data_5Y07 # _model_server_result.job_id nL1ctapOTX_wFu8up7Ww8w _model_server_result.datetime_utc '2024-10-19 21:30:14' _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 5y07 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 5Y07 # _exptl.entry_id 5Y07 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.07 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _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 105.87 _cell.angle_gamma 90 _cell.entry_id 5Y07 _cell.length_a 48.301 _cell.length_b 86.292 _cell.length_c 48.553 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y07 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 F 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 THR 117 A THR 117 1_555 D NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc2 A O ILE 120 A ILE 120 1_555 D NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 C O1 PRP . A PRP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc4 C O2 PRP . A PRP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc5 C O3 PRP . A PRP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc6 C O2B PRP . A PRP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc7 D NA NA . A NA 202 1_555 I O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc8 D NA NA . A NA 202 1_555 I O HOH . A HOH 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc9 E MG MG . A MG 203 1_555 I O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc10 E MG MG . A MG 203 1_555 I O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc11 B O THR 117 B THR 117 1_555 G NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc12 B O ILE 120 B ILE 120 1_555 G NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc13 F O1 PRP . B PRP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc14 F O2 PRP . B PRP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc15 F O3 PRP . B PRP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc16 F O3B PRP . B PRP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc17 G NA NA . B NA 202 1_555 J O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc18 G NA NA . B NA 202 1_555 J O HOH . B HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc19 G NA NA . B NA 202 1_555 J O HOH . B HOH 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc20 H MG MG . B MG 203 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc21 H MG MG . B MG 203 1_555 J O HOH . B HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? # _chem_comp.formula 'C5 H13 O14 P3' _chem_comp.formula_weight 390.07 _chem_comp.id PRP _chem_comp.mon_nstd_flag n _chem_comp.name 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID;1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose;1-O-pyrophosphono-5-O-phosphono-D-ribose;1-O-pyrophosphono-5-O-phosphono-ribose' # 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 C1 C2 PRP sing 277 n n C1 O1 PRP sing 278 n n C1 O4 PRP sing 279 n n C1 H1 PRP sing 280 n n C2 C3 PRP sing 281 n n C2 O2 PRP sing 282 n n C2 H2 PRP sing 283 n n C3 C4 PRP sing 284 n n C3 O3 PRP sing 285 n n C3 H3 PRP sing 286 n n C4 C5 PRP sing 287 n n C4 O4 PRP sing 288 n n C4 H4 PRP sing 289 n n C5 O5 PRP sing 290 n n C5 H51 PRP sing 291 n n C5 H52 PRP sing 292 n n O1 PA PRP sing 293 n n O2 HO2 PRP sing 294 n n O3 HO3 PRP sing 295 n n O5 P PRP sing 296 n n P O1P PRP doub 297 n n P O2P PRP sing 298 n n P O3P PRP sing 299 n n O2P HOP2 PRP sing 300 n n O3P HOP3 PRP sing 301 n n PA O1A PRP doub 302 n n PA O2A PRP sing 303 n n PA O3A PRP sing 304 n n O2A HOA2 PRP sing 305 n n O3A PB PRP sing 306 n n PB O1B PRP doub 307 n n PB O2B PRP sing 308 n n PB O3B PRP sing 309 n n O2B HOB2 PRP sing 310 n n O3B HOB3 PRP sing 311 n n # _pdbx_chem_comp_identifier.comp_id PRP _pdbx_chem_comp_identifier.identifier a-D-Ribf1PO35PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 5Y07 _atom_sites.fract_transf_matrix[1][1] 0.020704 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005884 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011589 _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] 0.021412 _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 C 2 PRP A 1 201 201 PRP PRP . D 3 NA A 1 202 202 NA NA . E 4 MG A 1 203 203 MG MG . F 2 PRP B 1 201 201 PRP PRP . G 3 NA B 1 202 202 NA NA . H 4 MG B 1 203 203 MG MG . I 5 HOH A 1 301 32 HOH HOH . I 5 HOH A 2 302 52 HOH HOH . I 5 HOH A 3 303 31 HOH HOH . I 5 HOH A 4 304 67 HOH HOH . I 5 HOH A 5 305 70 HOH HOH . I 5 HOH A 6 306 61 HOH HOH . I 5 HOH A 7 307 49 HOH HOH . I 5 HOH A 8 308 23 HOH HOH . I 5 HOH A 9 309 44 HOH HOH . I 5 HOH A 10 310 7 HOH HOH . I 5 HOH A 11 311 14 HOH HOH . I 5 HOH A 12 312 21 HOH HOH . I 5 HOH A 13 313 41 HOH HOH . I 5 HOH A 14 314 64 HOH HOH . I 5 HOH A 15 315 45 HOH HOH . I 5 HOH A 16 316 54 HOH HOH . I 5 HOH A 17 317 39 HOH HOH . I 5 HOH A 18 318 4 HOH HOH . I 5 HOH A 19 319 28 HOH HOH . I 5 HOH A 20 320 62 HOH HOH . I 5 HOH A 21 321 5 HOH HOH . I 5 HOH A 22 322 33 HOH HOH . I 5 HOH A 23 323 15 HOH HOH . I 5 HOH A 24 324 38 HOH HOH . I 5 HOH A 25 325 36 HOH HOH . I 5 HOH A 26 326 19 HOH HOH . I 5 HOH A 27 327 26 HOH HOH . I 5 HOH A 28 328 29 HOH HOH . I 5 HOH A 29 329 71 HOH HOH . I 5 HOH A 30 330 65 HOH HOH . I 5 HOH A 31 331 57 HOH HOH . I 5 HOH A 32 332 10 HOH HOH . I 5 HOH A 33 333 11 HOH HOH . I 5 HOH A 34 334 34 HOH HOH . I 5 HOH A 35 335 50 HOH HOH . I 5 HOH A 36 336 48 HOH HOH . J 5 HOH B 1 301 60 HOH HOH . J 5 HOH B 2 302 20 HOH HOH . J 5 HOH B 3 303 24 HOH HOH . J 5 HOH B 4 304 1 HOH HOH . J 5 HOH B 5 305 53 HOH HOH . J 5 HOH B 6 306 59 HOH HOH . J 5 HOH B 7 307 25 HOH HOH . J 5 HOH B 8 308 35 HOH HOH . J 5 HOH B 9 309 37 HOH HOH . J 5 HOH B 10 310 6 HOH HOH . J 5 HOH B 11 311 51 HOH HOH . J 5 HOH B 12 312 42 HOH HOH . J 5 HOH B 13 313 16 HOH HOH . J 5 HOH B 14 314 9 HOH HOH . J 5 HOH B 15 315 30 HOH HOH . J 5 HOH B 16 316 63 HOH HOH . J 5 HOH B 17 317 12 HOH HOH . J 5 HOH B 18 318 8 HOH HOH . J 5 HOH B 19 319 27 HOH HOH . J 5 HOH B 20 320 40 HOH HOH . J 5 HOH B 21 321 56 HOH HOH . J 5 HOH B 22 322 46 HOH HOH . J 5 HOH B 23 323 68 HOH HOH . J 5 HOH B 24 324 43 HOH HOH . J 5 HOH B 25 325 17 HOH HOH . J 5 HOH B 26 326 55 HOH HOH . J 5 HOH B 27 327 69 HOH HOH . J 5 HOH B 28 328 3 HOH HOH . J 5 HOH B 29 329 22 HOH HOH . J 5 HOH B 30 330 18 HOH HOH . J 5 HOH B 31 331 13 HOH HOH . J 5 HOH B 32 332 66 HOH HOH . J 5 HOH B 33 333 58 HOH HOH . J 5 HOH B 34 334 2 HOH HOH . J 5 HOH B 35 335 47 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 C C1 PRP . . . F 2 -7.119 -4.334 15.44 1 27.73 ? C1 PRP 201 B 1 HETATM 2 C C2 PRP . . . F 2 -5.88 -4.111 14.504 1 26.46 ? C2 PRP 201 B 1 HETATM 3 C C3 PRP . . . F 2 -5.606 -2.598 14.589 1 25.21 ? C3 PRP 201 B 1 HETATM 4 C C4 PRP . . . F 2 -7.01 -2.028 14.762 1 26.71 ? C4 PRP 201 B 1 HETATM 5 C C5 PRP . . . F 2 -7.579 -1.427 13.491 1 26.2 ? C5 PRP 201 B 1 HETATM 6 O O1 PRP . . . F 2 -6.788 -4.441 16.843 1 35.68 ? O1 PRP 201 B 1 HETATM 7 O O2 PRP . . . F 2 -4.701 -4.774 14.852 1 22.01 ? O2 PRP 201 B 1 HETATM 8 O O3 PRP . . . F 2 -4.876 -2.22 15.763 1 23.68 ? O3 PRP 201 B 1 HETATM 9 O O4 PRP . . . F 2 -7.832 -3.095 15.254 1 25.52 ? O4 PRP 201 B 1 HETATM 10 O O5 PRP . . . F 2 -8.96 -0.971 13.773 1 26.68 ? O5 PRP 201 B 1 HETATM 11 P P PRP . . . F 2 -9.313 0.611 13.783 1 24.27 ? P PRP 201 B 1 HETATM 12 O O1P PRP . . . F 2 -9.046 1.159 15.206 1 22.06 ? O1P PRP 201 B 1 HETATM 13 O O2P PRP . . . F 2 -8.49 1.135 12.569 1 21.41 ? O2P PRP 201 B 1 HETATM 14 O O3P PRP . . . F 2 -10.815 0.527 13.455 1 27.94 ? O3P PRP 201 B 1 HETATM 15 P PA PRP . . . F 2 -7.384 -5.426 18.175 1 54.95 ? PA PRP 201 B 1 HETATM 16 O O1A PRP . . . F 2 -7.444 -4.641 19.551 1 49.48 ? O1A PRP 201 B 1 HETATM 17 O O2A PRP . . . F 2 -8.624 -6.35 17.883 1 53.25 ? O2A PRP 201 B 1 HETATM 18 O O3A PRP . . . F 2 -6.436 -6.653 18.594 1 33.61 ? O3A PRP 201 B 1 HETATM 19 P PB PRP . . . F 2 -4.919 -6.958 18.381 1 27.77 ? PB PRP 201 B 1 HETATM 20 O O1B PRP . . . F 2 -4.602 -7.256 19.846 1 29.83 ? O1B PRP 201 B 1 HETATM 21 O O2B PRP . . . F 2 -4.967 -8.286 17.684 1 27.11 ? O2B PRP 201 B 1 HETATM 22 O O3B PRP . . . F 2 -4.093 -5.846 17.699 1 23.9 ? O3B PRP 201 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #