data_5L26 # _model_server_result.job_id CZLsmZPSOqzd1VyJATeZ3w _model_server_result.datetime_utc '2024-10-19 14:17:12' _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 5l26 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":503}' # _entry.id 5L26 # _exptl.entry_id 5L26 _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 3 _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 5L26 _cell.length_a 115.22 _cell.length_b 115.22 _cell.length_c 264.028 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L26 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,M,N,O,P,Q,R,S,T,U _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 M N N ? 3 Q 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 O ASN 155 A ASN 149 1_555 I NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc2 A OD1 ASN 155 A ASN 149 1_555 I NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 I NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 I NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc5 A O VAL 190 A VAL 184 1_555 I NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc6 I NA NA . A NA 506 1_555 S O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc7 B O ASN 155 B ASN 149 1_555 N NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc8 B OD1 ASN 155 B ASN 149 1_555 N NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc9 B O VAL 158 B VAL 152 1_555 N NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc10 B OG SER 189 B SER 183 1_555 N NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc11 B O VAL 190 B VAL 184 1_555 N NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc12 N NA NA . B NA 505 1_555 T O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc13 C O ASN 155 C ASN 149 1_555 R NA NA . C NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc14 C OD1 ASN 155 C ASN 149 1_555 R NA NA . C NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc15 C O VAL 158 C VAL 152 1_555 R NA NA . C NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc16 C OG SER 189 C SER 183 1_555 R NA NA . C NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc17 C O VAL 190 C VAL 184 1_555 R NA NA . C NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc18 R NA NA . C NA 504 1_555 U O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? # _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 506 n n N1 C6 URI sing 507 n n N1 C1' URI sing 508 n n C2 N3 URI sing 509 n n C2 O2 URI doub 510 n n N3 C4 URI sing 511 n n N3 H3 URI sing 512 n n C4 C5 URI sing 513 n n C4 O4 URI doub 514 n n C5 C6 URI doub 515 n n C5 H5 URI sing 516 n n C6 H6 URI sing 517 n n C1' C2' URI sing 518 n n C1' O4' URI sing 519 n n C1' H1' URI sing 520 n n C2' C3' URI sing 521 n n C2' O2' URI sing 522 n n C2' H2' URI sing 523 n n C3' C4' URI sing 524 n n C3' O3' URI sing 525 n n C3' H3' URI sing 526 n n C4' O4' URI sing 527 n n C4' C5' URI sing 528 n n C4' H4' URI sing 529 n n O2' HO2' URI sing 530 n n O3' HO3' URI sing 531 n n C5' O5' URI sing 532 n n C5' "H5'1" URI sing 533 n n C5' "H5'2" URI sing 534 n n O5' HO5' URI sing 535 n n # _atom_sites.entry_id 5L26 _atom_sites.fract_transf_matrix[1][1] 0.008679 _atom_sites.fract_transf_matrix[1][2] 0.005011 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010022 _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] 0.003787 _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 2 6ZL A 1 501 7 6ZL 6ZL . E 2 6ZL A 1 502 10 6ZL 6ZL . F 2 6ZL A 1 503 12 6ZL 6ZL . G 2 6ZL A 1 504 13 6ZL 6ZL . H 3 URI A 1 505 419 URI URI . I 4 NA A 1 506 1 NA NA . J 2 6ZL B 1 501 4 6ZL 6ZL . K 2 6ZL B 1 502 9 6ZL 6ZL . L 2 6ZL B 1 503 11 6ZL 6ZL . M 3 URI B 1 504 421 URI URI . N 4 NA B 1 505 3 NA NA . O 2 6ZL C 1 501 14 6ZL 6ZL . P 2 6ZL C 1 502 15 6ZL 6ZL . Q 3 URI C 1 503 420 URI URI . R 4 NA C 1 504 2 NA NA . S 5 HOH A 1 601 7 HOH HOH . T 5 HOH B 1 601 8 HOH HOH . U 5 HOH C 1 601 6 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 . . . Q 3 -116.754 54.245 10.317 1 70.66 ? N1 URI 503 C 1 HETATM 2 C C2 URI . . . Q 3 -117.331 54.527 11.541 1 79.58 ? C2 URI 503 C 1 HETATM 3 N N3 URI . . . Q 3 -118.389 55.401 11.499 1 83.39 ? N3 URI 503 C 1 HETATM 4 C C4 URI . . . Q 3 -118.918 56.01 10.38 1 83.39 ? C4 URI 503 C 1 HETATM 5 C C5 URI . . . Q 3 -118.267 55.669 9.152 1 69.35 ? C5 URI 503 C 1 HETATM 6 C C6 URI . . . Q 3 -117.233 54.821 9.163 1 66.37 ? C6 URI 503 C 1 HETATM 7 O O2 URI . . . Q 3 -116.937 54.04 12.587 1 85.23 ? O2 URI 503 C 1 HETATM 8 O O4 URI . . . Q 3 -119.876 56.775 10.503 1 91.59 ? O4 URI 503 C 1 HETATM 9 C C1' URI . . . Q 3 -115.605 53.311 10.297 1 75 ? C1' URI 503 C 1 HETATM 10 C C2' URI . . . Q 3 -116.045 51.847 10.363 1 80.01 ? C2' URI 503 C 1 HETATM 11 C C3' URI . . . Q 3 -116.069 51.474 8.886 1 73.35 ? C3' URI 503 C 1 HETATM 12 C C4' URI . . . Q 3 -114.893 52.257 8.326 1 67.43 ? C4' URI 503 C 1 HETATM 13 O O2' URI . . . Q 3 -115.045 51.111 11.053 1 78.86 ? O2' URI 503 C 1 HETATM 14 O O3' URI . . . Q 3 -115.972 50.08 8.647 1 74.02 ? O3' URI 503 C 1 HETATM 15 O O4' URI . . . Q 3 -114.898 53.492 9.088 1 73.89 ? O4' URI 503 C 1 HETATM 16 C C5' URI . . . Q 3 -114.952 52.568 6.852 1 67.17 ? C5' URI 503 C 1 HETATM 17 O O5' URI . . . Q 3 -116.169 53.215 6.507 1 71.9 ? O5' URI 503 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #