data_8IPM
#
_model_server_result.job_id            anOGONecWZJdJs3fJmjMjA 
_model_server_result.datetime_utc      '2025-04-26 05:29:43' 
_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          8ipm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    8IPM 
#
_exptl.entry_id    8IPM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              381.387 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SINEFUNGIN 
_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            8IPM 
_cell.length_a            71.22 
_cell.length_b            134.111 
_cell.length_c            93.026 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8IPM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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                      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
hydrog 'G-U MISPAIR' hydrog1 C N2 G 6 A G 3 1_555 C O2 U 11 A U 8 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 C N3 C 7 A C 4 1_555 C N1 G 10 A G 7 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 C N4 C 7 A C 4 1_555 C O6 G 10 A G 7 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 C O2 C 7 A C 4 1_555 C N2 G 10 A G 7 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-C MISPAIR' hydrog5 C N3 C 8 A C 5 1_555 C N4 C 9 A C 6 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-C MISPAIR' hydrog6 C N4 C 9 A C 6 1_555 C N3 C 8 A C 5 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 C N1 G 10 A G 7 1_555 C N3 C 7 A C 4 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 C N2 G 10 A G 7 1_555 C O2 C 7 A C 4 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 C O6 G 10 A G 7 1_555 C N4 C 7 A C 4 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'U-G MISPAIR' hydrog10 C O2 U 11 A U 8 1_555 C N2 G 6 A G 3 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'U-C MISPAIR' hydrog11 C N3 U 11 A U 8 1_555 C N3 C 7 A C 4 3_554 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C15 H23 N7 O5' 
_chem_comp.formula_weight    381.387 
_chem_comp.id                SFG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              SINEFUNGIN 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ADENOSYL-ORNITHINE 
#
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
N CA SFG sing 403 n n 
N HN1 SFG sing 404 n n 
N HN2 SFG sing 405 n n 
CA C SFG sing 406 n n 
CA CB SFG sing 407 n n 
CA HA SFG sing 408 n n 
C O SFG doub 409 n n 
C OXT SFG sing 410 n n 
OXT HXT SFG sing 411 n n 
CB CG SFG sing 412 n n 
CB HB1 SFG sing 413 n n 
CB HB2 SFG sing 414 n n 
CG CD SFG sing 415 n n 
CG HG1 SFG sing 416 n n 
CG HG2 SFG sing 417 n n 
CD NE SFG sing 418 n n 
CD C5' SFG sing 419 n n 
CD HD SFG sing 420 n n 
NE HNE1 SFG sing 421 n n 
NE HNE2 SFG sing 422 n n 
C5' C4' SFG sing 423 n n 
C5' "H5'1" SFG sing 424 n n 
C5' "H5'2" SFG sing 425 n n 
C4' O4' SFG sing 426 n n 
C4' C3' SFG sing 427 n n 
C4' H4' SFG sing 428 n n 
O4' C1' SFG sing 429 n n 
C3' O3' SFG sing 430 n n 
C3' C2' SFG sing 431 n n 
C3' H3' SFG sing 432 n n 
O3' HO3' SFG sing 433 n n 
C2' O2' SFG sing 434 n n 
C2' C1' SFG sing 435 n n 
C2' H2' SFG sing 436 n n 
O2' HO2' SFG sing 437 n n 
C1' N9 SFG sing 438 n n 
C1' H1' SFG sing 439 n n 
N9 C8 SFG sing 440 n y 
N9 C4 SFG sing 441 n y 
C8 N7 SFG doub 442 n y 
C8 H8 SFG sing 443 n n 
N7 C5 SFG sing 444 n y 
C5 C6 SFG sing 445 n y 
C5 C4 SFG doub 446 n y 
C6 N6 SFG sing 447 n n 
C6 N1 SFG doub 448 n y 
N6 HN61 SFG sing 449 n n 
N6 HN62 SFG sing 450 n n 
N1 C2 SFG sing 451 n y 
C2 N3 SFG doub 452 n y 
C2 H2 SFG sing 453 n n 
N3 C4 SFG sing 454 n y 
#
_atom_sites.entry_id                     8IPM 
_atom_sites.fract_transf_matrix[1][1]    0.014041 
_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]    0.007457 
_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]    0.01075 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          D 
_pdbx_nonpoly_scheme.entity_id        4 
_pdbx_nonpoly_scheme.mon_id           SFG 
_pdbx_nonpoly_scheme.pdb_strand_id    D 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      401 
_pdbx_nonpoly_scheme.auth_seq_num     401 
_pdbx_nonpoly_scheme.pdb_mon_id       SFG 
_pdbx_nonpoly_scheme.auth_mon_id      SFG 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 N SFG . . . D 4 20.52 35.904 -7.665 1 84.02 ? N SFG 401 D 1 
HETATM 2 C CA SFG . . . D 4 21.534 35.126 -8.347 1 94.65 ? CA SFG 401 D 1 
HETATM 3 C C SFG . . . D 4 21.699 35.628 -9.757 1 102.64 ? C SFG 401 D 1 
HETATM 4 O O SFG . . . D 4 21.686 36.864 -9.938 1 100.08 ? O SFG 401 D 1 
HETATM 5 O OXT SFG . . . D 4 21.827 34.816 -10.701 1 119.13 ? OXT SFG 401 D 1 
HETATM 6 C CB SFG . . . D 4 21.146 33.652 -8.311 1 93.75 ? CB SFG 401 D 1 
HETATM 7 C CG SFG . . . D 4 22.358 32.751 -8.504 1 83.75 ? CG SFG 401 D 1 
HETATM 8 C CD SFG . . . D 4 21.962 31.3 -8.743 1 93.66 ? CD SFG 401 D 1 
HETATM 9 N NE SFG . . . D 4 20.585 31.242 -9.195 1 109.38 ? NE SFG 401 D 1 
HETATM 10 C C5' SFG . . . D 4 22.126 30.515 -7.45 1 83.58 ? C5' SFG 401 D 1 
HETATM 11 C C4' SFG . . . D 4 23.513 30.746 -6.859 1 86.99 ? C4' SFG 401 D 1 
HETATM 12 O O4' SFG . . . D 4 23.511 30.305 -5.502 1 75.59 ? O4' SFG 401 D 1 
HETATM 13 C C3' SFG . . . D 4 24.606 29.975 -7.588 1 86.97 ? C3' SFG 401 D 1 
HETATM 14 O O3' SFG . . . D 4 25.673 30.85 -7.971 1 84.6 ? O3' SFG 401 D 1 
HETATM 15 C C2' SFG . . . D 4 25.124 28.955 -6.594 1 76.07 ? C2' SFG 401 D 1 
HETATM 16 O O2' SFG . . . D 4 26.554 28.912 -6.624 1 66.77 ? O2' SFG 401 D 1 
HETATM 17 C C1' SFG . . . D 4 24.613 29.436 -5.245 1 85.9 ? C1' SFG 401 D 1 
HETATM 18 N N9 SFG . . . D 4 24.163 28.282 -4.431 1 83.52 ? N9 SFG 401 D 1 
HETATM 19 C C8 SFG . . . D 4 23.219 27.394 -4.787 1 66.22 ? C8 SFG 401 D 1 
HETATM 20 N N7 SFG . . . D 4 23.045 26.456 -3.823 1 58.87 ? N7 SFG 401 D 1 
HETATM 21 C C5 SFG . . . D 4 23.897 26.74 -2.823 1 66.16 ? C5 SFG 401 D 1 
HETATM 22 C C6 SFG . . . D 4 24.234 26.157 -1.505 1 79.42 ? C6 SFG 401 D 1 
HETATM 23 N N6 SFG . . . D 4 23.608 25.048 -1.048 1 90.42 ? N6 SFG 401 D 1 
HETATM 24 N N1 SFG . . . D 4 25.187 26.768 -0.771 1 79.95 ? N1 SFG 401 D 1 
HETATM 25 C C2 SFG . . . D 4 25.817 27.87 -1.211 1 79.66 ? C2 SFG 401 D 1 
HETATM 26 N N3 SFG . . . D 4 25.565 28.453 -2.394 1 80.75 ? N3 SFG 401 D 1 
HETATM 27 C C4 SFG . . . D 4 24.633 27.943 -3.231 1 81.13 ? C4 SFG 401 D 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#