data_1Y90
# 
_entry.id   1Y90 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.387 
_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
# 
loop_
_database_2.database_id 
_database_2.database_code 
_database_2.pdbx_database_accession 
_database_2.pdbx_DOI 
PDB   1Y90         pdb_00001y90 10.2210/pdb1y90/pdb 
NDB   AR0053       ?            ?                   
RCSB  RCSB031267   ?            ?                   
WWPDB D_1000031267 ?            ?                   
# 
loop_
_pdbx_audit_revision_history.ordinal 
_pdbx_audit_revision_history.data_content_type 
_pdbx_audit_revision_history.major_revision 
_pdbx_audit_revision_history.minor_revision 
_pdbx_audit_revision_history.revision_date 
1 'Structure model' 1 0 2004-12-21 
2 'Structure model' 1 1 2008-04-30 
3 'Structure model' 1 2 2011-07-13 
4 'Structure model' 1 3 2024-02-14 
# 
_pdbx_audit_revision_details.ordinal             1 
_pdbx_audit_revision_details.revision_ordinal    1 
_pdbx_audit_revision_details.data_content_type   'Structure model' 
_pdbx_audit_revision_details.provider            repository 
_pdbx_audit_revision_details.type                'Initial release' 
_pdbx_audit_revision_details.description         ? 
_pdbx_audit_revision_details.details             ? 
# 
loop_
_pdbx_audit_revision_group.ordinal 
_pdbx_audit_revision_group.revision_ordinal 
_pdbx_audit_revision_group.data_content_type 
_pdbx_audit_revision_group.group 
1 2 'Structure model' 'Version format compliance' 
2 3 'Structure model' 'Version format compliance' 
3 4 'Structure model' 'Data collection'           
4 4 'Structure model' 'Database references'       
5 4 'Structure model' 'Derived calculations'      
# 
loop_
_pdbx_audit_revision_category.ordinal 
_pdbx_audit_revision_category.revision_ordinal 
_pdbx_audit_revision_category.data_content_type 
_pdbx_audit_revision_category.category 
1 4 'Structure model' chem_comp_atom         
2 4 'Structure model' chem_comp_bond         
3 4 'Structure model' database_2             
4 4 'Structure model' pdbx_struct_conn_angle 
5 4 'Structure model' struct_conn            
6 4 'Structure model' struct_site            
# 
loop_
_pdbx_audit_revision_item.ordinal 
_pdbx_audit_revision_item.revision_ordinal 
_pdbx_audit_revision_item.data_content_type 
_pdbx_audit_revision_item.item 
1  4 'Structure model' '_database_2.pdbx_DOI'                        
2  4 'Structure model' '_database_2.pdbx_database_accession'         
3  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id'  
4  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id'   
5  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 
6  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 
7  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id'  
8  4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id'  
9  4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id'   
10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 
11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 
12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id'  
13 4 'Structure model' '_pdbx_struct_conn_angle.value'               
14 4 'Structure model' '_struct_conn.conn_type_id'                   
15 4 'Structure model' '_struct_conn.id'                             
16 4 'Structure model' '_struct_conn.pdbx_dist_value'                
17 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag'         
18 4 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id'        
19 4 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id'        
20 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id'             
21 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id'             
22 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id'              
23 4 'Structure model' '_struct_conn.ptnr1_label_asym_id'            
24 4 'Structure model' '_struct_conn.ptnr1_label_atom_id'            
25 4 'Structure model' '_struct_conn.ptnr1_label_comp_id'            
26 4 'Structure model' '_struct_conn.ptnr1_label_seq_id'             
27 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id'             
28 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id'             
29 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id'              
30 4 'Structure model' '_struct_conn.ptnr2_label_asym_id'            
31 4 'Structure model' '_struct_conn.ptnr2_label_atom_id'            
32 4 'Structure model' '_struct_conn.ptnr2_label_comp_id'            
33 4 'Structure model' '_struct_conn.ptnr2_label_seq_id'             
34 4 'Structure model' '_struct_site.pdbx_auth_asym_id'              
35 4 'Structure model' '_struct_site.pdbx_auth_comp_id'              
36 4 'Structure model' '_struct_site.pdbx_auth_seq_id'               
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        1Y90 
_pdbx_database_status.recvd_initial_deposition_date   2004-12-14 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.status_code_sf                  REL 
_pdbx_database_status.SG_entry                        . 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.status_code_nmr_data            ? 
_pdbx_database_status.methods_development_category    ? 
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 1Y73 'HIV-1 Dis(Mal) Duplex Pt-Soaked'     unspecified 
PDB 1Y6T 'HIV-1 Dis(Mal) Duplex CoHexa-Soaked' unspecified 
PDB 1Y6S 'HIV-1 Dis(Mal) Duplex Ba-Soaked'     unspecified 
PDB 1NLC 'HIV-1 Dis(Mal) Duplex Zn-Soaked'     unspecified 
PDB 1O3Z 'HIV-1 Dis(Mal) Duplex RuHexa-Soaked' unspecified 
PDB 462D 'HIV-1 Dis(Mal) Duplex Mg-Native'     unspecified 
PDB 1Y95 .                                     unspecified 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Ennifar, E.' 1 
'Walter, P.'  2 
'Dumas, P.'   3 
# 
loop_
_citation.id 
_citation.title 
_citation.journal_abbrev 
_citation.journal_volume 
_citation.page_first 
_citation.page_last 
_citation.year 
_citation.journal_id_ASTM 
_citation.country 
_citation.journal_id_ISSN 
_citation.journal_id_CSD 
_citation.book_publisher 
_citation.pdbx_database_id_PubMed 
_citation.pdbx_database_id_DOI 
primary 'A crystallographic study of the binding of 13 metal ions to two related RNA duplexes' 'Nucleic Acids Res.'  31 2671 2682 
2003 NARHAD UK 0305-1048 0389 ? 12736317 10.1093/nar/gkg350              
1       
'The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges' 
'Structure Fold.Des.' 7  1439 1449 1999 FODEFH UK 0969-2126 1263 ? 10574792 '10.1016/S0969-2126(00)80033-7' 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Ennifar, E.'   1  ? 
primary 'Walter, P.'    2  ? 
primary 'Dumas, P.'     3  ? 
1       'Ennifar, E.'   4  ? 
1       'Yusupov, M.'   5  ? 
1       'Walter, P.'    6  ? 
1       'Marquet, R.'   7  ? 
1       'Ehresmann, B.' 8  ? 
1       'Ehresmann, C.' 9  ? 
1       'Dumas, P.'     10 ? 
# 
loop_
_entity.id 
_entity.type 
_entity.src_method 
_entity.pdbx_description 
_entity.formula_weight 
_entity.pdbx_number_of_molecules 
_entity.pdbx_ec 
_entity.pdbx_mutation 
_entity.pdbx_fragment 
_entity.details 
1 polymer     syn "5'-R(*CP*(5BU)P*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3'" 7481.368 2  ? ? ? 
'HIV-1 DIS RNA' 
2 non-polymer syn 'MANGANESE (II) ION'                                                                54.938   12 ? ? ? ? 
# 
_entity_poly.entity_id                      1 
_entity_poly.type                           polyribonucleotide 
_entity_poly.nstd_linkage                   no 
_entity_poly.nstd_monomer                   yes 
_entity_poly.pdbx_seq_one_letter_code       'C(5BU)UGCUGAGGUGCACACAGCAAG' 
_entity_poly.pdbx_seq_one_letter_code_can   CUUGCUGAGGUGCACACAGCAAG 
_entity_poly.pdbx_strand_id                 A,B 
_entity_poly.pdbx_target_identifier         ? 
# 
_pdbx_entity_nonpoly.entity_id   2 
_pdbx_entity_nonpoly.name        'MANGANESE (II) ION' 
_pdbx_entity_nonpoly.comp_id     MN 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1  C   n 
1 2  5BU n 
1 3  U   n 
1 4  G   n 
1 5  C   n 
1 6  U   n 
1 7  G   n 
1 8  A   n 
1 9  G   n 
1 10 G   n 
1 11 U   n 
1 12 G   n 
1 13 C   n 
1 14 A   n 
1 15 C   n 
1 16 A   n 
1 17 C   n 
1 18 A   n 
1 19 G   n 
1 20 C   n 
1 21 A   n 
1 22 A   n 
1 23 G   n 
# 
loop_
_chem_comp.id 
_chem_comp.type 
_chem_comp.mon_nstd_flag 
_chem_comp.name 
_chem_comp.pdbx_synonyms 
_chem_comp.formula 
_chem_comp.formula_weight 
5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 
A   'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE"       ? 'C10 H14 N5 O7 P'   347.221 
C   'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE"        ? 'C9 H14 N3 O8 P'    323.197 
G   'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE"       ? 'C10 H14 N5 O8 P'   363.221 
MN  non-polymer   . 'MANGANESE (II) ION'               ? 'Mn 2'              54.938  
U   'RNA linking' y "URIDINE-5'-MONOPHOSPHATE"         ? 'C9 H13 N2 O9 P'    324.181 
# 
loop_
_pdbx_poly_seq_scheme.asym_id 
_pdbx_poly_seq_scheme.entity_id 
_pdbx_poly_seq_scheme.seq_id 
_pdbx_poly_seq_scheme.mon_id 
_pdbx_poly_seq_scheme.ndb_seq_num 
_pdbx_poly_seq_scheme.pdb_seq_num 
_pdbx_poly_seq_scheme.auth_seq_num 
_pdbx_poly_seq_scheme.pdb_mon_id 
_pdbx_poly_seq_scheme.auth_mon_id 
_pdbx_poly_seq_scheme.pdb_strand_id 
_pdbx_poly_seq_scheme.pdb_ins_code 
_pdbx_poly_seq_scheme.hetero 
A 1 1  C   1  1  1  C   C   A . n 
A 1 2  5BU 2  2  2  5BU 5BU A . n 
A 1 3  U   3  3  3  U   U   A . n 
A 1 4  G   4  4  4  G   G   A . n 
A 1 5  C   5  5  5  C   C   A . n 
A 1 6  U   6  6  6  U   U   A . n 
A 1 7  G   7  7  7  G   G   A . n 
A 1 8  A   8  8  8  A   A   A . n 
A 1 9  G   9  9  9  G   G   A . n 
A 1 10 G   10 10 10 G   G   A . n 
A 1 11 U   11 11 11 U   U   A . n 
A 1 12 G   12 12 12 G   G   A . n 
A 1 13 C   13 13 13 C   C   A . n 
A 1 14 A   14 14 14 A   A   A . n 
A 1 15 C   15 15 15 C   C   A . n 
A 1 16 A   16 16 16 A   A   A . n 
A 1 17 C   17 17 17 C   C   A . n 
A 1 18 A   18 18 18 A   A   A . n 
A 1 19 G   19 19 19 G   G   A . n 
A 1 20 C   20 20 20 C   C   A . n 
A 1 21 A   21 21 21 A   A   A . n 
A 1 22 A   22 22 22 A   A   A . n 
A 1 23 G   23 23 23 G   G   A . n 
B 1 1  C   1  1  1  C   C   B . n 
B 1 2  5BU 2  2  2  5BU 5BU B . n 
B 1 3  U   3  3  3  U   U   B . n 
B 1 4  G   4  4  4  G   G   B . n 
B 1 5  C   5  5  5  C   C   B . n 
B 1 6  U   6  6  6  U   U   B . n 
B 1 7  G   7  7  7  G   G   B . n 
B 1 8  A   8  8  8  A   A   B . n 
B 1 9  G   9  9  9  G   G   B . n 
B 1 10 G   10 10 10 G   G   B . n 
B 1 11 U   11 11 11 U   U   B . n 
B 1 12 G   12 12 12 G   G   B . n 
B 1 13 C   13 13 13 C   C   B . n 
B 1 14 A   14 14 14 A   A   B . n 
B 1 15 C   15 15 15 C   C   B . n 
B 1 16 A   16 16 16 A   A   B . n 
B 1 17 C   17 17 17 C   C   B . n 
B 1 18 A   18 18 18 A   A   B . n 
B 1 19 G   19 19 19 G   G   B . n 
B 1 20 C   20 20 20 C   C   B . n 
B 1 21 A   21 21 21 A   A   B . n 
B 1 22 A   22 22 22 A   A   B . n 
B 1 23 G   23 23 23 G   G   B . n 
# 
loop_
_pdbx_nonpoly_scheme.asym_id 
_pdbx_nonpoly_scheme.entity_id 
_pdbx_nonpoly_scheme.mon_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_strand_id 
_pdbx_nonpoly_scheme.pdb_ins_code 
C 2 MN 1 101 101 MN MN A . 
D 2 MN 1 107 107 MN MN A . 
E 2 MN 1 109 109 MN MN A . 
F 2 MN 1 110 110 MN MN A . 
G 2 MN 1 111 111 MN MN A . 
H 2 MN 1 102 102 MN MN B . 
I 2 MN 1 103 103 MN MN B . 
J 2 MN 1 104 104 MN MN B . 
K 2 MN 1 105 105 MN MN B . 
L 2 MN 1 106 106 MN MN B . 
M 2 MN 1 108 108 MN MN B . 
N 2 MN 1 112 112 MN MN B . 
# 
loop_
_software.name 
_software.classification 
_software.version 
_software.citation_id 
_software.pdbx_ordinal 
CNS       refinement       0.4 ? 1 
DENZO     'data reduction' .   ? 2 
SCALEPACK 'data scaling'   .   ? 3 
CNS       phasing          .   ? 4 
# 
_cell.entry_id           1Y90 
_cell.length_a           59.080 
_cell.length_b           59.080 
_cell.length_c           63.659 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        120.00 
_cell.Z_PDB              12 
_cell.pdbx_unique_axis   ? 
# 
_symmetry.entry_id                         1Y90 
_symmetry.space_group_name_H-M             'P 31 2 1' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                152 
_symmetry.space_group_name_Hall            ? 
# 
_exptl.entry_id          1Y90 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      2.14 
_exptl_crystal.density_percent_sol   50 
_exptl_crystal.description           ? 
_exptl_crystal.F_000                 ? 
_exptl_crystal.preparation           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, SITTING DROP' 
_exptl_crystal_grow.temp            310 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              7.0 
_exptl_crystal_grow.pdbx_details    
'MPD, spermine, KCl, MgCl2, Na Cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 310K' 
_exptl_crystal_grow.pdbx_pH_range   . 
# 
loop_
_exptl_crystal_grow_comp.crystal_id 
_exptl_crystal_grow_comp.id 
_exptl_crystal_grow_comp.sol_id 
_exptl_crystal_grow_comp.name 
_exptl_crystal_grow_comp.volume 
_exptl_crystal_grow_comp.conc 
_exptl_crystal_grow_comp.details 
1 1  1 MPD             ? ? ? 
1 2  1 spermine        ? ? ? 
1 3  1 KCl             ? ? ? 
1 4  1 MgCl2           ? ? ? 
1 5  1 'Na Cacodylate' ? ? ? 
1 6  1 H2O             ? ? ? 
1 7  2 MPD             ? ? ? 
1 8  2 KCl             ? ? ? 
1 9  2 MgCl2           ? ? ? 
1 10 2 'Na Cacodylate' ? ? ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           120 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               'IMAGE PLATE' 
_diffrn_detector.type                   MACSCIENCE 
_diffrn_detector.pdbx_collection_date   ? 
_diffrn_detector.details                ? 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.monochromator                    mirror 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.54 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      'ROTATING ANODE' 
_diffrn_source.type                        ENRAF-NONIUS 
_diffrn_source.pdbx_synchrotron_site       ? 
_diffrn_source.pdbx_synchrotron_beamline   ? 
_diffrn_source.pdbx_wavelength             ? 
_diffrn_source.pdbx_wavelength_list        1.54 
# 
_reflns.entry_id                     1Y90 
_reflns.observed_criterion_sigma_I   0 
_reflns.observed_criterion_sigma_F   0 
_reflns.d_resolution_low             15 
_reflns.d_resolution_high            3.08 
_reflns.number_obs                   2446 
_reflns.number_all                   ? 
_reflns.percent_possible_obs         96.7 
_reflns.pdbx_Rmerge_I_obs            ? 
_reflns.pdbx_Rsym_value              0.052 
_reflns.pdbx_netI_over_sigmaI        ? 
_reflns.B_iso_Wilson_estimate        ? 
_reflns.pdbx_redundancy              3.0 
_reflns.R_free_details               ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             3.08 
_reflns_shell.d_res_low              ? 
_reflns_shell.percent_possible_all   92.1 
_reflns_shell.Rmerge_I_obs           ? 
_reflns_shell.pdbx_Rsym_value        0.112 
_reflns_shell.meanI_over_sigI_obs    ? 
_reflns_shell.pdbx_redundancy        ? 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.number_unique_all      ? 
_reflns_shell.number_measured_all    ? 
_reflns_shell.number_measured_obs    ? 
_reflns_shell.number_unique_obs      ? 
_reflns_shell.pdbx_chi_squared       ? 
_reflns_shell.pdbx_diffrn_id         ? 
_reflns_shell.pdbx_ordinal           1 
# 
_refine.entry_id                                 1Y90 
_refine.ls_number_reflns_obs                     2373 
_refine.ls_number_reflns_all                     2446 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          0.0 
_refine.pdbx_data_cutoff_high_absF               439218.88 
_refine.pdbx_data_cutoff_low_absF                0.000000 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             10.00 
_refine.ls_d_res_high                            3.08 
_refine.ls_percent_reflns_obs                    95.8 
_refine.ls_R_factor_obs                          0.194 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_R_work                       0.194 
_refine.ls_R_factor_R_free                       0.244 
_refine.ls_R_factor_R_free_error                 0.018 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 7.9 
_refine.ls_number_reflns_R_free                  187 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.occupancy_min                            ? 
_refine.occupancy_max                            ? 
_refine.correlation_coeff_Fo_to_Fc               ? 
_refine.correlation_coeff_Fo_to_Fc_free          ? 
_refine.B_iso_mean                               47.0 
_refine.aniso_B[1][1]                            0.98 
_refine.aniso_B[2][2]                            0.98 
_refine.aniso_B[3][3]                            -1.95 
_refine.aniso_B[1][2]                            2.11 
_refine.aniso_B[1][3]                            0.00 
_refine.aniso_B[2][3]                            0.00 
_refine.solvent_model_details                    'FLAT MODEL' 
_refine.solvent_model_param_ksol                 0.262868 
_refine.solvent_model_param_bsol                 16.3725 
_refine.pdbx_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.details                                  ? 
_refine.pdbx_starting_model                      ? 
_refine.pdbx_method_to_determine_struct          'FOURIER SYNTHESIS' 
_refine.pdbx_isotropic_thermal_model             RESTRAINED 
_refine.pdbx_stereochemistry_target_values       ? 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_R_Free_selection_details            RANDOM 
_refine.pdbx_overall_ESU_R                       ? 
_refine.pdbx_overall_ESU_R_Free                  ? 
_refine.overall_SU_ML                            ? 
_refine.overall_SU_B                             ? 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.overall_SU_R_free                        ? 
_refine.ls_wR_factor_R_free                      ? 
_refine.ls_wR_factor_R_work                      ? 
_refine.overall_FOM_free_R_set                   ? 
_refine.overall_FOM_work_R_set                   ? 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_refine.pdbx_overall_phase_error                 ? 
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI   ? 
_refine.pdbx_overall_SU_R_Blow_DPI               ? 
_refine.pdbx_overall_SU_R_free_Blow_DPI          ? 
# 
_refine_analyze.entry_id                        1Y90 
_refine_analyze.Luzzati_coordinate_error_obs    0.33 
_refine_analyze.Luzzati_sigma_a_obs             0.23 
_refine_analyze.Luzzati_d_res_low_obs           10.00 
_refine_analyze.Luzzati_coordinate_error_free   0.41 
_refine_analyze.Luzzati_sigma_a_free            0.28 
_refine_analyze.Luzzati_d_res_low_free          ? 
_refine_analyze.number_disordered_residues      ? 
_refine_analyze.occupancy_sum_hydrogen          ? 
_refine_analyze.occupancy_sum_non_hydrogen      ? 
_refine_analyze.pdbx_refine_id                  'X-RAY DIFFRACTION' 
# 
_refine_hist.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_hist.cycle_id                         LAST 
_refine_hist.pdbx_number_atoms_protein        0 
_refine_hist.pdbx_number_atoms_nucleic_acid   1050 
_refine_hist.pdbx_number_atoms_ligand         12 
_refine_hist.number_atoms_solvent             0 
_refine_hist.number_atoms_total               1062 
_refine_hist.d_res_high                       3.08 
_refine_hist.d_res_low                        10.00 
# 
loop_
_refine_ls_restr.type 
_refine_ls_restr.dev_ideal 
_refine_ls_restr.dev_ideal_target 
_refine_ls_restr.weight 
_refine_ls_restr.number 
_refine_ls_restr.pdbx_refine_id 
_refine_ls_restr.pdbx_restraint_function 
c_bond_d                0.004 ? ? ? 'X-RAY DIFFRACTION' ? 
c_bond_d_na             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_bond_d_prot           ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_d               ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_d_na            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_d_prot          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg             0.8   ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg_na          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg_prot        ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d      10.6  ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d      1.33  ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_mcbond_it             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_mcangle_it            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_scbond_it             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_scangle_it            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
# 
_refine_ls_shell.pdbx_total_number_of_bins_used   6 
_refine_ls_shell.d_res_high                       3.08 
_refine_ls_shell.d_res_low                        3.27 
_refine_ls_shell.number_reflns_R_work             345 
_refine_ls_shell.R_factor_R_work                  0.255 
_refine_ls_shell.percent_reflns_obs               92.9 
_refine_ls_shell.R_factor_R_free                  0.271 
_refine_ls_shell.R_factor_R_free_error            0.047 
_refine_ls_shell.percent_reflns_R_free            8.7 
_refine_ls_shell.number_reflns_R_free             33 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_ls_shell.number_reflns_all                ? 
_refine_ls_shell.R_factor_all                     ? 
# 
loop_
_pdbx_xplor_file.serial_no 
_pdbx_xplor_file.param_file 
_pdbx_xplor_file.topol_file 
_pdbx_xplor_file.pdbx_refine_id 
1 DNA-RNA_REP.PARAM.UPDATE2 DNA-RNA.TOP 'X-RAY DIFFRACTION' 
2 WATER_REP.PARAM           WATER.TOP   'X-RAY DIFFRACTION' 
3 ION.PARAM                 ION.TOP     'X-RAY DIFFRACTION' 
# 
_database_PDB_matrix.entry_id          1Y90 
_database_PDB_matrix.origx[1][1]       1.000000 
_database_PDB_matrix.origx[1][2]       0.000000 
_database_PDB_matrix.origx[1][3]       0.000000 
_database_PDB_matrix.origx[2][1]       0.000000 
_database_PDB_matrix.origx[2][2]       1.000000 
_database_PDB_matrix.origx[2][3]       0.000000 
_database_PDB_matrix.origx[3][1]       0.000000 
_database_PDB_matrix.origx[3][2]       0.000000 
_database_PDB_matrix.origx[3][3]       1.000000 
_database_PDB_matrix.origx_vector[1]   0.00000 
_database_PDB_matrix.origx_vector[2]   0.00000 
_database_PDB_matrix.origx_vector[3]   0.00000 
# 
_struct.entry_id                  1Y90 
_struct.title                     'HIV-1 Dis(Mal) Duplex Mn-Soaked' 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        1Y90 
_struct_keywords.pdbx_keywords   RNA 
_struct_keywords.text            'HIV-1, RNA, metal ions, bulge' 
# 
loop_
_struct_asym.id 
_struct_asym.pdbx_blank_PDB_chainid_flag 
_struct_asym.pdbx_modified 
_struct_asym.entity_id 
_struct_asym.details 
A N N 1 ? 
B N N 1 ? 
C N N 2 ? 
D N N 2 ? 
E N N 2 ? 
F N N 2 ? 
G N N 2 ? 
H N N 2 ? 
I N N 2 ? 
J N N 2 ? 
K N N 2 ? 
L N N 2 ? 
M N N 2 ? 
N N N 2 ? 
# 
_struct_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    1Y90 
_struct_ref.pdbx_db_accession          1Y90 
_struct_ref.pdbx_db_isoform            ? 
_struct_ref.pdbx_seq_one_letter_code   ? 
_struct_ref.pdbx_align_begin           ? 
# 
loop_
_struct_ref_seq.align_id 
_struct_ref_seq.ref_id 
_struct_ref_seq.pdbx_PDB_id_code 
_struct_ref_seq.pdbx_strand_id 
_struct_ref_seq.seq_align_beg 
_struct_ref_seq.pdbx_seq_align_beg_ins_code 
_struct_ref_seq.seq_align_end 
_struct_ref_seq.pdbx_seq_align_end_ins_code 
_struct_ref_seq.pdbx_db_accession 
_struct_ref_seq.db_align_beg 
_struct_ref_seq.pdbx_db_align_beg_ins_code 
_struct_ref_seq.db_align_end 
_struct_ref_seq.pdbx_db_align_end_ins_code 
_struct_ref_seq.pdbx_auth_seq_align_beg 
_struct_ref_seq.pdbx_auth_seq_align_end 
1 1 1Y90 A 1 ? 23 ? 1Y90 1 ? 23 ? 1 23 
2 1 1Y90 B 1 ? 23 ? 1Y90 1 ? 23 ? 1 23 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_defined_assembly 
_pdbx_struct_assembly.method_details       ? 
_pdbx_struct_assembly.oligomeric_details   dimeric 
_pdbx_struct_assembly.oligomeric_count     2 
# 
_pdbx_struct_assembly_gen.assembly_id       1 
_pdbx_struct_assembly_gen.oper_expression   1 
_pdbx_struct_assembly_gen.asym_id_list      A,B,C,D,E,F,G,H,I,J,K,L,M,N 
# 
_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]         1.0000000000 
_pdbx_struct_oper_list.matrix[1][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[1][3]         0.0000000000 
_pdbx_struct_oper_list.vector[1]            0.0000000000 
_pdbx_struct_oper_list.matrix[2][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[2][2]         1.0000000000 
_pdbx_struct_oper_list.matrix[2][3]         0.0000000000 
_pdbx_struct_oper_list.vector[2]            0.0000000000 
_pdbx_struct_oper_list.matrix[3][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][3]         1.0000000000 
_pdbx_struct_oper_list.vector[3]            0.0000000000 
# 
_struct_biol.id                    1 
_struct_biol.pdbx_parent_biol_id   ? 
_struct_biol.details               ? 
# 
loop_
_struct_conn.id 
_struct_conn.conn_type_id 
_struct_conn.pdbx_leaving_atom_flag 
_struct_conn.pdbx_PDB_id 
_struct_conn.ptnr1_label_asym_id 
_struct_conn.ptnr1_label_comp_id 
_struct_conn.ptnr1_label_seq_id 
_struct_conn.ptnr1_label_atom_id 
_struct_conn.pdbx_ptnr1_label_alt_id 
_struct_conn.pdbx_ptnr1_PDB_ins_code 
_struct_conn.pdbx_ptnr1_standard_comp_id 
_struct_conn.ptnr1_symmetry 
_struct_conn.ptnr2_label_asym_id 
_struct_conn.ptnr2_label_comp_id 
_struct_conn.ptnr2_label_seq_id 
_struct_conn.ptnr2_label_atom_id 
_struct_conn.pdbx_ptnr2_label_alt_id 
_struct_conn.pdbx_ptnr2_PDB_ins_code 
_struct_conn.ptnr1_auth_asym_id 
_struct_conn.ptnr1_auth_comp_id 
_struct_conn.ptnr1_auth_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_ptnr3_label_atom_id 
_struct_conn.pdbx_ptnr3_label_seq_id 
_struct_conn.pdbx_ptnr3_label_comp_id 
_struct_conn.pdbx_ptnr3_label_asym_id 
_struct_conn.pdbx_ptnr3_label_alt_id 
_struct_conn.pdbx_ptnr3_PDB_ins_code 
_struct_conn.details 
_struct_conn.pdbx_dist_value 
_struct_conn.pdbx_value_order 
_struct_conn.pdbx_role 
covale1  covale both ? A C   1  "O3'" ? ? ? 1_555 A 5BU 2  P  ? ? A C   1  A 5BU 2   1_555 ? ? ? ? ? ? ?            1.605 ? ? 
covale2  covale both ? A 5BU 2  "O3'" ? ? ? 1_555 A U   3  P  ? ? A 5BU 2  A U   3   1_555 ? ? ? ? ? ? ?            1.602 ? ? 
covale3  covale both ? B C   1  "O3'" ? ? ? 1_555 B 5BU 2  P  ? ? B C   1  B 5BU 2   1_555 ? ? ? ? ? ? ?            1.609 ? ? 
covale4  covale both ? B 5BU 2  "O3'" ? ? ? 1_555 B U   3  P  ? ? B 5BU 2  B U   3   1_555 ? ? ? ? ? ? ?            1.607 ? ? 
metalc1  metalc ?    ? A A   8  OP2   ? ? ? 1_555 D MN  .  MN ? ? A A   8  A MN  107 1_555 ? ? ? ? ? ? ?            2.426 ? ? 
metalc2  metalc ?    ? A G   9  N7    ? ? ? 1_555 D MN  .  MN ? ? A G   9  A MN  107 1_555 ? ? ? ? ? ? ?            2.564 ? ? 
metalc3  metalc ?    ? A G   9  OP1   ? ? ? 1_555 H MN  .  MN ? ? A G   9  B MN  102 1_555 ? ? ? ? ? ? ?            2.513 ? ? 
metalc4  metalc ?    ? B G   4  O6    ? ? ? 1_555 J MN  .  MN ? ? B G   4  B MN  104 1_555 ? ? ? ? ? ? ?            2.688 ? ? 
metalc5  metalc ?    ? B A   8  OP2   B ? ? 1_555 L MN  .  MN ? ? B A   8  B MN  106 1_555 ? ? ? ? ? ? ?            2.332 ? ? 
metalc6  metalc ?    ? B A   8  OP2   A ? ? 1_555 L MN  .  MN ? ? B A   8  B MN  106 1_555 ? ? ? ? ? ? ?            2.603 ? ? 
metalc7  metalc ?    ? B G   9  OP1   B ? ? 1_555 H MN  .  MN ? ? B G   9  B MN  102 1_555 ? ? ? ? ? ? ?            2.255 ? ? 
metalc8  metalc ?    ? B G   9  OP2   A ? ? 1_555 H MN  .  MN ? ? B G   9  B MN  102 1_555 ? ? ? ? ? ? ?            2.483 ? ? 
metalc9  metalc ?    ? B G   9  N7    B ? ? 1_555 L MN  .  MN ? ? B G   9  B MN  106 1_555 ? ? ? ? ? ? ?            2.223 ? ? 
metalc10 metalc ?    ? B G   9  N7    A ? ? 1_555 L MN  .  MN ? ? B G   9  B MN  106 1_555 ? ? ? ? ? ? ?            2.349 ? ? 
hydrog1  hydrog ?    ? A C   1  N3    ? ? ? 1_555 B G   23 N1 ? ? A C   1  B G   23  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog2  hydrog ?    ? A C   1  N4    ? ? ? 1_555 B G   23 O6 ? ? A C   1  B G   23  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog3  hydrog ?    ? A C   1  O2    ? ? ? 1_555 B G   23 N2 ? ? A C   1  B G   23  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog4  hydrog ?    ? A 5BU 2  N3    ? ? ? 1_555 B A   22 N1 ? ? A 5BU 2  B A   22  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog5  hydrog ?    ? A 5BU 2  O4    ? ? ? 1_555 B A   22 N6 ? ? A 5BU 2  B A   22  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog6  hydrog ?    ? A U   3  N3    ? ? ? 1_555 B A   21 N1 ? ? A U   3  B A   21  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog7  hydrog ?    ? A U   3  O4    ? ? ? 1_555 B A   21 N6 ? ? A U   3  B A   21  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog8  hydrog ?    ? A G   4  N1    ? ? ? 1_555 B C   20 N3 ? ? A G   4  B C   20  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog9  hydrog ?    ? A G   4  N2    ? ? ? 1_555 B C   20 O2 ? ? A G   4  B C   20  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog10 hydrog ?    ? A G   4  O6    ? ? ? 1_555 B C   20 N4 ? ? A G   4  B C   20  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog11 hydrog ?    ? A C   5  N3    ? ? ? 1_555 B G   19 N1 ? ? A C   5  B G   19  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog12 hydrog ?    ? A C   5  N4    ? ? ? 1_555 B G   19 O6 ? ? A C   5  B G   19  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog13 hydrog ?    ? A C   5  O2    ? ? ? 1_555 B G   19 N2 ? ? A C   5  B G   19  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog14 hydrog ?    ? A U   6  N3    ? ? ? 1_555 B A   18 N1 ? ? A U   6  B A   18  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog15 hydrog ?    ? A U   6  O4    ? ? ? 1_555 B A   18 N6 ? ? A U   6  B A   18  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog16 hydrog ?    ? A G   7  N1    ? ? ? 1_555 B C   17 N3 ? ? A G   7  B C   17  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog17 hydrog ?    ? A G   7  N2    ? ? ? 1_555 B C   17 O2 ? ? A G   7  B C   17  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog18 hydrog ?    ? A G   7  O6    ? ? ? 1_555 B C   17 N4 ? ? A G   7  B C   17  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog19 hydrog ?    ? A G   9  N1    ? ? ? 1_555 B A   16 N1 ? ? A G   9  B A   16  1_555 ? ? ? ? ? ? TYPE_8_PAIR  ?     ? ? 
hydrog20 hydrog ?    ? A G   9  O6    ? ? ? 1_555 B A   16 N6 ? ? A G   9  B A   16  1_555 ? ? ? ? ? ? TYPE_8_PAIR  ?     ? ? 
hydrog21 hydrog ?    ? A G   10 N1    ? ? ? 1_555 B C   15 N3 ? ? A G   10 B C   15  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog22 hydrog ?    ? A G   10 N2    ? ? ? 1_555 B C   15 O2 ? ? A G   10 B C   15  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog23 hydrog ?    ? A G   10 O6    ? ? ? 1_555 B C   15 N4 ? ? A G   10 B C   15  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog24 hydrog ?    ? A U   11 N3    ? ? ? 1_555 B A   14 N1 ? ? A U   11 B A   14  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog25 hydrog ?    ? A U   11 O4    ? ? ? 1_555 B A   14 N6 ? ? A U   11 B A   14  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog26 hydrog ?    ? A G   12 N1    ? ? ? 1_555 B C   13 N3 ? ? A G   12 B C   13  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog27 hydrog ?    ? A G   12 N2    ? ? ? 1_555 B C   13 O2 ? ? A G   12 B C   13  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog28 hydrog ?    ? A G   12 O6    ? ? ? 1_555 B C   13 N4 ? ? A G   12 B C   13  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog29 hydrog ?    ? A C   13 N3    ? ? ? 1_555 B G   12 N1 ? ? A C   13 B G   12  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog30 hydrog ?    ? A C   13 N4    ? ? ? 1_555 B G   12 O6 ? ? A C   13 B G   12  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog31 hydrog ?    ? A C   13 O2    ? ? ? 1_555 B G   12 N2 ? ? A C   13 B G   12  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog32 hydrog ?    ? A A   14 N1    ? ? ? 1_555 B U   11 N3 ? ? A A   14 B U   11  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog33 hydrog ?    ? A A   14 N6    ? ? ? 1_555 B U   11 O4 ? ? A A   14 B U   11  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog34 hydrog ?    ? A C   15 N3    ? ? ? 1_555 B G   10 N1 ? ? A C   15 B G   10  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog35 hydrog ?    ? A C   15 N4    ? ? ? 1_555 B G   10 O6 ? ? A C   15 B G   10  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog36 hydrog ?    ? A C   15 O2    ? ? ? 1_555 B G   10 N2 ? ? A C   15 B G   10  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog37 hydrog ?    ? A A   16 N1    ? ? ? 1_555 B G   9  N1 A ? A A   16 B G   9   1_555 ? ? ? ? ? ? TYPE_8_PAIR  ?     ? ? 
hydrog38 hydrog ?    ? A A   16 N6    ? ? ? 1_555 B G   9  O6 A ? A A   16 B G   9   1_555 ? ? ? ? ? ? TYPE_8_PAIR  ?     ? ? 
hydrog39 hydrog ?    ? A C   17 N3    ? ? ? 1_555 B G   7  N1 A ? A C   17 B G   7   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog40 hydrog ?    ? A C   17 N4    ? ? ? 1_555 B G   7  O6 A ? A C   17 B G   7   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog41 hydrog ?    ? A C   17 O2    ? ? ? 1_555 B G   7  N2 A ? A C   17 B G   7   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog42 hydrog ?    ? A A   18 N1    ? ? ? 1_555 B U   6  N3 ? ? A A   18 B U   6   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog43 hydrog ?    ? A A   18 N6    ? ? ? 1_555 B U   6  O4 ? ? A A   18 B U   6   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog44 hydrog ?    ? A G   19 N1    ? ? ? 1_555 B C   5  N3 ? ? A G   19 B C   5   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog45 hydrog ?    ? A G   19 N2    ? ? ? 1_555 B C   5  O2 ? ? A G   19 B C   5   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog46 hydrog ?    ? A G   19 O6    ? ? ? 1_555 B C   5  N4 ? ? A G   19 B C   5   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog47 hydrog ?    ? A C   20 N3    ? ? ? 1_555 B G   4  N1 ? ? A C   20 B G   4   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog48 hydrog ?    ? A C   20 N4    ? ? ? 1_555 B G   4  O6 ? ? A C   20 B G   4   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog49 hydrog ?    ? A C   20 O2    ? ? ? 1_555 B G   4  N2 ? ? A C   20 B G   4   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog50 hydrog ?    ? A A   21 N1    ? ? ? 1_555 B U   3  N3 ? ? A A   21 B U   3   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog51 hydrog ?    ? A A   21 N6    ? ? ? 1_555 B U   3  O4 ? ? A A   21 B U   3   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog52 hydrog ?    ? A A   22 N1    ? ? ? 1_555 B 5BU 2  N3 ? ? A A   22 B 5BU 2   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog53 hydrog ?    ? A A   22 N6    ? ? ? 1_555 B 5BU 2  O4 ? ? A A   22 B 5BU 2   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog54 hydrog ?    ? A G   23 N1    ? ? ? 1_555 B C   1  N3 ? ? A G   23 B C   1   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog55 hydrog ?    ? A G   23 N2    ? ? ? 1_555 B C   1  O2 ? ? A G   23 B C   1   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog56 hydrog ?    ? A G   23 O6    ? ? ? 1_555 B C   1  N4 ? ? A G   23 B C   1   1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
covale ? ? 
metalc ? ? 
hydrog ? ? 
# 
loop_
_pdbx_struct_conn_angle.id 
_pdbx_struct_conn_angle.ptnr1_label_atom_id 
_pdbx_struct_conn_angle.ptnr1_label_alt_id 
_pdbx_struct_conn_angle.ptnr1_label_asym_id 
_pdbx_struct_conn_angle.ptnr1_label_comp_id 
_pdbx_struct_conn_angle.ptnr1_label_seq_id 
_pdbx_struct_conn_angle.ptnr1_auth_atom_id 
_pdbx_struct_conn_angle.ptnr1_auth_asym_id 
_pdbx_struct_conn_angle.ptnr1_auth_comp_id 
_pdbx_struct_conn_angle.ptnr1_auth_seq_id 
_pdbx_struct_conn_angle.ptnr1_PDB_ins_code 
_pdbx_struct_conn_angle.ptnr1_symmetry 
_pdbx_struct_conn_angle.ptnr2_label_atom_id 
_pdbx_struct_conn_angle.ptnr2_label_alt_id 
_pdbx_struct_conn_angle.ptnr2_label_asym_id 
_pdbx_struct_conn_angle.ptnr2_label_comp_id 
_pdbx_struct_conn_angle.ptnr2_label_seq_id 
_pdbx_struct_conn_angle.ptnr2_auth_atom_id 
_pdbx_struct_conn_angle.ptnr2_auth_asym_id 
_pdbx_struct_conn_angle.ptnr2_auth_comp_id 
_pdbx_struct_conn_angle.ptnr2_auth_seq_id 
_pdbx_struct_conn_angle.ptnr2_PDB_ins_code 
_pdbx_struct_conn_angle.ptnr2_symmetry 
_pdbx_struct_conn_angle.ptnr3_label_atom_id 
_pdbx_struct_conn_angle.ptnr3_label_alt_id 
_pdbx_struct_conn_angle.ptnr3_label_asym_id 
_pdbx_struct_conn_angle.ptnr3_label_comp_id 
_pdbx_struct_conn_angle.ptnr3_label_seq_id 
_pdbx_struct_conn_angle.ptnr3_auth_atom_id 
_pdbx_struct_conn_angle.ptnr3_auth_asym_id 
_pdbx_struct_conn_angle.ptnr3_auth_comp_id 
_pdbx_struct_conn_angle.ptnr3_auth_seq_id 
_pdbx_struct_conn_angle.ptnr3_PDB_ins_code 
_pdbx_struct_conn_angle.ptnr3_symmetry 
_pdbx_struct_conn_angle.value 
_pdbx_struct_conn_angle.value_esd 
1  OP2 ? A A 8 ? A A 8 ? 1_555 MN ? D MN . ? A MN 107 ? 1_555 N7  ? A G 9 ? A G 9 ? 1_555 78.8  ? 
2  OP1 ? A G 9 ? A G 9 ? 1_555 MN ? H MN . ? B MN 102 ? 1_555 OP1 B B G 9 ? B G 9 ? 1_555 138.4 ? 
3  OP1 ? A G 9 ? A G 9 ? 1_555 MN ? H MN . ? B MN 102 ? 1_555 OP2 A B G 9 ? B G 9 ? 1_555 157.9 ? 
4  OP1 B B G 9 ? B G 9 ? 1_555 MN ? H MN . ? B MN 102 ? 1_555 OP2 A B G 9 ? B G 9 ? 1_555 42.9  ? 
5  OP2 B B A 8 ? B A 8 ? 1_555 MN ? L MN . ? B MN 106 ? 1_555 OP2 A B A 8 ? B A 8 ? 1_555 13.2  ? 
6  OP2 B B A 8 ? B A 8 ? 1_555 MN ? L MN . ? B MN 106 ? 1_555 N7  B B G 9 ? B G 9 ? 1_555 71.2  ? 
7  OP2 A B A 8 ? B A 8 ? 1_555 MN ? L MN . ? B MN 106 ? 1_555 N7  B B G 9 ? B G 9 ? 1_555 58.1  ? 
8  OP2 B B A 8 ? B A 8 ? 1_555 MN ? L MN . ? B MN 106 ? 1_555 N7  A B G 9 ? B G 9 ? 1_555 82.3  ? 
9  OP2 A B A 8 ? B A 8 ? 1_555 MN ? L MN . ? B MN 106 ? 1_555 N7  A B G 9 ? B G 9 ? 1_555 69.3  ? 
10 N7  B B G 9 ? B G 9 ? 1_555 MN ? L MN . ? B MN 106 ? 1_555 N7  A B G 9 ? B G 9 ? 1_555 13.2  ? 
# 
loop_
_struct_site.id 
_struct_site.pdbx_evidence_code 
_struct_site.pdbx_auth_asym_id 
_struct_site.pdbx_auth_comp_id 
_struct_site.pdbx_auth_seq_id 
_struct_site.pdbx_auth_ins_code 
_struct_site.pdbx_num_residues 
_struct_site.details 
AC1 Software B MN 102 ? 3 'BINDING SITE FOR RESIDUE MN B 102' 
AC2 Software B MN 104 ? 2 'BINDING SITE FOR RESIDUE MN B 104' 
AC3 Software B MN 105 ? 2 'BINDING SITE FOR RESIDUE MN B 105' 
AC4 Software B MN 106 ? 2 'BINDING SITE FOR RESIDUE MN B 106' 
AC5 Software A MN 107 ? 2 'BINDING SITE FOR RESIDUE MN A 107' 
AC6 Software B MN 108 ? 1 'BINDING SITE FOR RESIDUE MN B 108' 
AC7 Software A MN 109 ? 1 'BINDING SITE FOR RESIDUE MN A 109' 
AC8 Software A MN 110 ? 1 'BINDING SITE FOR RESIDUE MN A 110' 
AC9 Software B MN 112 ? 1 'BINDING SITE FOR RESIDUE MN B 112' 
# 
loop_
_struct_site_gen.id 
_struct_site_gen.site_id 
_struct_site_gen.pdbx_num_res 
_struct_site_gen.label_comp_id 
_struct_site_gen.label_asym_id 
_struct_site_gen.label_seq_id 
_struct_site_gen.pdbx_auth_ins_code 
_struct_site_gen.auth_comp_id 
_struct_site_gen.auth_asym_id 
_struct_site_gen.auth_seq_id 
_struct_site_gen.label_atom_id 
_struct_site_gen.label_alt_id 
_struct_site_gen.symmetry 
_struct_site_gen.details 
1  AC1 3 G A 9  ? G A 9  . ? 1_555 ? 
2  AC1 3 A B 8  ? A B 8  . ? 1_555 ? 
3  AC1 3 G B 9  ? G B 9  . ? 1_555 ? 
4  AC2 2 U B 3  ? U B 3  . ? 1_555 ? 
5  AC2 2 G B 4  ? G B 4  . ? 1_555 ? 
6  AC3 2 U B 6  ? U B 6  . ? 1_555 ? 
7  AC3 2 G B 7  ? G B 7  . ? 1_555 ? 
8  AC4 2 A B 8  ? A B 8  . ? 1_555 ? 
9  AC4 2 G B 9  ? G B 9  . ? 1_555 ? 
10 AC5 2 A A 8  ? A A 8  . ? 1_555 ? 
11 AC5 2 G A 9  ? G A 9  . ? 1_555 ? 
12 AC6 1 G B 12 ? G B 12 . ? 1_555 ? 
13 AC7 1 A A 21 ? A A 21 . ? 3_764 ? 
14 AC8 1 A A 22 ? A A 22 . ? 1_555 ? 
15 AC9 1 A B 22 ? A B 22 . ? 1_555 ? 
# 
_pdbx_validate_planes.id              1 
_pdbx_validate_planes.PDB_model_num   1 
_pdbx_validate_planes.auth_comp_id    U 
_pdbx_validate_planes.auth_asym_id    A 
_pdbx_validate_planes.auth_seq_id     3 
_pdbx_validate_planes.PDB_ins_code    ? 
_pdbx_validate_planes.label_alt_id    ? 
