data_7DFH
#
_model_server_result.job_id            wdX1VJvxxAVP3h0lSE0iMg 
_model_server_result.datetime_utc      '2025-01-28 02:04:35' 
_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          7dfh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":1201}' 
#
_entry.id    7DFH 
#
_exptl.entry_id    7DFH 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              324.185 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'RIBAVIRIN MONOPHOSPHATE' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,G,H,I,J,K,L,M,N,O 
_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                      9 
_struct_asym.id                             N 
_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 E O3' G 8 P G 20 1_555 N P RVP . P RVP 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? 
metalc ? metalc1 A OD1 ASN 210 A ASN 209 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc2 A ND1 HIS 296 A HIS 295 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc3 A SG CYS 302 A CYS 301 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? 
metalc ? metalc4 A SG CYS 307 A CYS 306 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? 
metalc ? metalc5 A SG CYS 311 A CYS 310 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? 
metalc ? metalc6 A SG CYS 488 A CYS 487 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? 
metalc ? metalc7 A SG CYS 646 A CYS 645 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? 
metalc ? metalc8 A SG CYS 647 A CYS 646 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc9 A OD2 ASP 761 A ASP 760 1_555 J MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc10 I MG MG . A MG 1003 1_555 L O6 POP . A POP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc11 I MG MG . A MG 1003 1_555 L O2 POP . A POP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? 
metalc ? metalc12 J MG MG . A MG 1004 1_555 N O2P RVP . P RVP 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 
hydrog WATSON-CRICK hydrog1 E N1 G 1 P G 13 1_555 F N3 C 12 T C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 E N2 G 1 P G 13 1_555 F O2 C 12 T C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 E O6 G 1 P G 13 1_555 F N4 C 12 T C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 E N3 C 2 P C 14 1_555 F N1 G 11 T G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 E N4 C 2 P C 14 1_555 F O6 G 11 T G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 E O2 C 2 P C 14 1_555 F N2 G 11 T G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 E N3 U 3 P U 15 1_555 F N1 A 10 T A 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 E O4 U 3 P U 15 1_555 F N6 A 10 T A 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 E N1 A 4 P A 16 1_555 F N3 U 9 T U 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 E N6 A 4 P A 16 1_555 F O4 U 9 T U 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 E N3 U 5 P U 17 1_555 F N1 A 8 T A 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 E O4 U 5 P U 17 1_555 F N6 A 8 T A 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 E N1 G 6 P G 18 1_555 F N3 C 7 T C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 E N2 G 6 P G 18 1_555 F O2 C 7 T C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 E O6 G 6 P G 18 1_555 F N4 C 7 T C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'U-A PAIR' hydrog16 E N3 U 7 P U 19 1_555 F N1 A 6 T A 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'G-C PAIR' hydrog17 E N1 G 8 P G 20 1_555 F N3 C 5 T C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C8 H13 N4 O8 P' 
_chem_comp.formula_weight    324.185 
_chem_comp.id                RVP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'RIBAVIRIN MONOPHOSPHATE' 
_chem_comp.type              non-polymer 
_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
P O1P RVP sing 402 n n 
P O2P RVP sing 403 n n 
P O3P RVP doub 404 n n 
P O5' RVP sing 405 n n 
O1P HOP1 RVP sing 406 n n 
O2P HOP2 RVP sing 407 n n 
O5' C5' RVP sing 408 n n 
C5' C4' RVP sing 409 n n 
C5' "H5'1" RVP sing 410 n n 
C5' "H5'2" RVP sing 411 n n 
C4' O4' RVP sing 412 n n 
C4' C3' RVP sing 413 n n 
C4' H4' RVP sing 414 n n 
O4' C1' RVP sing 415 n n 
C3' O3' RVP sing 416 n n 
C3' C2' RVP sing 417 n n 
C3' H3' RVP sing 418 n n 
O3' "HO'3" RVP sing 419 n n 
C2' O2' RVP sing 420 n n 
C2' C1' RVP sing 421 n n 
C2' H2' RVP sing 422 n n 
O2' "HO'2" RVP sing 423 n n 
C1' N9 RVP sing 424 n n 
C1' H1' RVP sing 425 n n 
N9 C8 RVP sing 426 n y 
N9 N4 RVP sing 427 n y 
C8 N7 RVP doub 428 n y 
C8 HC8 RVP sing 429 n n 
N7 C5 RVP sing 430 n y 
C5 C6 RVP sing 431 n n 
C5 N4 RVP doub 432 n y 
C6 O6 RVP doub 433 n n 
C6 N1 RVP sing 434 n n 
N1 HN1 RVP sing 435 n n 
N1 HN2 RVP sing 436 n n 
#
_atom_sites.entry_id                     7DFH 
_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
G 6 ZN A 1 1001 1001 ZN ZN . 
