data_9BFD
#
_model_server_result.job_id            '_AihVG-2NzlOjtFPuIJqeg' 
_model_server_result.datetime_utc      '2025-01-05 04:53:43' 
_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          9bfd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1101}' 
#
_entry.id    9BFD 
#
_exptl.entry_id    9BFD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              444.336 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine" 
_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            9BFD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9BFD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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    ? 
_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                      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
covale ? covale1 A OG SER 563 A SER 563 1_555 C P2 A1AN1 . A A1AN1 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.614 ? 
covale ? covale2 C P1 A1AN1 . A A1AN1 1101 1_555 B OG SER 1007 B SER 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? 
#
_chem_comp.formula           'C15 H21 N6 O8 P' 
_chem_comp.formula_weight    444.336 
_chem_comp.id                PR8 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     prolyl-adenylate 
#
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
O10 C PR8 sing 387 n n 
C O PR8 doub 388 n n 
C CA PR8 sing 389 n n 
CA N PR8 sing 390 n n 
CD N PR8 sing 391 n n 
N HN PR8 sing 392 n n 
O2P P PR8 doub 393 n n 
O5' P PR8 sing 394 n n 
P O1P PR8 sing 395 n n 
P O10 PR8 sing 396 n n 
C2 N1 PR8 doub 397 n y 
N1 C6 PR8 sing 398 n y 
C2 N3 PR8 sing 399 n y 
C2 H2 PR8 sing 400 n n 
N3 C4 PR8 doub 401 n y 
C4 N9 PR8 sing 402 n y 
C4 C5 PR8 sing 403 n y 
C6 C5 PR8 doub 404 n y 
C5 N7 PR8 sing 405 n y 
C6 N6 PR8 sing 406 n n 
N6 HN6 PR8 sing 407 n n 
N6 HN6A PR8 sing 408 n n 
C8 N7 PR8 doub 409 n y 
N9 C8 PR8 sing 410 n y 
C8 H8 PR8 sing 411 n n 
C1' N9 PR8 sing 412 n n 
CB CA PR8 sing 413 n n 
CA HA PR8 sing 414 n n 
CB CG PR8 sing 415 n n 
CB HB PR8 sing 416 n n 
CB HBA PR8 sing 417 n n 
CG CD PR8 sing 418 n n 
CD HD PR8 sing 419 n n 
CD HDA PR8 sing 420 n n 
CG HG PR8 sing 421 n n 
CG HGA PR8 sing 422 n n 
C2' C1' PR8 sing 423 n n 
C1' O4' PR8 sing 424 n n 
C1' H1' PR8 sing 425 n n 
O1P HO1P PR8 sing 426 n n 
O2' C2' PR8 sing 427 n n 
C2' C3' PR8 sing 428 n n 
C2' H2' PR8 sing 429 n n 
O2' HO2' PR8 sing 430 n n 
O3' C3' PR8 sing 431 n n 
C3' C4' PR8 sing 432 n n 
C3' H3' PR8 sing 433 n n 
O3' HO3' PR8 sing 434 n n 
C4' O4' PR8 sing 435 n n 
C4' C5' PR8 sing 436 n n 
C4' H4' PR8 sing 437 n n 
C5' O5' PR8 sing 438 n n 
C5' H5' PR8 sing 439 n n 
C5' "H5'A" PR8 sing 440 n n 
#
_atom_sites.entry_id                     9BFD 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 3 A1AN1 A 1 1101 1102 A1AN1 DRG . 
D 4 PR8 B 1 1101 1101 PR8 INH . 
#
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 C PR8 . . . D 4 114.312 135.536 86.122 1 49.38 ? C PR8 1101 B 1 
HETATM 2 N N PR8 . . . D 4 115.224 134.368 84.146 1 50.6 ? N PR8 1101 B 1 
HETATM 3 O O PR8 . . . D 4 114.786 134.828 86.972 1 47.63 ? O PR8 1101 B 1 
HETATM 4 P P PR8 . . . D 4 114.015 137.608 87.707 1 58.15 ? P PR8 1101 B 1 
HETATM 5 N N1 PR8 . . . D 4 121.074 131.589 89.798 1 47.95 ? N1 PR8 1101 B 1 
HETATM 6 C C2 PR8 . . . D 4 120.559 132.335 90.784 1 49.03 ? C2 PR8 1101 B 1 
HETATM 7 N N3 PR8 . . . D 4 119.635 133.29 90.724 1 48.02 ? N3 PR8 1101 B 1 
HETATM 8 C C4 PR8 . . . D 4 119.194 133.443 89.466 1 41.57 ? C4 PR8 1101 B 1 
HETATM 9 C C5 PR8 . . . D 4 119.625 132.758 88.351 1 36.75 ? C5 PR8 1101 B 1 
HETATM 10 C C6 PR8 . . . D 4 120.631 131.793 88.535 1 36.93 ? C6 PR8 1101 B 1 
HETATM 11 N N6 PR8 . . . D 4 121.135 131.052 87.553 1 38.43 ? N6 PR8 1101 B 1 
HETATM 12 N N7 PR8 . . . D 4 118.963 133.219 87.221 1 48.68 ? N7 PR8 1101 B 1 
HETATM 13 C C8 PR8 . . . D 4 118.187 134.182 87.661 1 55.44 ? C8 PR8 1101 B 1 
HETATM 14 N N9 PR8 . . . D 4 118.303 134.38 89.015 1 48.38 ? N9 PR8 1101 B 1 
HETATM 15 C CA PR8 . . . D 4 114.078 135.115 84.68 1 47.3 ? CA PR8 1101 B 1 
HETATM 16 C CB PR8 . . . D 4 112.868 134.183 84.524 1 48.58 ? CB PR8 1101 B 1 
HETATM 17 C CD PR8 . . . D 4 114.781 133.038 83.727 1 45.16 ? CD PR8 1101 B 1 
HETATM 18 C CG PR8 . . . D 4 113.303 133.21 83.455 1 43.42 ? CG PR8 1101 B 1 
HETATM 19 C C1' PR8 . . . D 4 117.492 135.248 89.856 1 43.59 ? C1' PR8 1101 B 1 
HETATM 20 O O10 PR8 . . . D 4 113.993 136.815 86.299 1 50.61 ? O10 PR8 1101 B 1 
HETATM 21 O O1P PR8 . . . D 4 113.146 138.808 87.531 1 49.94 ? O1P PR8 1101 B 1 
HETATM 22 C C2' PR8 . . . D 4 118.194 135.997 90.991 1 41.02 ? C2' PR8 1101 B 1 
HETATM 23 O O2' PR8 . . . D 4 117.755 135.517 92.242 1 45.51 ? O2' PR8 1101 B 1 
HETATM 24 O O2P PR8 . . . D 4 113.744 136.676 88.841 1 52.78 ? O2P PR8 1101 B 1 
HETATM 25 C C3' PR8 . . . D 4 117.744 137.448 90.775 1 41.13 ? C3' PR8 1101 B 1 
HETATM 26 O O3' PR8 . . . D 4 117.519 138.197 91.962 1 43.48 ? O3' PR8 1101 B 1 
HETATM 27 C C4' PR8 . . . D 4 116.477 137.29 89.928 1 41.96 ? C4' PR8 1101 B 1 
HETATM 28 O O4' PR8 . . . D 4 116.859 136.212 89.047 1 44.42 ? O4' PR8 1101 B 1 
HETATM 29 C C5' PR8 . . . D 4 116.056 138.512 89.149 1 44.63 ? C5' PR8 1101 B 1 
HETATM 30 O O5' PR8 . . . D 4 115.519 138.145 87.853 1 46.82 ? O5' PR8 1101 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    86 
_model_server_stats.query_time_ms           448 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           30 
#