data_1OPR # _model_server_result.job_id dn_tva0Ywc-NRQU3GuYZHw _model_server_result.datetime_utc '2025-09-09 02:05:00' _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 1opr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":221}' # _entry.id 1OPR # _exptl.entry_id 1OPR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.07 _entity.id 4 _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 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 1OPR _cell.length_a 47.3 _cell.length_b 47.3 _cell.length_c 216.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1OPR _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 metalc ? metalc1 D O1 PRP . A PRP 221 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? metalc ? metalc2 D O2 PRP . A PRP 221 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc3 D O3A PRP . A PRP 221 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc4 D O3B PRP . A PRP 221 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc5 D O3 PRP . A PRP 221 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc6 B MG MG . A MG 300 1_555 E O HOH . A HOH 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? # _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 292 n n C1 O1 PRP sing 293 n n C1 O4 PRP sing 294 n n C1 H1 PRP sing 295 n n C2 C3 PRP sing 296 n n C2 O2 PRP sing 297 n n C2 H2 PRP sing 298 n n C3 C4 PRP sing 299 n n C3 O3 PRP sing 300 n n C3 H3 PRP sing 301 n n C4 C5 PRP sing 302 n n C4 O4 PRP sing 303 n n C4 H4 PRP sing 304 n n C5 O5 PRP sing 305 n n C5 H51 PRP sing 306 n n C5 H52 PRP sing 307 n n O1 PA PRP sing 308 n n O2 HO2 PRP sing 309 n n O3 HO3 PRP sing 310 n n O5 P PRP sing 311 n n P O1P PRP doub 312 n n P O2P PRP sing 313 n n P O3P PRP sing 314 n n O2P HOP2 PRP sing 315 n n O3P HOP3 PRP sing 316 n n PA O1A PRP doub 317 n n PA O2A PRP sing 318 n n PA O3A PRP sing 319 n n O2A HOA2 PRP sing 320 n n O3A PB PRP sing 321 n n PB O1B PRP doub 322 n n PB O2B PRP sing 323 n n PB O3B PRP sing 324 n n O2B HOB2 PRP sing 325 n n O3B HOB3 PRP sing 326 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 1OPR _atom_sites.fract_transf_matrix[1][1] 0.021142 _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] 0.021142 _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] 0.004617 _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 B 2 MG A 1 300 300 MG MG . C 3 ORO A 1 220 220 ORO ORO . D 4 PRP A 1 221 221 PRP PRP . E 5 HOH A 1 501 501 HOH HOH . E 5 HOH A 2 502 502 HOH HOH . E 5 HOH A 3 503 503 HOH HOH . E 5 HOH A 4 504 504 HOH HOH . E 5 HOH A 5 505 505 HOH HOH . E 5 HOH A 6 506 506 HOH HOH . E 5 HOH A 7 507 507 HOH HOH . E 5 HOH A 8 508 508 HOH HOH . E 5 HOH A 9 509 509 HOH HOH . E 5 HOH A 10 510 510 HOH HOH . E 5 HOH A 11 511 511 HOH HOH . E 5 HOH A 12 512 512 HOH HOH . E 5 HOH A 13 513 513 HOH HOH . E 5 HOH A 14 514 514 HOH HOH . E 5 HOH A 15 515 515 HOH HOH . E 5 HOH A 16 516 516 HOH HOH . E 5 HOH A 17 517 517 HOH HOH . E 5 HOH A 18 518 518 HOH HOH . E 5 HOH A 19 519 519 HOH HOH . E 5 HOH A 20 520 520 