H 6 ZN A 1 1002 1002 ZN ZN . 
I 7 MG A 1 1003 1003 MG MG . 
J 7 MG A 1 1004 1004 MG MG . 
K 7 MG A 1 1005 1005 MG MG . 
L 8 POP A 1 1006 1301 POP POP . 
M 8 POP A 1 1007 1302 POP POP . 
N 9 RVP P 1 1201 1201 RVP LIG . 
O 10 HOH A 1 1101 1105 HOH HOH . 
O 10 HOH A 2 1102 1104 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 P P RVP . . . N 9 130.565 129.306 138.285 1 0.5 ? P RVP 1201 P 1 
HETATM 2 O O1P RVP . . . N 9 130.366 129.276 139.769 1 0.5 ? O1P RVP 1201 P 1 
HETATM 3 O O2P RVP . . . N 9 131.491 128.369 137.711 1 0.5 ? O2P RVP 1201 P 1 
HETATM 4 O O5' RVP . . . N 9 130.648 130.596 138.248 1 0.5 ? O5' RVP 1201 P 1 
HETATM 5 C C5' RVP . . . N 9 130.319 131.537 136.945 1 0.5 ? C5' RVP 1201 P 1 
HETATM 6 C C4' RVP . . . N 9 129.914 132.907 137.172 1 0.5 ? C4' RVP 1201 P 1 
HETATM 7 O O4' RVP . . . N 9 128.626 133.309 137.696 1 0.5 ? O4' RVP 1201 P 1 
HETATM 8 C C3' RVP . . . N 9 130.931 133.395 138.211 1 0.5 ? C3' RVP 1201 P 1 
HETATM 9 O O3' RVP . . . N 9 132.189 133.657 137.604 1 0.5 ? O3' RVP 1201 P 1 
HETATM 10 C C2' RVP . . . N 9 130.273 134.677 138.732 1 0.5 ? C2' RVP 1201 P 1 
HETATM 11 O O2' RVP . . . N 9 130.468 135.783 137.875 1 0.5 ? O2' RVP 1201 P 1 
HETATM 12 C C1' RVP . . . N 9 128.794 134.281 138.703 1 0.5 ? C1' RVP 1201 P 1 
HETATM 13 N N9 RVP . . . N 9 128.38 133.707 139.992 1 0.5 ? N9 RVP 1201 P 1 
HETATM 14 C C8 RVP . . . N 9 128.6 132.465 140.496 1 0.5 ? C8 RVP 1201 P 1 
HETATM 15 N N7 RVP . . . N 9 128.056 132.382 141.692 1 0.5 ? N7 RVP 1201 P 1 
HETATM 16 C C5 RVP . . . N 9 127.495 133.59 141.927 1 0.5 ? C5 RVP 1201 P 1 
HETATM 17 C C6 RVP . . . N 9 126.761 133.971 143.164 1 0.5 ? C6 RVP 1201 P 1 
HETATM 18 O O6 RVP . . . N 9 126.423 133.108 143.994 1 0.5 ? O6 RVP 1201 P 1 
HETATM 19 N N1 RVP . . . N 9 126.506 135.258 143.327 1 0.5 ? N1 RVP 1201 P 1 
HETATM 20 N N4 RVP . . . N 9 127.676 134.415 140.913 1 0.5 ? N4 RVP 1201 P 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           530 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#