data_4ZOK # _model_server_result.job_id zGcup4TiLVpkf288TPodbw _model_server_result.datetime_utc '2025-09-07 02:04:38' _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 4zok # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 4ZOK # _exptl.entry_id 4ZOK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.07 _entity.id 3 _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 110.9 _cell.angle_gamma 90 _cell.entry_id 4ZOK _cell.length_a 94.6 _cell.length_b 77.7 _cell.length_c 101.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZOK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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,K _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 E N N ? 3 I 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 OG SER 120 A SER 119 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc2 A OD1 ASP 252 A ASP 251 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc3 A OD2 ASP 252 A ASP 251 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc4 A OE2 GLU 253 A GLU 252 1_555 C MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc5 C MG MG . A MG 400 1_555 E O1A PRP . A PRP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc6 C MG MG . A MG 400 1_555 E O3B PRP . A PRP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc7 C MG MG . A MG 400 1_555 J O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc8 C MG MG . A MG 400 1_555 J O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc9 D MG MG . A MG 401 1_555 J O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc10 D MG MG . A MG 401 1_555 J O HOH . A HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc11 D MG MG . A MG 401 1_555 J O HOH . A HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc12 B OG SER 120 B SER 119 1_555 G MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc13 B OD1 ASP 252 B ASP 251 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc14 B OD2 ASP 252 B ASP 251 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc15 B OE1 GLU 253 B GLU 252 1_555 G MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc16 B OE1 GLU 253 B GLU 252 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc17 G MG MG . B MG 400 1_555 I O3B PRP . B PRP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc18 G MG MG . B MG 400 1_555 I O2A PRP . B PRP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc19 G MG MG . B MG 400 1_555 K O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc20 G MG MG . B MG 400 1_555 K O HOH . B HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc21 H MG MG . B MG 401 1_555 K O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc22 H MG MG . B MG 401 1_555 K O HOH . B HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? # _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 317 n n C1 O1 PRP sing 318 n n C1 O4 PRP sing 319 n n C1 H1 PRP sing 320 n n C2 C3 PRP sing 321 n n C2 O2 PRP sing 322 n n C2 H2 PRP sing 323 n n C3 C4 PRP sing 324 n n C3 O3 PRP sing 325 n n C3 H3 PRP sing 326 n n C4 C5 PRP sing 327 n n C4 O4 PRP sing 328 