data_6PFB # _model_server_result.job_id zFZztWaGQtToIJE-oEzNBA _model_server_result.datetime_utc '2024-11-25 08:28:13' _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 6pfb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":602}' # _entry.id 6PFB # _exptl.entry_id 6PFB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 326.172 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.75 _cell.angle_gamma 90 _cell.entry_id 6PFB _cell.length_a 213.994 _cell.length_b 116.238 _cell.length_c 221.672 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PFB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,F,G,H,I,J,K,L,M 1 1 C,D,N,O,P,Q,R,S,T,U 2 1 E,V,W,X,Y 3 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_658 -x+1,y,-z+3 -1 0 0 0 1 0 0 0 -1 158.925217 0 662.732004 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 K N N ? 3 O N N ? 3 S N N ? 3 W N N # _chem_comp.formula 'C9 H12 F N2 O8 P' _chem_comp.formula_weight 326.172 _chem_comp.id UFP _chem_comp.mon_nstd_flag . _chem_comp.name "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna 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 UFP sing 551 n n N1 C6 UFP sing 552 n n N1 C1' UFP sing 553 n n C2 N3 UFP sing 554 n n C2 O2 UFP doub 555 n n N3 C4 UFP sing 556 n n N3 HN3 UFP sing 557 n n C4 C5 UFP sing 558 n n C4 O4 UFP doub 559 n n C5 C6 UFP doub 560 n n C5 F5 UFP sing 561 n n C6 H6 UFP sing 562 n n C1' C2' UFP sing 563 n n C1' O4' UFP sing 564 n n C1' H1' UFP sing 565 n n C2' C3' UFP sing 566 n n C2' "H2'1" UFP sing 567 n n C2' "H2'2" UFP sing 568 n n C3' C4' UFP sing 569 n n C3' O3' UFP sing 570 n n C3' H3' UFP sing 571 n n C4' O4' UFP sing 572 n n C4' C5' UFP sing 573 n n C4' H4' UFP sing 574 n n O3' HO3' UFP sing 575 n n C5' O5' UFP sing 576 n n C5' "H5'1" UFP sing 577 n n C5' "H5'2" UFP sing 578 n n O5' P UFP sing 579 n n P O1P UFP doub 580 n n P O2P UFP sing 581 n n P O3P UFP sing 582 n n O2P HOP2 UFP sing 583 n n O3P HOP3 UFP sing 584 n n # _atom_sites.entry_id 6PFB _atom_sites.fract_transf_matrix[1][1] 0.004673 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000389 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008603 _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] 0.004527 _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 F 2 NDP A 1 601 601 NDP NDP . G 3 UFP A 1 602 602 UFP UFP . H 4 OG4 A 1 603 603 OG4 TS7 . I 5 MTX A 1 604 604 MTX MTX . J 2 NDP B 1 601 601 NDP NDP . K 3 UFP B 1 602 602 UFP UFP . L 4 OG4 B 1 603 603 OG4 TS7 . M 5 MTX B 1 604 604 MTX MTX . N 2 NDP C 1 601 601 NDP NDP . O 3 UFP C 1 602 602 UFP UFP . P 4 OG4 C 1 603 603 OG4 TS7 . Q 5 MTX C 1 604 604 MTX MTX . R 2 NDP D 1 601 601 NDP NDP . S 3 UFP D 1 602 602 UFP UFP . T 4 OG4 D 1 603 603 OG4 TS7 . U 5 MTX D 1 604 604 MTX MTX . V 2 NDP E 1 601 601 NDP NDP . W 3 UFP E 1 602 602 UFP UFP . X 4 OG4 E 1 603 603 OG4 TS7 . Y 5 MTX E 1 604 604 MTX MTX . # 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 UFP . . . S 3 58.263 51.675 264.298 1 96.93 ? N1 UFP 602 D 1 HETATM 2 C C2 UFP . . . S 3 58.496 52.441 265.403 1 102 ? C2 UFP 602 D 1 HETATM 3 N N3 UFP . . . S 3 59.634 52.289 266.112 1 111.82 ? N3 UFP 602 D 1 HETATM 4 C C4 UFP . . . S 3 60.568 51.383 265.758 1 112.97 ? C4 UFP 602 D 1 HETATM 5 C C5 UFP . . . S 3 60.341 50.578 264.618 1 100.56 ? C5 UFP 602 D 1 HETATM 6 C C6 UFP . . . S 3 59.198 50.743 263.927 1 89.23 ? C6 UFP 602 D 1 HETATM 7 O O2 UFP . . . S 3 57.72 53.288 265.812 1 96.53 ? O2 UFP 602 D 1 HETATM 8 O O4 UFP . . . S 3 61.59 51.258 266.408 1 113.68 ? O4 UFP 602 D 1 HETATM 9 F F5 UFP . . . S 3 61.252 49.656 264.226 1 106.32 ? F5 UFP 602 D 1 HETATM 10 C C1' UFP . . . S 3 57.067 51.723 263.423 1 105.55 ? C1' UFP 602 D 1 HETATM 11 C C2' UFP . . . S 3 56.566 53.128 263.015 1 100.44 ? C2' UFP 602 D 1 HETATM 12 C C3' UFP . . . S 3 55.668 52.743 261.829 1 82.73 ? C3' UFP 602 D 1 HETATM 13 C C4' UFP . . . S 3 56.557 51.716 261.107 1 87.74 ? C4' UFP 602 D 1 HETATM 14 O O3' UFP . . . S 3 54.477 52.102 262.284 1 84.06 ? O3' UFP 602 D 1 HETATM 15 O O4' UFP . . . S 3 57.387 51.117 262.143 1 109.32 ? O4' UFP 602 D 1 HETATM 16 C C5' UFP . . . S 3 57.421 52.401 260.044 1 85.56 ? C5' UFP 602 D 1 HETATM 17 O O5' UFP . . . S 3 56.754 52.346 258.781 1 78.87 ? O5' UFP 602 D 1 HETATM 18 P P UFP . . . S 3 57.148 53.672 257.958 1 95.15 ? P UFP 602 D 1 HETATM 19 O O1P UFP . . . S 3 56.037 54.04 257.052 1 95.59 ? O1P UFP 602 D 1 HETATM 20 O O2P UFP . . . S 3 58.47 53.391 257.088 1 75.89 ? O2P UFP 602 D 1 HETATM 21 O O3P UFP . . . S 3 57.427 54.876 258.986 1 61.99 ? O3P UFP 602 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #