data_8APF # _model_server_result.job_id bv380g_3vBOvRaO1-fy_iA _model_server_result.datetime_utc '2024-11-15 07:58:29' _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 8apf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"PB","auth_seq_id":401}' # _entry.id 8APF # _exptl.entry_id 8APF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 484.141 _entity.id 31 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _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 8APF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8APF _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 42-meric _pdbx_struct_assembly.oligomeric_count 42 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB _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 31 _struct_asym.id PB _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 V C AME 1 e AME 1 1_555 V N GLN 2 e GLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 KA OG1 THR 213 A1 THR 213 1_555 RB MG MG . A1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 QB O2G ATP . A1 ATP 601 1_555 RB MG MG . A1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc3 QB O2B ATP . A1 ATP 601 1_555 RB MG MG . A1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc4 LA OG1 THR 213 B1 THR 213 1_555 TB MG MG . B1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc5 SB O2G ATP . B1 ATP 601 1_555 TB MG MG . B1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc6 SB O2B ATP . B1 ATP 601 1_555 TB MG MG . B1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc7 MA OG1 THR 213 C1 THR 213 1_555 VB MG MG . C1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc8 UB O2G ATP . C1 ATP 601 1_555 VB MG MG . C1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc9 UB O2B ATP . C1 ATP 601 1_555 VB MG MG . C1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc10 NA OG1 THR 190 D1 THR 190 1_555 XB MG MG . D1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc11 NA OE2 GLU 215 D1 GLU 215 1_555 XB MG MG . D1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc12 WB O2G ATP . D1 ATP 601 1_555 XB MG MG . D1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc13 WB O2B ATP . D1 ATP 601 1_555 XB MG MG . D1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc14 OA OG1 THR 190 E1 THR 190 1_555 ZB MG MG . E1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc15 YB O3B ADP . E1 ADP 601 1_555 ZB MG MG . E1 MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 8APF _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 QA 26 CDL L 1 101 12 CDL CDL . RA 26 CDL M 1 201 1 CDL CDL . SA 27 PEE M 1 202 2 PEE PEE . TA 26 CDL c 1 201 3 CDL CDL . UA 26 CDL e 1 401 2 CDL CDL . VA 26 CDL e 1 402 5 CDL CDL . WA 26 CDL e 1 403 7 CDL CDL . XA 26 CDL e 1 404 10 CDL CDL . YA 26 CDL e 1 405 11 CDL CDL . ZA 28 LMT e 1 406 1 LMT LMT . AB 29 Q7G e 1 407 2 Q7G GD0 . BB 26 CDL f 1 201 9 CDL CDL . CB 27 PEE f 1 202 1 PEE PEE . DB 30 PC1 f 1 203 2 PC1 PC1 . EB 30 PC1 i 1 201 4 PC1 PC1 . FB 26 CDL j 1 201 4 CDL CDL . GB 30 PC1 j 1 202 3 PC1 PC1 . HB 28 LMT j 1 203 2 LMT LMT . IB 26 CDL l 1 101 12 CDL CDL . JB 27 PEE m 1 201 2 PEE PEE . KB 26 CDL m 1 202 1 CDL CDL . LB 29 Q7G n 1 201 1 Q7G GD0 . MB 30 PC1 p 1 201 1 PC1 PC1 . NB 26 CDL q 1 101 6 CDL CDL . OB 26 CDL q 1 102 8 CDL CDL . PB 31 UTP G1 1 401 1 UTP UTP . QB 32 ATP A1 1 601 5 ATP ATP . RB 33 MG A1 1 602 6 MG MG . SB 32 ATP B1 1 601 1 ATP ATP . TB 33 MG B1 1 602 2 MG MG . UB 32 ATP C1 1 601 3 ATP ATP . VB 33 MG C1 1 602 4 MG MG . WB 32 ATP D1 1 601 7 ATP ATP . XB 33 MG D1 1 602 8 MG MG . YB 34 ADP E1 1 601 1 ADP ADP . ZB 33 