n n C4 H4 PRP sing 329 n n C5 O5 PRP sing 330 n n C5 H51 PRP sing 331 n n C5 H52 PRP sing 332 n n O1 PA PRP sing 333 n n O2 HO2 PRP sing 334 n n O3 HO3 PRP sing 335 n n O5 P PRP sing 336 n n P O1P PRP doub 337 n n P O2P PRP sing 338 n n P O3P PRP sing 339 n n O2P HOP2 PRP sing 340 n n O3P HOP3 PRP sing 341 n n PA O1A PRP doub 342 n n PA O2A PRP sing 343 n n PA O3A PRP sing 344 n n O2A HOA2 PRP sing 345 n n O3A PB PRP sing 346 n n PB O1B PRP doub 347 n n PB O2B PRP sing 348 n n PB O3B PRP sing 349 n n O2B HOB2 PRP sing 350 n n O3B HOB3 PRP sing 351 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 4ZOK _atom_sites.fract_transf_matrix[1][1] 0.010571 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004037 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01287 _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] 0.010546 _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 MG A 1 400 400 MG MG . D 2 MG A 1 401 401 MG MG . E 3 PRP A 1 402 402 PRP PRP . F 4 62L A 1 403 403 62L 62L . G 2 MG B 1 400 400 MG MG . H 2 MG B 1 401 401 MG MG . I 3 PRP B 1 402 402 PRP PRP . J 5 HOH A 1 501 75 HOH HOH . J 5 HOH A 2 502 29 HOH HOH . J 5 HOH A 3 503 108 HOH HOH . J 5 HOH A 4 504 102 HOH HOH . J 5 HOH A 5 505 106 HOH HOH . J 5 HOH A 6 506 11 HOH HOH . J 5 HOH A 7 507 61 HOH HOH . J 5 HOH A 8 508 95 HOH HOH . J 5 HOH A 9 509 86 HOH HOH . J 5 HOH A 10 510 25 HOH HOH . J 5 HOH A 11 511 3 HOH HOH . J 5 HOH A 12 512 37 HOH HOH . J 5 HOH A 13 513 9 HOH HOH . J 5 HOH A 14 514 32 HOH HOH . J 5 HOH A 15 515 42 HOH HOH . J 5 HOH A 16 516 5 HOH HOH . J 5 HOH A 17 517 22 HOH HOH . J 5 HOH A 18 518 41 HOH HOH . J 5 HOH A 19 519 66 HOH HOH . J 5 HOH A 20 520 109 HOH HOH . J 5 HOH A 21 521 90 HOH HOH . J 5 HOH A 22 522 13 HOH HOH . J 5 HOH A 23 523 21 HOH HOH . J 5 HOH A 24 524 2 HOH HOH . J 5 HOH A 25 525 1 HOH HOH . J 5 HOH A 26 526 20 HOH HOH . J 5 HOH A 27 527 17 HOH HOH . J 5 HOH A 28 528 14 HOH HOH . J 5 HOH A 29 529 81 HOH HOH . J 5 HOH A 30 530 60 HOH HOH . J 5 HOH A 31 531 35 HOH HOH . J 5 HOH A 32 532 8 HOH HOH . J 5 HOH A 33 533 15 HOH HOH . J 5 HOH A 34 534 78 HOH HOH . J 5 HOH A 35 535 10 HOH HOH . J 5 HOH A 36 536 34 HOH HOH . J 5 HOH A 37 537 31 HOH HOH . J 5 HOH A 38 538 59 HOH HOH . J 5 HOH A 39 539 91 HOH HOH . J 5 HOH A 40 540 6 HOH HOH . J 5 HOH A 41 541 28 HOH HOH . J 5 HOH A 42 542 30 HOH HOH . J 5 HOH A 43 543 4 HOH HOH . J 5 HOH A 44 544 39 HOH HOH . J 5 HOH A 45 545 23 HOH HOH . J 5 HOH A 46 546 18 HOH HOH . J 5 HOH A 47 547 33 HOH HOH . J 5 HOH A 48 548 40 HOH HOH . J 5 HOH A 49 549 73 HOH HOH . J 5 HOH A 50 550 19 HOH HOH . J 5 HOH A 51 551 26 HOH HOH . J 5 HOH A 52 552 55 HOH HOH . J 5 HOH A 53 553 38 HOH HOH . J 5 HOH A 54 554 12 HOH HOH . J 5 HOH A 55 555 101 HOH HOH . J 5 HOH A 56 556 98 HOH HOH . J 5 HOH A 57 557 7 HOH HOH . J 5 HOH A 58 558 100 HOH HOH . J 5 HOH A 59 559 94 HOH HOH . J 5 HOH A 60 560 57 HOH HOH . J 5 HOH A 61 561 24 HOH HOH . J 5 HOH A 62 562 107 HOH HOH . J 5 HOH A 63 563 67 HOH HOH . J 5 HOH A 64 564 27 HOH HOH . J 5 HOH A 65 565 64 HOH HOH . J 5 HOH A 66 566 99 HOH HOH . J 5 HOH A 67 567 36 HOH HOH . K 5 HOH B 1 501 58 HOH HOH . K 5 HOH B 2 502 82 HOH HOH . K 5 HOH B 3 503 103 HOH HOH . K 5 HOH B 4 504 44 HOH HOH . K 5 HOH B 5 505 104 HOH HOH . K 5 HOH B 6 506 50 HOH HOH . K 5 HOH B 7 507 110 HOH HOH . K 5 HOH B 8 508 46 HOH HOH . K 5 HOH B 9 509 70 HOH HOH . K 5 HOH B 10 510 76 HOH HOH . K 5 HOH B 11 511 77 HOH HOH . K 5 HOH B 12 512 51 HOH HOH . K 5 HOH B 13 513 47 HOH HOH . K 5 HOH B 14 514 83 HOH HOH . K 5 HOH B 15 515 52 HOH HOH . K 5 HOH B 16 516 43 HOH HOH . K 5 HOH B 17 517 80 HOH HOH . K 5 HOH B 18 518 49 HOH HOH . K 5 HOH B 19 519 63 HOH HOH . K 5 HOH B 20 520 79 HOH HOH . K 5 HOH B 21 521 48 HOH HOH . K 5 HOH B 22 522 69 HOH HOH . K 5 HOH B 23 523 53 HOH HOH . K 5 HOH B 24 524 68 HOH HOH . K 5 HOH B 25 525 62 HOH HOH . K 5 HOH B 26 526 88 HOH HOH . K 5 HOH B 27 527 45 HOH HOH . K 5 HOH B 28 528 105 HOH HOH . K 5 HOH B 29 529 16 HOH HOH . K 5 HOH B 30 530 84 HOH HOH . K 5 HOH B 31 531 72 HOH HOH . K 5 HOH B 32 532 96 HOH HOH . K 5 HOH B 33 533 74 HOH HOH . K 5 HOH B 34 534 54 HOH HOH . K 5 HOH B 35 535 56 HOH HOH . K 5 HOH B 36 536 71 HOH HOH . K 5 HOH B 37 537 87 HOH HOH . K 5 HOH B 38 538 93 HOH HOH . K 5 HOH B 39 539 65 HOH HOH . K 5 HOH B 40 540 89 HOH HOH . K 5 HOH B 41 541 97 HOH HOH . K 5 HOH B 42 542 85 HOH HOH . K 5 HOH B 43 543 92 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 . . . E 3 1.628 7.505 31.827 1 39.09 ? C1 PRP 402 A 1 HETATM 2 C C2 PRP . . . E 3 2.256 6.872 30.64 1 41.6 ? C2 PRP 402 A 1 HETATM 3 C C3 PRP . . . E 3 2.49 7.965 29.688 1 39.35 ? C3 PRP 402 A 1 HETATM 4 C C4 PRP . . . E 3 1.481 9.008 30.005 1 39.79 ? C4 PRP 402 A 1 HETATM 5 C C5 PRP . . . E 3 0.361 8.981 29.023 1 40 ? C5 PRP 402 A 1 HETATM 6 O O1 PRP . . . E 3 2.602 7.789 32.767 1 41.93 ? O1 PRP 402 A 1 HETATM 7 O O2 PRP . . . E 3 3.498 6.246 31.001 1 38.32 ? O2 PRP 402 A 1 HETATM 8 O O3 PRP . . . E 3 3.81 8.501 29.865 1 36.06 ? O3 PRP 402 A 1 HETATM 9 O O4 PRP . . . E 3 0.984 8.727 31.351 1 48.38 ? O4 PRP 402 A 1 HETATM 10 O O5 PRP . . . E 3 -0.054 7.655 28.786 1 50.65 ? O5 PRP 402 A 1 HETATM 11 P P PRP . . . E 3 -0.587 7.268 27.346 1 50.61 ? P PRP 402 A 1 HETATM 12 O O1P PRP . . . E 3 0.316 7.643 26.233 1 41.63 ? O1P PRP 402 A 1 HETATM 13 O O2P PRP . . . E 3 -0.815 5.819 27.154 1 45.29 ? O2P PRP 402 A 1 HETATM 14 O O3P PRP . . . E 3 -1.884 7.89 26.998 1 47.62 ? O3P PRP 402 A 1 HETATM 15 P PA PRP . . . E 3 2.457 9.058 33.702 1 29.41 ? PA PRP 402 A 1 HETATM 16 O O1A PRP . . . E 3 1.137 9.097 34.371 1 29.78 ? O1A PRP 402 A 1 HETATM 17 O O2A PRP . . . E 3 3.368 8.969 34.863 1 42.83 ? O2A PRP 402 A 1 HETATM 18 O O3A PRP . . . E 3 2.725 10.373 32.871 1 39.93 ? O3A PRP 402 A 1 HETATM 19 P PB PRP . . . E 3 1.907 11.711 33.05 1 36.44 ? PB PRP 402 A 1 HETATM 20 O O1B PRP . . . E 3 1.504 12.324 31.765 1 43.98 ? O1B PRP 402 A 1 HETATM 21 O O2B PRP . . . E 3 2.647 12.773 33.766 1 29.95 ? O2B PRP 402 A 1 HETATM 22 O O3B PRP . . . E 3 0.644 11.572 33.811 1 21.88 ? O3B PRP 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 22 #