data_1L1R
#
_model_server_result.job_id            yc22s5cdIf7pgzwwbQx8NA 
_model_server_result.datetime_utc      '2025-03-04 22:59:58' 
_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          1l1r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    1L1R 
#
_exptl.entry_id    1L1R 
_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         120 
_cell.entry_id            1L1R 
_cell.length_a            54.325 
_cell.length_b            54.325 
_cell.length_c            108.744 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1L1R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_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' 5_675 x-y+1,-y+2,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 94.09366 72.496 
#
_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 O3A PRP . A PRP 301 1_555 B MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? 
metalc ? metalc2 D O1 PRP . A PRP 301 1_555 B MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc3 D O2 PRP . A PRP 301 1_555 B MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? 
metalc ? metalc4 D O3 PRP . A PRP 301 1_555 B MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? 
metalc ? metalc5 D O3B PRP . A PRP 301 1_555 B MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? 
metalc ? metalc6 B MG MG . A MG 400 1_555 E O HOH . A HOH 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc7 B MG MG . A MG 400 1_555 E O HOH . A HOH 464 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
#
_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 294 n n 
C1 O1 PRP sing 295 n n 
C1 O4 PRP sing 296 n n 
C1 H1 PRP sing 297 n n 
C2 C3 PRP sing 298 n n 
C2 O2 PRP sing 299 n n 
C2 H2 PRP sing 300 n n 
C3 C4 PRP sing 301 n n 
C3 O3 PRP sing 302 n n 
C3 H3 PRP sing 303 n n 
C4 C5 PRP sing 304 n n 
C4 O4 PRP sing 305 n n 
C4 H4 PRP sing 306 n n 
C5 O5 PRP sing 307 n n 
C5 H51 PRP sing 308 n n 
C5 H52 PRP sing 309 n n 
O1 PA PRP sing 310 n n 
O2 HO2 PRP sing 311 n n 
O3 HO3 PRP sing 312 n n 
O5 P PRP sing 313 n n 
P O1P PRP doub 314 n n 
P O2P PRP sing 315 n n 
P O3P PRP sing 316 n n 
O2P HOP2 PRP sing 317 n n 
O3P HOP3 PRP sing 318 n n 
PA O1A PRP doub 319 n n 
PA O2A PRP sing 320 n n 
PA O3A PRP sing 321 n n 
O2A HOA2 PRP sing 322 n n 
O3A PB PRP sing 323 n n 
PB O1B PRP doub 324 n n 
PB O2B PRP sing 325 n n 
PB O3B PRP sing 326 n n 
O2B HOB2 PRP sing 327 n n 
O3B HOB3 PRP sing 328 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                     1L1R 
_atom_sites.fract_transf_matrix[1][1]    0.018408 
_atom_sites.fract_transf_matrix[1][2]    0.010628 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021255 
_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]    0.009196 
_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 1 400 400 MG MG . 
C 3 9DA A 1 201 201 9DA 9DA . 
D 4 PRP A 1 301 301 PRP PRP . 
E 5 HOH A 1 401 401 HOH HOH . 
E 5 HOH A 2 402 402 HOH HOH . 
E 5 HOH A 3 403 403 HOH HOH . 
E 5 HOH A 4 404 404 HOH HOH . 
E 5 HOH A 5 405 405 HOH HOH . 
E 5 HOH A 6 406 406 HOH HOH . 
E 5 HOH A 7 407 407 HOH HOH . 
E 5 HOH A 8 408 408 HOH HOH . 
E 5 HOH A 9 409 409 HOH HOH . 
E 5 HOH A 10 410 410 HOH HOH . 
E 5 HOH A 11 411 411 HOH HOH . 
E 5 HOH A 12 412 412 HOH HOH . 
E 5 HOH A 13 413 413 HOH HOH . 
E 5 HOH A 14 414 414 HOH HOH . 
E 5 HOH A 15 415 415 HOH HOH . 
E 5 HOH A 16 416 416 HOH HOH . 
E 5 HOH A 17 417 417 HOH HOH . 
E 5 HOH A 18 418 418 HOH HOH . 
E 5 HOH A 19 419 419 HOH HOH . 
E 5 HOH A 20 420 420 HOH HOH . 
E 5 HOH A 21 421 421 HOH HOH . 
E 5 HOH A 22 422 422 HOH HOH . 
E 5 HOH A 23 424 424 HOH HOH . 
E 5 HOH A 24 425 425 HOH HOH . 
E 5 HOH A 25 426 426 HOH HOH . 
E 5 HOH A 26 427 427 HOH HOH . 
E 5 HOH A 27 428 428 HOH HOH . 
E 5 HOH A 28 429 429 HOH HOH . 
E 5 HOH A 29 430 430 HOH HOH . 
E 5 HOH A 30 431 431 HOH HOH . 
E 5 HOH A 31 432 432 HOH HOH . 
E 5 HOH A 32 433 433 HOH HOH . 
E 5 HOH A 33 434 434 HOH HOH . 
E 5 HOH A 34 435 435 HOH HOH . 
E 5 HOH A 35 436 436 HOH HOH . 
E 5 HOH A 36 437 437 HOH HOH . 
E 5 HOH A 37 438 438 HOH HOH . 
E 5 HOH A 38 439 439 HOH HOH . 
E 5 HOH A 39 440 440 HOH HOH . 
E 5 HOH A 40 441 441 HOH HOH . 
E 5 HOH A 41 442 442 HOH HOH . 
E 5 HOH A 42 443 443 HOH HOH . 
E 5 HOH A 43 444 444 HOH HOH . 
E 5 HOH A 44 445 445 HOH HOH . 
E 5 HOH A 45 446 446 HOH HOH . 
E 5 HOH A 46 447 447 HOH HOH . 
E 5 HOH A 47 448 448 HOH HOH . 
E 5 HOH A 48 449 449 HOH HOH . 
E 5 HOH A 49 450 450 HOH HOH . 
E 5 HOH A 50 451 451 HOH HOH . 
E 5 HOH A 51 452 452 HOH HOH . 
E 5 HOH A 52 453 453 HOH HOH . 
E 5 HOH A 53 454 454 HOH HOH . 
E 5 HOH A 54 455 455 HOH HOH . 
E 5 HOH A 55 456 456 HOH HOH . 
E 5 HOH A 56 457 457 HOH HOH . 
E 5 HOH A 57 458 458 HOH HOH . 
E 5 HOH A 58 459 459 HOH HOH . 
E 5 HOH A 59 460 460 HOH HOH . 
E 5 HOH A 60 461 461 HOH HOH . 
E 5 HOH A 61 462 462 HOH HOH . 
E 5 HOH A 62 463 463 HOH HOH . 
E 5 HOH A 63 464 464 HOH HOH . 
E 5 HOH A 64 465 465 HOH HOH . 
E 5 HOH A 65 466 466 HOH HOH . 
E 5 HOH A 66 467 467 HOH HOH . 
E 5 HOH A 67 468 468 HOH HOH . 
E 5 HOH A 68 469 469 HOH HOH . 
E 5 HOH A 69 470 470 HOH HOH . 
E 5 HOH A 70 471 471 HOH HOH . 
E 5 HOH A 71 472 472 HOH HOH . 
E 5 HOH A 72 473 473 HOH HOH . 
E 5 HOH A 73 474 474 HOH HOH . 
E 5 HOH A 74 475 475 HOH HOH . 
E 5 HOH A 75 476 476 HOH HOH . 
E 5 HOH A 76 477 477 HOH HOH . 
E 5 HOH A 77 478 478 HOH HOH . 
E 5 HOH A 78 479 479 HOH HOH . 
E 5 HOH A 79 480 480 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 7.281 36.583 36.714 1 34.24 ? C1 PRP 301 A 1 
HETATM 2 C C2 PRP . . . D 4 8.802 36.315 36.685 1 33.85 ? C2 PRP 301 A 1 
HETATM 3 C C3 PRP . . . D 4 9.043 35.843 35.259 1 33.36 ? C3 PRP 301 A 1 
HETATM 4 C C4 PRP . . . D 4 7.787 35.109 34.878 1 34.11 ? C4 PRP 301 A 1 
HETATM 5 C C5 PRP . . . D 4 7.961 33.753 34.956 1 35.66 ? C5 PRP 301 A 1 
HETATM 6 O O1 PRP . . . D 4 7.086 37.951 36.255 1 35.27 ? O1 PRP 301 A 1 
HETATM 7 O O2 PRP . . . D 4 9.503 37.515 37.025 1 32.13 ? O2 PRP 301 A 1 
HETATM 8 O O3 PRP . . . D 4 9.236 36.996 34.413 1 29.9 ? O3 PRP 301 A 1 
HETATM 9 O O4 PRP . . . D 4 6.739 35.632 35.823 1 36.42 ? O4 PRP 301 A 1 
HETATM 10 O O5 PRP . . . D 4 6.781 32.983 34.75 1 35.38 ? O5 PRP 301 A 1 
HETATM 11 P P PRP . . . D 4 6.591 31.988 33.5 1 33.63 ? P PRP 301 A 1 
HETATM 12 O O1P PRP . . . D 4 7.863 31.168 33.307 1 32.35 ? O1P PRP 301 A 1 
HETATM 13 O O2P PRP . . . D 4 6.198 32.815 32.282 1 35.11 ? O2P PRP 301 A 1 
HETATM 14 O O3P PRP . . . D 4 5.453 31.105 34.008 1 37.05 ? O3P PRP 301 A 1 
HETATM 15 P PA PRP . . . D 4 5.692 38.734 36.485 1 39.41 ? PA PRP 301 A 1 
HETATM 16 O O1A PRP . . . D 4 4.799 38.429 35.337 1 37.04 ? O1A PRP 301 A 1 
HETATM 17 O O2A PRP . . . D 4 5.174 38.381 37.838 1 39.73 ? O2A PRP 301 A 1 
HETATM 18 O O3A PRP . . . D 4 6.168 40.262 36.367 1 36.94 ? O3A PRP 301 A 1 
HETATM 19 P PB PRP . . . D 4 7.165 41.142 37.345 1 38.54 ? PB PRP 301 A 1 
HETATM 20 O O1B PRP . . . D 4 6.986 40.569 38.761 1 38.17 ? O1B PRP 301 A 1 
HETATM 21 O O2B PRP . . . D 4 6.733 42.581 37.194 1 35.44 ? O2B PRP 301 A 1 
HETATM 22 O O3B PRP . . . D 4 8.537 40.908 36.817 1 36.69 ? O3B PRP 301 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           22 
#