HOH HOH . E 5 HOH A 21 521 521 HOH HOH . E 5 HOH A 22 522 522 HOH HOH . E 5 HOH A 23 523 523 HOH HOH . E 5 HOH A 24 524 524 HOH HOH . E 5 HOH A 25 525 525 HOH HOH . E 5 HOH A 26 526 526 HOH HOH . E 5 HOH A 27 527 527 HOH HOH . E 5 HOH A 28 528 528 HOH HOH . E 5 HOH A 29 529 529 HOH HOH . E 5 HOH A 30 530 530 HOH HOH . E 5 HOH A 31 531 531 HOH HOH . E 5 HOH A 32 532 532 HOH HOH . E 5 HOH A 33 533 533 HOH HOH . E 5 HOH A 34 534 534 HOH HOH . E 5 HOH A 35 535 535 HOH HOH . E 5 HOH A 36 536 536 HOH HOH . E 5 HOH A 37 537 537 HOH HOH . E 5 HOH A 38 538 538 HOH HOH . E 5 HOH A 39 539 539 HOH HOH . E 5 HOH A 40 540 540 HOH HOH . E 5 HOH A 41 541 541 HOH HOH . E 5 HOH A 42 542 542 HOH HOH . E 5 HOH A 43 543 543 HOH HOH . E 5 HOH A 44 544 544 HOH HOH . E 5 HOH A 45 545 545 HOH HOH . E 5 HOH A 46 546 546 HOH HOH . E 5 HOH A 47 547 547 HOH HOH . E 5 HOH A 48 548 548 HOH HOH . E 5 HOH A 49 549 549 HOH HOH . E 5 HOH A 50 550 550 HOH HOH . E 5 HOH A 51 551 551 HOH HOH . E 5 HOH A 52 552 552 HOH HOH . E 5 HOH A 53 553 553 HOH HOH . E 5 HOH A 54 554 554 HOH HOH . E 5 HOH A 55 555 555 HOH HOH . E 5 HOH A 56 556 556 HOH HOH . E 5 HOH A 57 557 557 HOH HOH . E 5 HOH A 58 558 558 HOH HOH . E 5 HOH A 59 559 559 HOH HOH . E 5 HOH A 60 560 560 HOH HOH . E 5 HOH A 61 561 561 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 . . . D 4 19.066 27.491 11.303 1 37.78 ? C1 PRP 221 A 1 HETATM 2 C C2 PRP . . . D 4 20.381 28.281 11.184 1 36.18 ? C2 PRP 221 A 1 HETATM 3 C C3 PRP . . . D 4 21.231 27.686 12.317 1 36.98 ? C3 PRP 221 A 1 HETATM 4 C C4 PRP . . . D 4 20.237 26.833 13.112 1 36.55 ? C4 PRP 221 A 1 HETATM 5 C C5 PRP . . . D 4 20.382 26.808 14.611 1 34.95 ? C5 PRP 221 A 1 HETATM 6 O O1 PRP . . . D 4 19.202 26.109 10.742 1 39.92 ? O1 PRP 221 A 1 HETATM 7 O O2 PRP . . . D 4 21.019 28.041 9.948 1 34.23 ? O2 PRP 221 A 1 HETATM 8 O O3 PRP . . . D 4 22.246 26.858 11.74 1 38.04 ? O3 PRP 221 A 1 HETATM 9 O O4 PRP . . . D 4 18.928 27.317 12.701 1 37.57 ? O4 PRP 221 A 1 HETATM 10 O O5 PRP . . . D 4 19.339 25.994 15.096 1 35.83 ? O5 PRP 221 A 1 HETATM 11 P P PRP . . . D 4 19.355 25.118 16.448 1 34.99 ? P PRP 221 A 1 HETATM 12 O O1P PRP . . . D 4 20.687 25.459 17.085 1 33.99 ? O1P PRP 221 A 1 HETATM 13 O O2P PRP . . . D 4 19.436 23.698 16.027 1 32.57 ? O2P PRP 221 A 1 HETATM 14 O O3P PRP . . . D 4 18 25.311 17.03 1 34.5 ? O3P PRP 221 A 1 HETATM 15 P PA PRP . . . D 4 18.506 25.646 9.374 1 41.32 ? PA PRP 221 A 1 HETATM 16 O O1A PRP . . . D 4 18.38 24.176 9.624 1 42.42 ? O1A PRP 221 A 1 HETATM 17 O O2A PRP . . . D 4 17.162 26.257 9.408 1 41.59 ? O2A PRP 221 A 1 HETATM 18 O O3A PRP . . . D 4 19.312 26.314 8.293 1 40.31 ? O3A PRP 221 A 1 HETATM 19 P PB PRP . . . D 4 19.459 25.943 6.839 1 38.58 ? PB PRP 221 A 1 HETATM 20 O O1B PRP . . . D 4 18.822 27.007 6.061 1 37.36 ? O1B PRP 221 A 1 HETATM 21 O O2B PRP . . . D 4 18.755 24.688 6.467 1 39.95 ? O2B PRP 221 A 1 HETATM 22 O O3B PRP . . . D 4 20.93 25.822 6.535 1 36.23 ? O3B PRP 221 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #