data_9DEU
#
_model_server_result.job_id            9OYFLl8X8UCWdlVSgfBfUw 
_model_server_result.datetime_utc      '2025-01-22 14:57:08' 
_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          9deu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    9DEU 
#
_exptl.entry_id    9DEU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              489.374 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one 
_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            9DEU 
_cell.length_a            53.647 
_cell.length_b            105.194 
_cell.length_c            73.792 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9DEU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    'C 2c 2' 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 A SG CYS 9 A CYS 9 1_555 E ZN ZN . A ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? 
metalc ? metalc2 A SG CYS 10 A CYS 10 1_555 E ZN ZN . A ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc3 A OD2 ASP 13 A ASP 13 1_555 E ZN ZN . A ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? 
metalc ? metalc4 A SG CYS 87 A CYS 87 1_555 C FE2 SF4 . A SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc5 A SG CYS 90 A CYS 90 1_555 C FE3 SF4 . A SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc6 A SG CYS 169 A CYS 169 1_555 C FE1 SF4 . A SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc7 A SG CYS 171 A CYS 171 1_555 C FE4 SF4 . A SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
#
_chem_comp.formula           'C17 H24 N5 O10 P' 
_chem_comp.formula_weight    489.374 
_chem_comp.id                56B 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
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
N2 C2 56B sing 1 n n 
C2 N1 56B sing 2 n n 
C2 N3 56B doub 3 n n 
N1 C6 56B sing 4 n n 
N3 C4 56B sing 5 n n 
C6 O6 56B doub 6 n n 
C6 C5 56B sing 7 n n 
C4 C5 56B doub 8 n y 
C4 N9 56B sing 9 n y 
C5 C7 56B sing 10 n y 
O4' C1' 56B sing 11 n n 
O4' C4' 56B sing 12 n n 
O3' C3' 56B sing 13 n n 
C1' N9 56B sing 14 n n 
C1' C2' 56B sing 15 n n 
N9 C8 56B sing 16 n y 
C4' C3' 56B sing 17 n n 
C4' C5' 56B sing 18 n n 
C7 C8 56B doub 19 n y 
C7 C9 56B sing 20 n n 
O2' C2' 56B sing 21 n n 
C3' C2' 56B sing 22 n n 
N10 C9 56B sing 23 n n 
N10 C10 56B sing 24 n n 
C12 C13 56B sing 25 n n 
C12 O12 56B sing 26 n n 
C12 C11 56B sing 27 n n 
C13 C14 56B doub 28 n n 
C14 C10 56B sing 29 n n 
C5' O5' 56B sing 30 n n 
C10 C11 56B sing 31 n n 
C11 O11 56B sing 32 n n 
OP2 P 56B sing 33 n n 
O5' P 56B sing 34 n n 
P OP1 56B doub 35 n n 
C2' H1 56B sing 36 n n 
O2' H2 56B sing 37 n n 
C1' H3 56B sing 38 n n 
N10 H4 56B sing 39 n n 
O11 H6 56B sing 40 n n 
C8 H7 56B sing 41 n n 
O12 H8 56B sing 42 n n 
N2 H9 56B sing 43 n n 
N2 H10 56B sing 44 n n 
C9 H11 56B sing 45 n n 
C9 H12 56B sing 46 n n 
N1 H13 56B sing 47 n n 
C10 H14 56B sing 48 n n 
C11 H15 56B sing 49 n n 
OP2 H16 56B sing 50 n n 
C12 H17 56B sing 51 n n 
C13 H18 56B sing 52 n n 
C14 H21 56B sing 53 n n 
O3' H23 56B sing 54 n n 
C4' H24 56B sing 55 n n 
C5' H25 56B sing 56 n n 
C5' H26 56B sing 57 n n 
C3' H27 56B sing 58 n n 
P OP3 56B sing 59 n n 
OP3 HOP3 56B sing 60 n n 
#
_atom_sites.entry_id                     9DEU 
_atom_sites.fract_transf_matrix[1][1]    0.01864 
_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]    0.009506 
_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]    0.013552 
_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 56B A 1 201 201 56B 56B . 
C 3 SF4 A 1 202 501 SF4 SF4 . 
D 4 CL A 1 203 503 CL CL . 
E 5 ZN A 1 204 1 ZN ZN . 
F 6 HOH A 1 301 76 HOH HOH . 
F 6 HOH A 2 302 53 HOH HOH . 
F 6 HOH A 3 303 34 HOH HOH . 
F 6 HOH A 4 304 72 HOH HOH . 
F 6 HOH A 5 305 19 HOH HOH . 
F 6 HOH A 6 306 39 HOH HOH . 
F 6 HOH A 7 307 33 HOH HOH . 
F 6 HOH A 8 308 61 HOH HOH . 
F 6 HOH A 9 309 70 HOH HOH . 
F 6 HOH A 10 310 30 HOH HOH . 
F 6 HOH A 11 311 24 HOH HOH . 
F 6 HOH A 12 312 3 HOH HOH . 
F 6 HOH A 13 313 23 HOH HOH . 
F 6 HOH A 14 314 28 HOH HOH . 
F 6 HOH A 15 315 4 HOH HOH . 
F 6 HOH A 16 316 44 HOH HOH . 
F 6 HOH A 17 317 8 HOH HOH . 
F 6 HOH A 18 318 12 HOH HOH . 
F 6 HOH A 19 319 15 HOH HOH . 
F 6 HOH A 20 320 46 HOH HOH . 
F 6 HOH A 21 321 5 HOH HOH . 
F 6 HOH A 22 322 2 HOH HOH . 
F 6 HOH A 23 323 1 HOH HOH . 
F 6 HOH A 24 324 73 HOH HOH . 
F 6 HOH A 25 325 11 HOH HOH . 
F 6 HOH A 26 326 16 HOH HOH . 
F 6 HOH A 27 327 18 HOH HOH . 
F 6 HOH A 28 328 7 HOH HOH . 
F 6 HOH A 29 329 10 HOH HOH . 
F 6 HOH A 30 330 9 HOH HOH . 
F 6 HOH A 31 331 37 HOH HOH . 
F 6 HOH A 32 332 69 HOH HOH . 
F 6 HOH A 33 333 35 HOH HOH . 
F 6 HOH A 34 334 20 HOH HOH . 
F 6 HOH A 35 335 17 HOH HOH . 
F 6 HOH A 36 336 38 HOH HOH . 
F 6 HOH A 37 337 29 HOH HOH . 
F 6 HOH A 38 338 55 HOH HOH . 
F 6 HOH A 39 339 22 HOH HOH . 
F 6 HOH A 40 340 31 HOH HOH . 
F 6 HOH A 41 341 42 HOH HOH . 
F 6 HOH A 42 342 6 HOH HOH . 
F 6 HOH A 43 343 49 HOH HOH . 
F 6 HOH A 44 344 21 HOH HOH . 
F 6 HOH A 45 345 13 HOH HOH . 
F 6 HOH A 46 346 57 HOH HOH . 
F 6 HOH A 47 347 75 HOH HOH . 
F 6 HOH A 48 348 65 HOH HOH . 
F 6 HOH A 49 349 36 HOH HOH . 
F 6 HOH A 50 350 41 HOH HOH . 
F 6 HOH A 51 351 63 HOH HOH . 
F 6 HOH A 52 352 40 HOH HOH . 
F 6 HOH A 53 353 48 HOH HOH . 
F 6 HOH A 54 354 32 HOH HOH . 
F 6 HOH A 55 355 43 HOH HOH . 
F 6 HOH A 56 356 67 HOH HOH . 
F 6 HOH A 57 357 60 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 N N9 56B . . . B 2 -11.485 -11.039 -10.351 1 116.26 ? N9 56B 201 A 1 
HETATM 2 C C2' 56B . . . B 2 -12.07 -10.849 -12.815 1 123.59 ? C2' 56B 201 A 1 
HETATM 3 O O2' 56B . . . B 2 -11.274 -11.832 -13.439 1 121.2 ? O2' 56B 201 A 1 
HETATM 4 P P 56B . . . B 2 -16.161 -6.921 -12.645 1 148.51 ? P 56B 201 A 1 
HETATM 5 C C1' 56B . . . B 2 -11.381 -10.254 -11.586 1 123.33 ? C1' 56B 201 A 1 
HETATM 6 N N10 56B . . . B 2 -13.416 -12.374 -6.305 1 84.64 ? N10 56B 201 A 1 
HETATM 7 O O11 56B . . . B 2 -13.414 -14.769 -3.585 1 74.05 ? O11 56B 201 A 1 
HETATM 8 C C8 56B . . . B 2 -12.634 -11.589 -9.822 1 108.95 ? C8 56B 201 A 1 
HETATM 9 N N3 56B . . . B 2 -9.159 -10.923 -9.691 1 115.25 ? N3 56B 201 A 1 
HETATM 10 O O12 56B . . . B 2 -13.629 -12.778 -1.685 1 67.71 ? O12 56B 201 A 1 
HETATM 11 C C7 56B . . . B 2 -12.359 -12.225 -8.627 1 101.44 ? C7 56B 201 A 1 
HETATM 12 N N2 56B . . . B 2 -7.053 -10.987 -8.748 1 111.88 ? N2 56B 201 A 1 
HETATM 13 O O6 56B . . . B 2 -10.307 -13.106 -6.386 1 97.12 ? O6 56B 201 A 1 
HETATM 14 C C9 56B . . . B 2 -13.275 -12.967 -7.663 1 89.72 ? C9 56B 201 A 1 
HETATM 15 N N1 56B . . . B 2 -8.767 -12.034 -7.624 1 107.24 ? N1 56B 201 A 1 
HETATM 16 O O4' 56B . . . B 2 -11.989 -8.993 -11.372 1 127.06 ? O4' 56B 201 A 1 
HETATM 17 C C10 56B . . . B 2 -12.744 -13.132 -5.241 1 81.95 ? C10 56B 201 A 1 
HETATM 18 O O5' 56B . . . B 2 -14.902 -7.753 -13.147 1 137.81 ? O5' 56B 201 A 1 
HETATM 19 C C11 56B . . . B 2 -13.711 -13.469 -4.101 1 75.35 ? C11 56B 201 A 1 
HETATM 20 O OP2 56B . . . B 2 -15.88 -6.397 -11.288 1 141.77 ? OP2 56B 201 A 1 
HETATM 21 C C12 56B . . . B 2 -13.469 -12.362 -3.043 1 72.52 ? C12 56B 201 A 1 
HETATM 22 C C13 56B . . . B 2 -12.052 -11.902 -3.293 1 77.76 ? C13 56B 201 A 1 
HETATM 23 O OP1 56B . . . B 2 -17.385 -7.711 -12.888 1 149.92 -1 OP1 56B 201 A 1 
HETATM 24 C C14 56B . . . B 2 -11.642 -12.323 -4.529 1 81.72 ? C14 56B 201 A 1 
HETATM 25 O O3' 56B . . . B 2 -11.006 -9.203 -14.161 1 122.06 ? O3' 56B 201 A 1 
HETATM 26 C C5 56B . . . B 2 -10.936 -12.048 -8.423 1 105.53 ? C5 56B 201 A 1 
HETATM 27 C C4 56B . . . B 2 -10.44 -11.307 -9.513 1 112.51 ? C4 56B 201 A 1 
HETATM 28 C C2 56B . . . B 2 -8.346 -11.309 -8.706 1 113.8 ? C2 56B 201 A 1 
HETATM 29 C C6 56B . . . B 2 -10.061 -12.453 -7.398 1 102.92 ? C6 56B 201 A 1 
HETATM 30 C C4' 56B . . . B 2 -12.706 -8.6 -12.57 1 128.4 ? C4' 56B 201 A 1 
HETATM 31 C C5' 56B . . . B 2 -14.179 -8.598 -12.259 1 131.94 ? C5' 56B 201 A 1 
HETATM 32 C C3' 56B . . . B 2 -12.28 -9.594 -13.644 1 124.95 ? C3' 56B 201 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           32 
#