data_7VTE # _model_server_result.job_id 5Sd8Tn9XyT8giJoXotyXFg _model_server_result.datetime_utc '2024-12-06 09:50:19' _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 7vte # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":402}' # _entry.id 7VTE # _exptl.entry_id 7VTE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE _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 120 _cell.entry_id 7VTE _cell.length_a 185.689 _cell.length_b 185.689 _cell.length_c 50.754 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VTE _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall 'P 3' _symmetry.space_group_name_H-M 'P 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 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 F N N ? 3 H N N ? 3 J N N ? 3 L N 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 metalc ? metalc1 A OD1 ASN 250 A ASN 250 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc2 A O THR 252 A THR 252 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc3 A O ALA 286 A ALA 286 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc4 A O CYS 289 A CYS 289 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc5 A O TYR 291 A TYR 291 1_555 E K K . A K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc6 B O ASN 250 B ASN 250 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc7 B OD1 ASN 250 B ASN 250 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc8 B O THR 252 B THR 252 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc9 B O ALA 286 B ALA 286 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc10 B O CYS 289 B CYS 289 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc11 B O TYR 291 B TYR 291 1_555 G K K . B K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.01 ? metalc ? metalc12 C OD1 ASN 250 C ASN 250 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc13 C O THR 252 C THR 252 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc14 C O ALA 286 C ALA 286 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc15 C O CYS 289 C CYS 289 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.226 ? metalc ? metalc16 C O TYR 291 C TYR 291 1_555 I K K . C K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc17 D OD1 ASN 250 D ASN 250 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc18 D O THR 252 D THR 252 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc19 D O ALA 286 D ALA 286 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc20 D O CYS 289 D CYS 289 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.188 ? metalc ? metalc21 D O TYR 291 D TYR 291 1_555 K K K . D K 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? # _chem_comp.formula 'C9 H12 N2 O6' _chem_comp.formula_weight 244.201 _chem_comp.id URI _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE _chem_comp.type non-polymer _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 URI sing 358 n n N1 C6 URI sing 359 n n N1 C1' URI sing 360 n n C2 N3 URI sing 361 n n C2 O2 URI doub 362 n n N3 C4 URI sing 363 n n N3 H3 URI sing 364 n n C4 C5 URI sing 365 n n C4 O4 URI doub 366 n n C5 C6 URI doub 367 n n C5 H5 URI sing 368 n n C6 H6 URI sing 369 n n C1' C2' URI sing 370 n n C1' O4' URI sing 371 n n C1' H1' URI sing 372 n n C2' C3' URI sing 373 n n C2' O2' URI sing 374 n n C2' H2' URI sing 375 n n C3' C4' URI sing 376 n n C3' O3' URI sing 377 n n C3' H3' URI sing 378 n n C4' O4' URI sing 379 n n C4' C5' URI sing 380 n n C4' H4' URI sing 381 n n O2' HO2' URI sing 382 n n O3' HO3' URI sing 383 n n C5' O5' URI sing 384 n n C5' "H5'1" URI sing 385 n n C5' "H5'2" URI sing 386 n n O5' HO5' URI sing 387 n n # _atom_sites.entry_id 7VTE _atom_sites.fract_transf_matrix[1][1] 0.005385 _atom_sites.fract_transf_matrix[1][2] 0.003109 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006218 _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] 0.019703 _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 2 K A 1 401 403 K K . F 3 URI A 1 402 402 URI URI . G 2 K B 1 401 403 K K . H 3 URI B 1 402 402 URI URI . I 2 K C 1 401 403 K K . J 3 URI C 1 402 402 URI URI . K 2 K D 1 401 403 K K . L 3 URI D 1 402 402 URI URI . M 4 HOH A 1 501 10 HOH HOH . M 4 HOH A 2 502 31 HOH HOH . M 4 HOH A 3 503 1 HOH HOH . M 4 HOH A 4 504 11 HOH HOH . M 4 HOH A 5 505 20 HOH HOH . M 4 HOH A 6 506 21 HOH HOH . M 4 HOH A 7 507 6 HOH HOH . M 4 HOH A 8 508 15 HOH HOH . M 4 HOH A 9 509 33 HOH HOH . M 4 HOH A 10 510 18 HOH HOH . M 4 HOH A 11 511 29 HOH HOH . N 4 HOH B 1 501 14 HOH HOH . N 4 HOH B 2 502 9 HOH HOH . N 4 HOH B 3 503 37 HOH HOH . N 4 HOH B 4 504 26 HOH HOH . N 4 HOH B 5 505 5 HOH HOH . N 4 HOH B 6 506 22 HOH HOH . N 4 HOH B 7 507 7 HOH HOH . N 4 HOH B 8 508 24 HOH HOH . O 4 HOH C 1 501 23 HOH HOH . O 4 HOH C 2 502 36 HOH HOH . O 4 HOH C 3 503 25 HOH HOH . O 4 HOH C 4 504 32 HOH HOH . O 4 HOH C 5 505 16 HOH HOH . O 4 HOH C 6 506 4 HOH HOH . O 4 HOH C 7 507 12 HOH HOH . O 4 HOH C 8 508 3 HOH HOH . O 4 HOH C 9 509 27 HOH HOH . O 4 HOH C 10 510 34 HOH HOH . P 4 HOH D 1 501 38 HOH HOH . P 4 HOH D 2 502 19 HOH HOH . P 4 HOH D 3 503 13 HOH HOH . P 4 HOH D 4 504 2 HOH HOH . P 4 HOH D 5 505 30 HOH HOH . P 4 HOH D 6 506 17 HOH HOH . P 4 HOH D 7 507 8 HOH HOH . P 4 HOH D 8 508 28 HOH HOH . P 4 HOH D 9 509 35 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 N N1 URI . . . H 3 106.765 -24.423 5.025 1 113.5 ? N1 URI 402 B 1 HETATM 2 C C2 URI . . . H 3 107.723 -23.734 4.3 1 109.91 ? C2 URI 402 B 1 HETATM 3 N N3 URI . . . H 3 108.399 -24.465 3.351 1 111.27 ? N3 URI 402 B 1 HETATM 4 C C4 URI . . . H 3 108.207 -25.8 3.054 1 111.21 ? C4 URI 402 B 1 HETATM 5 C C5 URI . . . H 3 107.186 -26.441 3.839 1 119.32 ? C5 URI 402 B 1 HETATM 6 C C6 URI . . . H 3 106.512 -25.756 4.773 1 119.97 ? C6 URI 402 B 1 HETATM 7 O O2 URI . . . H 3 107.962 -22.554 4.495 1 103.34 ? O2 URI 402 B 1 HETATM 8 O O4 URI . . . H 3 108.893 -26.319 2.164 1 100.44 ? O4 URI 402 B 1 HETATM 9 C C1' URI . . . H 3 106.025 -23.648 6.039 1 97.62 ? C1' URI 402 B 1 HETATM 10 C C2' URI . . . H 3 104.546 -24.015 6.15 1 92.48 ? C2' URI 402 B 1 HETATM 11 C C3' URI . . . H 3 104.223 -23.642 7.599 1 90.32 ? C3' URI 402 B 1 HETATM 12 C C4' URI . . . H 3 105.557 -23.836 8.331 1 98.5 ? C4' URI 402 B 1 HETATM 13 O O2' URI . . . H 3 103.788 -23.295 5.199 1 65.06 ? O2' URI 402 B 1 HETATM 14 O O3' URI . . . H 3 103.843 -22.267 7.644 1 75.8 ? O3' URI 402 B 1 HETATM 15 O O4' URI . . . H 3 106.589 -23.897 7.309 1 86.01 ? O4' URI 402 B 1 HETATM 16 C C5' URI . . . H 3 105.665 -25.056 9.213 1 107.8 ? C5' URI 402 B 1 HETATM 17 O O5' URI . . . H 3 106.816 -24.987 10.052 1 115.13 ? O5' URI 402 B 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 675 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #