1B UDP . . . E 5 132.426 118.263 110.754 1 59.34 ? O1B UDP 801 A 1 HETATM 24 O O2B UDP . . . E 5 134.408 119.104 112.029 1 59.34 ? O2B UDP 801 A 1 HETATM 25 O O3B UDP . . . E 5 132.093 119.321 113.021 1 59.34 ? O3B UDP 801 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #