data_7DSJ
#
_model_server_result.job_id            XaYMGDq76xJv0ChgH6SDMw 
_model_server_result.datetime_utc      '2024-10-20 05:33:02' 
_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          7dsj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    7DSJ 
#
_exptl.entry_id    7DSJ 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            7DSJ 
_cell.length_a            78.328 
_cell.length_b            89.488 
_cell.length_c            110.299 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7DSJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
_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 E 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 123 A SER 121 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? 
metalc ? metalc2 A OE2 GLU 261 A GLU 259 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc3 C O1A PRP . A PRP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc4 C O3B PRP . A PRP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc5 D MG MG . A MG 402 1_555 G O HOH . A HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc6 D MG MG . A MG 402 1_555 G O HOH . A HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc7 B OG SER 123 B SER 121 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc8 B OE1 GLU 261 B GLU 259 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? 
metalc ? metalc9 B OE2 GLU 261 B GLU 259 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc10 E O2A PRP . B PRP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc11 E O2B PRP . B PRP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc12 F MG MG . B MG 402 1_555 H O HOH . B HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? 
metalc ? metalc13 F MG MG . B MG 402 1_555 H O HOH . B HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
#
_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                     7DSJ 
_atom_sites.fract_transf_matrix[1][1]    0.012767 
_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]    0.011175 
_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]    0.009066 
_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 1 401 1 PRP PRP . 
D 3 MG A 1 402 2 MG MG . 
E 2 PRP B 1 401 2 PRP PRP . 
F 3 MG B 1 402 1 MG MG . 
G 4 HOH A 1 501 89 HOH HOH . 
G 4 HOH A 2 502 115 HOH HOH . 
G 4 HOH A 3 503 133 HOH HOH . 
G 4 HOH A 4 504 111 HOH HOH . 
G 4 HOH A 5 505 9 HOH HOH . 
G 4 HOH A 6 506 15 HOH HOH . 
G 4 HOH A 7 507 32 HOH HOH . 
G 4 HOH A 8 508 33 HOH HOH . 
G 4 HOH A 9 509 131 HOH HOH . 
G 4 HOH A 10 510 92 HOH HOH . 
G 4 HOH A 11 511 38 HOH HOH . 
G 4 HOH A 12 512 91 HOH HOH . 
G 4 HOH A 13 513 26 HOH HOH . 
G 4 HOH A 14 514 69 HOH HOH . 
G 4 HOH A 15 515 56 HOH HOH . 
G 4 HOH A 16 516 20 HOH HOH . 
G 4 HOH A 17 517 14 HOH HOH . 
G 4 HOH A 18 518 37 HOH HOH . 
G 4 HOH A 19 519 72 HOH HOH . 
G 4 HOH A 20 520 3 HOH HOH . 
G 4 HOH A 21 521 106 HOH HOH . 
G 4 HOH A 22 522 85 HOH HOH . 
G 4 HOH A 23 523 64 HOH HOH . 
G 4 HOH A 24 524 105 HOH HOH . 
G 4 HOH A 25 525 87 HOH HOH . 
G 4 HOH A 26 526 8 HOH HOH . 
G 4 HOH A 27 527 73 HOH HOH . 
G 4 HOH A 28 528 23 HOH HOH . 
G 4 HOH A 29 529 29 HOH HOH . 
G 4 HOH A 30 530 21 HOH HOH . 
G 4 HOH A 31 531 43 HOH HOH . 
G 4 HOH A 32 532 35 HOH HOH . 
G 4 HOH A 33 533 101 HOH HOH . 
G 4 HOH A 34 534 51 HOH HOH . 
G 4 HOH A 35 535 28 HOH HOH . 
G 4 HOH A 36 536 12 HOH HOH . 
G 4 HOH A 37 537 94 HOH HOH . 
G 4 HOH A 38 538 17 HOH HOH . 
G 4 HOH A 39 539 42 HOH HOH . 
G 4 HOH A 40 540 102 HOH HOH . 
G 4 HOH A 41 541 70 HOH HOH . 
G 4 HOH A 42 542 114 HOH HOH . 
G 4 HOH A 43 543 130 HOH HOH . 
G 4 HOH A 44 544 110 HOH HOH . 
G 4 HOH A 45 545 86 HOH HOH . 
G 4 HOH A 46 546 25 HOH HOH . 
G 4 HOH A 47 547 71 HOH HOH . 
G 4 HOH A 48 548 76 HOH HOH . 
G 4 HOH A 49 549 99 HOH HOH . 
G 4 HOH A 50 550 118 HOH HOH . 
G 4 HOH A 51 551 68 HOH HOH . 
G 4 HOH A 52 552 132 HOH HOH . 
G 4 HOH A 53 553 77 HOH HOH . 
G 4 HOH A 54 554 117 HOH HOH . 
G 4 HOH A 55 555 113 HOH HOH . 
G 4 HOH A 56 556 128 HOH HOH . 
G 4 HOH A 57 557 103 HOH HOH . 
G 4 HOH A 58 558 109 HOH HOH . 
G 4 HOH A 59 559 116 HOH HOH . 
H 4 HOH B 1 501 52 HOH HOH . 
H 4 HOH B 2 502 93 HOH HOH . 
H 4 HOH B 3 503 55 HOH HOH . 
H 4 HOH B 4 504 125 HOH HOH . 
H 4 HOH B 5 505 16 HOH HOH . 
H 4 HOH B 6 506 81 HOH HOH . 
H 4 HOH B 7 507 10 HOH HOH . 
H 4 HOH B 8 508 65 HOH HOH . 
H 4 HOH B 9 509 34 HOH HOH . 
H 4 HOH B 10 510 57 HOH HOH . 
H 4 HOH B 11 511 108 HOH HOH . 
H 4 HOH B 12 512 63 HOH HOH . 
H 4 HOH B 13 513 27 HOH HOH . 
H 4 HOH B 14 514 78 HOH HOH . 
H 4 HOH B 15 515 62 HOH HOH . 
H 4 HOH B 16 516 95 HOH HOH . 
H 4 HOH B 17 517 96 HOH HOH . 
H 4 HOH B 18 518 100 HOH HOH . 
H 4 HOH B 19 519 7 HOH HOH . 
H 4 HOH B 20 520 13 HOH HOH . 
H 4 HOH B 21 521 19 HOH HOH . 
H 4 HOH B 22 522 39 HOH HOH . 
H 4 HOH B 23 523 107 HOH HOH . 
H 4 HOH B 24 524 84 HOH HOH . 
H 4 HOH B 25 525 98 HOH HOH . 
H 4 HOH B 26 526 47 HOH HOH . 
H 4 HOH B 27 527 6 HOH HOH . 
H 4 HOH B 28 528 36 HOH HOH . 
H 4 HOH B 29 529 5 HOH HOH . 
H 4 HOH B 30 530 18 HOH HOH . 
H 4 HOH B 31 531 61 HOH HOH . 
H 4 HOH B 32 532 40 HOH HOH . 
H 4 HOH B 33 533 45 HOH HOH . 
H 4 HOH B 34 534 30 HOH HOH . 
H 4 HOH B 35 535 1 HOH HOH . 
H 4 HOH B 36 536 80 HOH HOH . 
H 4 HOH B 37 537 83 HOH HOH . 
H 4 HOH B 38 538 4 HOH HOH . 
H 4 HOH B 39 539 67 HOH HOH . 
H 4 HOH B 40 540 22 HOH HOH . 
H 4 HOH B 41 541 82 HOH HOH . 
H 4 HOH B 42 542 50 HOH HOH . 
H 4 HOH B 43 543 59 HOH HOH . 
H 4 HOH B 44 544 53 HOH HOH . 
H 4 HOH B 45 545 31 HOH HOH . 
H 4 HOH B 46 546 60 HOH HOH . 
H 4 HOH B 47 547 88 HOH HOH . 
H 4 HOH B 48 548 24 HOH HOH . 
H 4 HOH B 49 549 2 HOH HOH . 
H 4 HOH B 50 550 97 HOH HOH . 
H 4 HOH B 51 551 104 HOH HOH . 
H 4 HOH B 52 552 11 HOH HOH . 
H 4 HOH B 53 553 48 HOH HOH . 
H 4 HOH B 54 554 46 HOH HOH . 
H 4 HOH B 55 555 74 HOH HOH . 
H 4 HOH B 56 556 124 HOH HOH . 
H 4 HOH B 57 557 90 HOH HOH . 
H 4 HOH B 58 558 66 HOH HOH . 
H 4 HOH B 59 559 58 HOH HOH . 
H 4 HOH B 60 560 123 HOH HOH . 
H 4 HOH B 61 561 75 HOH HOH . 
H 4 HOH B 62 562 41 HOH HOH . 
H 4 HOH B 63 563 54 HOH HOH . 
H 4 HOH B 64 564 127 HOH HOH . 
H 4 HOH B 65 565 121 HOH HOH . 
H 4 HOH B 66 566 112 HOH HOH . 
H 4 HOH B 67 567 79 HOH HOH . 
H 4 HOH B 68 568 44 HOH HOH . 
H 4 HOH B 69 569 129 HOH HOH . 
H 4 HOH B 70 570 119 HOH HOH . 
H 4 HOH B 71 571 126 HOH HOH . 
H 4 HOH B 72 572 120 HOH HOH . 
H 4 HOH B 73 573 49 HOH HOH . 
H 4 HOH B 74 574 122 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 2 3.107 42.878 -41.304 1 79.44 ? C1 PRP 401 B 1 
HETATM 2 C C2 PRP . . . E 2 2.193 43.915 -40.604 1 83.64 ? C2 PRP 401 B 1 
HETATM 3 C C3 PRP . . . E 2 3.048 44.448 -39.448 1 84.74 ? C3 PRP 401 B 1 
HETATM 4 C C4 PRP . . . E 2 4.448 43.892 -39.694 1 81.87 ? C4 PRP 401 B 1 
HETATM 5 C C5 PRP . . . E 2 5.023 43.36 -38.416 1 84.72 ? C5 PRP 401 B 1 
HETATM 6 O O1 PRP . . . E 2 3.471 43.218 -42.648 1 77.51 ? O1 PRP 401 B 1 
HETATM 7 O O2 PRP . . . E 2 1.622 44.939 -41.472 1 73.07 ? O2 PRP 401 B 1 
HETATM 8 O O3 PRP . . . E 2 3.075 45.876 -39.305 1 85.15 ? O3 PRP 401 B 1 
HETATM 9 O O4 PRP . . . E 2 4.328 42.774 -40.568 1 81.42 ? O4 PRP 401 B 1 
HETATM 10 O O5 PRP . . . E 2 6.363 43.744 -38.175 1 82.38 ? O5 PRP 401 B 1 
HETATM 11 P P PRP . . . E 2 6.87 43.401 -36.688 1 78.62 ? P PRP 401 B 1 
HETATM 12 O O1P PRP . . . E 2 7.234 41.942 -36.777 1 75.78 ? O1P PRP 401 B 1 
HETATM 13 O O2P PRP . . . E 2 7.992 44.387 -36.47 1 84.41 ? O2P PRP 401 B 1 
HETATM 14 O O3P PRP . . . E 2 5.683 43.644 -35.764 1 87.13 ? O3P PRP 401 B 1 
HETATM 15 P PA PRP . . . E 2 2.671 42.662 -43.947 1 61.05 ? PA PRP 401 B 1 
HETATM 16 O O1A PRP . . . E 2 1.345 43.41 -43.946 1 65.49 ? O1A PRP 401 B 1 
HETATM 17 O O2A PRP . . . E 2 2.697 41.142 -43.924 1 55.73 ? O2A PRP 401 B 1 
HETATM 18 O O3A PRP . . . E 2 3.541 43.297 -45.202 1 69.31 ? O3A PRP 401 B 1 
HETATM 19 P PB PRP . . . E 2 5.108 43.14 -45.72 1 69.05 ? PB PRP 401 B 1 
HETATM 20 O O1B PRP . . . E 2 5.105 44.07 -46.964 1 47.46 ? O1B PRP 401 B 1 
HETATM 21 O O2B PRP . . . E 2 5.33 41.644 -45.996 1 50.65 ? O2B PRP 401 B 1 
HETATM 22 O O3B PRP . . . E 2 5.99 43.554 -44.53 1 66.41 ? O3B PRP 401 B 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    37 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           22 
#