MG E1 1 602 2 MG MG . # 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 P PA UTP . . . PB 31 301.194 215.11 200.88 1 131.19 ? PA UTP 401 G1 1 HETATM 2 O O1A UTP . . . PB 31 300.186 215.05 199.802 1 131.19 ? O1A UTP 401 G1 1 HETATM 3 O O2A UTP . . . PB 31 301.14 216.371 201.741 1 131.19 ? O2A UTP 401 G1 1 HETATM 4 O O3A UTP . . . PB 31 302.674 215.004 200.303 1 131.19 ? O3A UTP 401 G1 1 HETATM 5 O O5' UTP . . . PB 31 301.053 213.862 201.882 1 131.19 ? O5' UTP 401 G1 1 HETATM 6 P PB UTP . . . PB 31 303.824 216.069 200.023 1 131.19 ? PB UTP 401 G1 1 HETATM 7 O O1B UTP . . . PB 31 304.16 216.733 201.356 1 131.19 ? O1B UTP 401 G1 1 HETATM 8 O O2B UTP . . . PB 31 303.474 216.98 198.916 1 131.19 ? O2B UTP 401 G1 1 HETATM 9 O O3B UTP . . . PB 31 305.052 215.13 199.645 1 131.19 ? O3B UTP 401 G1 1 HETATM 10 P PG UTP . . . PB 31 306.627 215.378 199.59 1 131.19 ? PG UTP 401 G1 1 HETATM 11 O O1G UTP . . . PB 31 307.226 213.992 199.336 1 131.19 ? O1G UTP 401 G1 1 HETATM 12 O O2G UTP . . . PB 31 306.975 216.377 198.544 1 131.19 ? O2G UTP 401 G1 1 HETATM 13 O O3G UTP . . . PB 31 306.995 215.825 201.008 1 131.19 ? O3G UTP 401 G1 1 HETATM 14 C C5' UTP . . . PB 31 300.812 212.496 201.483 1 131.19 ? C5' UTP 401 G1 1 HETATM 15 C C4' UTP . . . PB 31 301.911 211.628 202.041 1 131.19 ? C4' UTP 401 G1 1 HETATM 16 O O4' UTP . . . PB 31 301.578 210.235 201.838 1 131.19 ? O4' UTP 401 G1 1 HETATM 17 C C1' UTP . . . PB 31 302.548 209.618 201.012 1 131.19 ? C1' UTP 401 G1 1 HETATM 18 C C2' UTP . . . PB 31 303.301 210.749 200.316 1 131.19 ? C2' UTP 401 G1 1 HETATM 19 O O2' UTP . . . PB 31 304.626 210.346 199.985 1 131.19 ? O2' UTP 401 G1 1 HETATM 20 C C3' UTP . . . PB 31 303.285 211.825 201.402 1 131.19 ? C3' UTP 401 G1 1 HETATM 21 O O3' UTP . . . PB 31 304.325 211.628 202.354 1 131.19 ? O3' UTP 401 G1 1 HETATM 22 N N1 UTP . . . PB 31 301.858 208.713 200.081 1 131.19 ? N1 UTP 401 G1 1 HETATM 23 C C6 UTP . . . PB 31 300.543 208.924 199.731 1 131.19 ? C6 UTP 401 G1 1 HETATM 24 C C2 UTP . . . PB 31 302.571 207.643 199.582 1 131.19 ? C2 UTP 401 G1 1 HETATM 25 O O2 UTP . . . PB 31 303.742 207.434 199.868 1 131.19 ? O2 UTP 401 G1 1 HETATM 26 N N3 UTP . . . PB 31 301.871 206.823 198.731 1 131.19 ? N3 UTP 401 G1 1 HETATM 27 C C4 UTP . . . PB 31 300.556 206.967 198.338 1 131.19 ? C4 UTP 401 G1 1 HETATM 28 O O4 UTP . . . PB 31 300.054 206.141 197.562 1 131.19 ? O4 UTP 401 G1 1 HETATM 29 C C5 UTP . . . PB 31 299.884 208.103 198.894 1 131.19 ? C5 UTP 401 G1 1 HETATM 30 H "H5'1" UTP . . . PB 31 299.848 212.151 201.852 1 131.19 ? "H5'1" UTP 401 G1 1 HETATM 31 H "H5'2" UTP . . . PB 31 300.763 212.502 200.395 1 131.19 ? "H5'2" UTP 401 G1 1 HETATM 32 H H4' UTP . . . PB 31 301.953 211.732 203.124 1 131.19 ? H4' UTP 401 G1 1 HETATM 33 H H1' UTP . . . PB 31 303.186 209.022 201.664 1 131.19 ? H1' UTP 401 G1 1 HETATM 34 H H2' UTP . . . PB 31 302.886 211.1 199.372 1 131.19 ? H2' UTP 401 G1 1 HETATM 35 H HA UTP . . . PB 31 304.6 209.488 199.486 1 131.19 ? HA UTP 401 G1 1 HETATM 36 H H3' UTP . . . PB 31 303.39 212.811 200.953 1 131.19 ? H3' UTP 401 G1 1 HETATM 37 H HB UTP . . . PB 31 304.055 210.847 202.905 1 131.19 ? HB UTP 401 G1 1 HETATM 38 H H6 UTP . . . PB 31 300.049 209.793 200.163 1 131.19 ? H6 UTP 401 G1 1 HETATM 39 H H3 UTP . . . PB 31 302.382 206.028 198.361 1 131.19 ? H3 UTP 401 G1 1 HETATM 40 H H5 UTP . . . PB 31 298.844 208.266 198.615 1 131.19 ? H5 UTP 401 G1 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 47 _model_server_stats.create_model_time_ms 577 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 40 #