_pdbx_validate_planes.rmsd            0.067 
_pdbx_validate_planes.type            'SIDE CHAIN' 
# 
loop_
_pdbx_validate_polymer_linkage.id 
_pdbx_validate_polymer_linkage.PDB_model_num 
_pdbx_validate_polymer_linkage.auth_atom_id_1 
_pdbx_validate_polymer_linkage.auth_asym_id_1 
_pdbx_validate_polymer_linkage.auth_comp_id_1 
_pdbx_validate_polymer_linkage.auth_seq_id_1 
_pdbx_validate_polymer_linkage.PDB_ins_code_1 
_pdbx_validate_polymer_linkage.label_alt_id_1 
_pdbx_validate_polymer_linkage.auth_atom_id_2 
_pdbx_validate_polymer_linkage.auth_asym_id_2 
_pdbx_validate_polymer_linkage.auth_comp_id_2 
_pdbx_validate_polymer_linkage.auth_seq_id_2 
_pdbx_validate_polymer_linkage.PDB_ins_code_2 
_pdbx_validate_polymer_linkage.label_alt_id_2 
_pdbx_validate_polymer_linkage.dist 
1 1 "O3'" B U 6 ? ? P B G 7  ? B 2.60 
2 1 "O3'" B G 9 ? A P B G 10 ? ? 2.62 
# 
loop_
_pdbx_struct_mod_residue.id 
_pdbx_struct_mod_residue.label_asym_id 
_pdbx_struct_mod_residue.label_comp_id 
_pdbx_struct_mod_residue.label_seq_id 
_pdbx_struct_mod_residue.auth_asym_id 
_pdbx_struct_mod_residue.auth_comp_id 
_pdbx_struct_mod_residue.auth_seq_id 
_pdbx_struct_mod_residue.PDB_ins_code 
_pdbx_struct_mod_residue.parent_comp_id 
_pdbx_struct_mod_residue.details 
1 A 5BU 2 A 5BU 2 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 
2 B 5BU 2 B 5BU 2 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_ordinal 
5BU P      P  N N 1   
5BU OP1    O  N N 2   
5BU OP2    O  N N 3   
5BU OP3    O  N N 4   
5BU "O5'"  O  N N 5   
5BU "C5'"  C  N N 6   
5BU "C4'"  C  N R 7   
5BU "O4'"  O  N N 8   
5BU "C3'"  C  N S 9   
5BU "O3'"  O  N N 10  
5BU "C2'"  C  N R 11  
5BU "O2'"  O  N N 12  
5BU "C1'"  C  N R 13  
5BU N1     N  N N 14  
5BU C2     C  N N 15  
5BU O2     O  N N 16  
5BU N3     N  N N 17  
5BU C4     C  N N 18  
5BU O4     O  N N 19  
5BU C5     C  N N 20  
5BU C6     C  N N 21  
5BU BR     BR N N 22  
5BU HOP2   H  N N 23  
5BU HOP3   H  N N 24  
5BU "H5'"  H  N N 25  
5BU "H5''" H  N N 26  
5BU "H4'"  H  N N 27  
5BU "H3'"  H  N N 28  
5BU "HO3'" H  N N 29  
5BU "H2'"  H  N N 30  
5BU "HO2'" H  N N 31  
5BU "H1'"  H  N N 32  
5BU H3     H  N N 33  
5BU H6     H  N N 34  
A   OP3    O  N N 35  
A   P      P  N N 36  
A   OP1    O  N N 37  
A   OP2    O  N N 38  
A   "O5'"  O  N N 39  
A   "C5'"  C  N N 40  
A   "C4'"  C  N R 41  
A   "O4'"  O  N N 42  
A   "C3'"  C  N S 43  
A   "O3'"  O  N N 44  
A   "C2'"  C  N R 45  
A   "O2'"  O  N N 46  
A   "C1'"  C  N R 47  
A   N9     N  Y N 48  
A   C8     C  Y N 49  
A   N7     N  Y N 50  
A   C5     C  Y N 51  
A   C6     C  Y N 52  
A   N6     N  N N 53  
A   N1     N  Y N 54  
A   C2     C  Y N 55  
A   N3     N  Y N 56  
A   C4     C  Y N 57  
A   HOP3   H  N N 58  
A   HOP2   H  N N 59  
A   "H5'"  H  N N 60  
A   "H5''" H  N N 61  
A   "H4'"  H  N N 62  
A   "H3'"  H  N N 63  
A   "HO3'" H  N N 64  
A   "H2'"  H  N N 65  
A   "HO2'" H  N N 66  
A   "H1'"  H  N N 67  
A   H8     H  N N 68  
A   H61    H  N N 69  
A   H62    H  N N 70  
A   H2     H  N N 71  
C   OP3    O  N N 72  
C   P      P  N N 73  
C   OP1    O  N N 74  
C   OP2    O  N N 75  
C   "O5'"  O  N N 76  
C   "C5'"  C  N N 77  
C   "C4'"  C  N R 78  
C   "O4'"  O  N N 79  
C   "C3'"  C  N S 80  
C   "O3'"  O  N N 81  
C   "C2'"  C  N R 82  
C   "O2'"  O  N N 83  
C   "C1'"  C  N R 84  
C   N1     N  N N 85  
C   C2     C  N N 86  
C   O2     O  N N 87  
C   N3     N  N N 88  
C   C4     C  N N 89  
C   N4     N  N N 90  
C   C5     C  N N 91  
C   C6     C  N N 92  
C   HOP3   H  N N 93  
C   HOP2   H  N N 94  
C   "H5'"  H  N N 95  
C   "H5''" H  N N 96  
C   "H4'"  H  N N 97  
C   "H3'"  H  N N 98  
C   "HO3'" H  N N 99  
C   "H2'"  H  N N 100 
C   "HO2'" H  N N 101 
C   "H1'"  H  N N 102 
C   H41    H  N N 103 
C   H42    H  N N 104 
C   H5     H  N N 105 
C   H6     H  N N 106 
G   OP3    O  N N 107 
G   P      P  N N 108 
G   OP1    O  N N 109 
G   OP2    O  N N 110 
G   "O5'"  O  N N 111 
G   "C5'"  C  N N 112 
G   "C4'"  C  N R 113 
G   "O4'"  O  N N 114 
G   "C3'"  C  N S 115 
G   "O3'"  O  N N 116 
G   "C2'"  C  N R 117 
G   "O2'"  O  N N 118 
G   "C1'"  C  N R 119 
G   N9     N  Y N 120 
G   C8     C  Y N 121 
G   N7     N  Y N 122 
G   C5     C  Y N 123 
G   C6     C  N N 124 
G   O6     O  N N 125 
G   N1     N  N N 126 
G   C2     C  N N 127 
G   N2     N  N N 128 
G   N3     N  N N 129 
G   C4     C  Y N 130 
G   HOP3   H  N N 131 
G   HOP2   H  N N 132 
G   "H5'"  H  N N 133 
G   "H5''" H  N N 134 
G   "H4'"  H  N N 135 
G   "H3'"  H  N N 136 
G   "HO3'" H  N N 137 
G   "H2'"  H  N N 138 
G   "HO2'" H  N N 139 
G   "H1'"  H  N N 140 
G   H8     H  N N 141 
G   H1     H  N N 142 
G   H21    H  N N 143 
G   H22    H  N N 144 
MN  MN     MN N N 145 
U   OP3    O  N N 146 
U   P      P  N N 147 
U   OP1    O  N N 148 
U   OP2    O  N N 149 
U   "O5'"  O  N N 150 
U   "C5'"  C  N N 151 
U   "C4'"  C  N R 152 
U   "O4'"  O  N N 153 
U   "C3'"  C  N S 154 
U   "O3'"  O  N N 155 
U   "C2'"  C  N R 156 
U   "O2'"  O  N N 157 
U   "C1'"  C  N R 158 
U   N1     N  N N 159 
U   C2     C  N N 160 
U   O2     O  N N 161 
U   N3     N  N N 162 
U   C4     C  N N 163 
U   O4     O  N N 164 
U   C5     C  N N 165 
U   C6     C  N N 166 
U   HOP3   H  N N 167 
U   HOP2   H  N N 168 
U   "H5'"  H  N N 169 
U   "H5''" H  N N 170 
U   "H4'"  H  N N 171 
U   "H3'"  H  N N 172 
U   "HO3'" H  N N 173 
U   "H2'"  H  N N 174 
U   "HO2'" H  N N 175 
U   "H1'"  H  N N 176 
U   H3     H  N N 177 
U   H5     H  N N 178 
U   H6     H  N N 179 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
5BU P     OP1    doub N N 1   
5BU P     OP2    sing N N 2   
5BU P     OP3    sing N N 3   
5BU P     "O5'"  sing N N 4   
5BU OP2   HOP2   sing N N 5   
5BU OP3   HOP3   sing N N 6   
5BU "O5'" "C5'"  sing N N 7   
5BU "C5'" "C4'"  sing N N 8   
5BU "C5'" "H5'"  sing N N 9   
5BU "C5'" "H5''" sing N N 10  
5BU "C4'" "O4'"  sing N N 11  
5BU "C4'" "C3'"  sing N N 12  
5BU "C4'" "H4'"  sing N N 13  
5BU "O4'" "C1'"  sing N N 14  
5BU "C3'" "O3'"  sing N N 15  
5BU "C3'" "C2'"  sing N N 16  
5BU "C3'" "H3'"  sing N N 17  
5BU "O3'" "HO3'" sing N N 18  
5BU "C2'" "O2'"  sing N N 19  
5BU "C2'" "C1'"  sing N N 20  
5BU "C2'" "H2'"  sing N N 21  
5BU "O2'" "HO2'" sing N N 22  
5BU "C1'" N1     sing N N 23  
5BU "C1'" "H1'"  sing N N 24  
5BU N1    C2     sing N N 25  
5BU N1    C6     sing N N 26  
5BU C2    O2     doub N N 27  
5BU C2    N3     sing N N 28  
5BU N3    C4     sing N N 29  
5BU N3    H3     sing N N 30  
5BU C4    O4     doub N N 31  
5BU C4    C5     sing N N 32  
5BU C5    C6     doub N N 33  
5BU C5    BR     sing N N 34  
5BU C6    H6     sing N N 35  
A   OP3   P      sing N N 36  
A   OP3   HOP3   sing N N 37  
A   P     OP1    doub N N 38  
A   P     OP2    sing N N 39  
A   P     "O5'"  sing N N 40  
A   OP2   HOP2   sing N N 41  
A   "O5'" "C5'"  sing N N 42  
A   "C5'" "C4'"  sing N N 43  
A   "C5'" "H5'"  sing N N 44  
A   "C5'" "H5''" sing N N 45  
A   "C4'" "O4'"  sing N N 46  
A   "C4'" "C3'"  sing N N 47  
A   "C4'" "H4'"  sing N N 48  
A   "O4'" "C1'"  sing N N 49  
A   "C3'" "O3'"  sing N N 50  
A   "C3'" "C2'"  sing N N 51  
A   "C3'" "H3'"  sing N N 52  
A   "O3'" "HO3'" sing N N 53  
A   "C2'" "O2'"  sing N N 54  
A   "C2'" "C1'"  sing N N 55  
A   "C2'" "H2'"  sing N N 56  
A   "O2'" "HO2'" sing N N 57  
A   "C1'" N9     sing N N 58  
A   "C1'" "H1'"  sing N N 59  
A   N9    C8     sing Y N 60  
A   N9    C4     sing Y N 61  
A   C8    N7     doub Y N 62  
A   C8    H8     sing N N 63  
A   N7    C5     sing Y N 64  
A   C5    C6     sing Y N 65  
A   C5    C4     doub Y N 66  
A   C6    N6     sing N N 67  
A   C6    N1     doub Y N 68  
A   N6    H61    sing N N 69  
A   N6    H62    sing N N 70  
A   N1    C2     sing Y N 71  
A   C2    N3     doub Y N 72  
A   C2    H2     sing N N 73  
A   N3    C4     sing Y N 74  
C   OP3   P      sing N N 75  
C   OP3   HOP3   sing N N 76  
C   P     OP1    doub N N 77  
C   P     OP2    sing N N 78  
C   P     "O5'"  sing N N 79  
C   OP2   HOP2   sing N N 80  
C   "O5'" "C5'"  sing N N 81  
C   "C5'" "C4'"  sing N N 82  
C   "C5'" "H5'"  sing N N 83  
C   "C5'" "H5''" sing N N 84  
C   "C4'" "O4'"  sing N N 85  
C   "C4'" "C3'"  sing N N 86  
C   "C4'" "H4'"  sing N N 87  
C   "O4'" "C1'"  sing N N 88  
C   "C3'" "O3'"  sing N N 89  
C   "C3'" "C2'"  sing N N 90  
C   "C3'" "H3'"  sing N N 91  
C   "O3'" "HO3'" sing N N 92  
C   "C2'" "O2'"  sing N N 93  
C   "C2'" "C1'"  sing N N 94  
C   "C2'" "H2'"  sing N N 95  
C   "O2'" "HO2'" sing N N 96  
C   "C1'" N1     sing N N 97  
C   "C1'" "H1'"  sing N N 98  
C   N1    C2     sing N N 99  
C   N1    C6     sing N N 100 
C   C2    O2     doub N N 101 
C   C2    N3     sing N N 102 
C   N3    C4     doub N N 103 
C   C4    N4     sing N N 104 
C   C4    C5     sing N N 105 
C   N4    H41    sing N N 106 
C   N4    H42    sing N N 107 
C   C5    C6     doub N N 108 
C   C5    H5     sing N N 109 
C   C6    H6     sing N N 110 
G   OP3   P      sing N N 111 
G   OP3   HOP3   sing N N 112 
G   P     OP1    doub N N 113 
G   P     OP2    sing N N 114 
G   P     "O5'"  sing N N 115 
G   OP2   HOP2   sing N N 116 
G   "O5'" "C5'"  sing N N 117 
G   "C5'" "C4'"  sing N N 118 
G   "C5'" "H5'"  sing N N 119 
G   "C5'" "H5''" sing N N 120 
G   "C4'" "O4'"  sing N N 121 
G   "C4'" "C3'"  sing N N 122 
G   "C4'" "H4'"  sing N N 123 
G   "O4'" "C1'"  sing N N 124 
G   "C3'" "O3'"  sing N N 125 
G   "C3'" "C2'"  sing N N 126 
G   "C3'" "H3'"  sing N N 127 
G   "O3'" "HO3'" sing N N 128 
G   "C2'" "O2'"  sing N N 129 
G   "C2'" "C1'"  sing N N 130 
G   "C2'" "H2'"  sing N N 131 
G   "O2'" "HO2'" sing N N 132 
G   "C1'" N9     sing N N 133 
G   "C1'" "H1'"  sing N N 134 
G   N9    C8     sing Y N 135 
G   N9    C4     sing Y N 136 
G   C8    N7     doub Y N 137 
G   C8    H8     sing N N 138 
G   N7    C5     sing Y N 139 
G   C5    C6     sing N N 140 
G   C5    C4     doub Y N 141 
G   C6    O6     doub N N 142 
G   C6    N1     sing N N 143 
G   N1    C2     sing N N 144 
G   N1    H1     sing N N 145 
G   C2    N2     sing N N 146 
G   C2    N3     doub N N 147 
G   N2    H21    sing N N 148 
G   N2    H22    sing N N 149 
G   N3    C4     sing N N 150 
U   OP3   P      sing N N 151 
U   OP3   HOP3   sing N N 152 
U   P     OP1    doub N N 153 
U   P     OP2    sing N N 154 
U   P     "O5'"  sing N N 155 
U   OP2   HOP2   sing N N 156 
U   "O5'" "C5'"  sing N N 157 
U   "C5'" "C4'"  sing N N 158 
U   "C5'" "H5'"  sing N N 159 
U   "C5'" "H5''" sing N N 160 
U   "C4'" "O4'"  sing N N 161 
U   "C4'" "C3'"  sing N N 162 
U   "C4'" "H4'"  sing N N 163 
U   "O4'" "C1'"  sing N N 164 
U   "C3'" "O3'"  sing N N 165 
U   "C3'" "C2'"  sing N N 166 
U   "C3'" "H3'"  sing N N 167 
U   "O3'" "HO3'" sing N N 168 
U   "C2'" "O2'"  sing N N 169 
U   "C2'" "C1'"  sing N N 170 
U   "C2'" "H2'"  sing N N 171 
U   "O2'" "HO2'" sing N N 172 
U   "C1'" N1     sing N N 173 
U   "C1'" "H1'"  sing N N 174 
U   N1    C2     sing N N 175 
U   N1    C6     sing N N 176 
U   C2    O2     doub N N 177 
U   C2    N3     sing N N 178 
U   N3    C4     sing N N 179 
U   N3    H3     sing N N 180 
U   C4    O4     doub N N 181 
U   C4    C5     sing N N 182 
U   C5    C6     doub N N 183 
U   C5    H5     sing N N 184 
U   C6    H6     sing N N 185 
# 
loop_
_ndb_struct_conf_na.entry_id 
_ndb_struct_conf_na.feature 
1Y90 'double helix'         
1Y90 'a-form double helix'  
1Y90 'bulge loop'           
1Y90 'mismatched base pair' 
# 
loop_
_ndb_struct_na_base_pair.model_number 
_ndb_struct_na_base_pair.i_label_asym_id 
_ndb_struct_na_base_pair.i_label_comp_id 
_ndb_struct_na_base_pair.i_label_seq_id 
_ndb_struct_na_base_pair.i_symmetry 
_ndb_struct_na_base_pair.j_label_asym_id 
_ndb_struct_na_base_pair.j_label_comp_id 
_ndb_struct_na_base_pair.j_label_seq_id 
_ndb_struct_na_base_pair.j_symmetry 
_ndb_struct_na_base_pair.shear 
_ndb_struct_na_base_pair.stretch 
_ndb_struct_na_base_pair.stagger 
_ndb_struct_na_base_pair.buckle 
_ndb_struct_na_base_pair.propeller 
_ndb_struct_na_base_pair.opening 
_ndb_struct_na_base_pair.pair_number 
_ndb_struct_na_base_pair.pair_name 
_ndb_struct_na_base_pair.i_auth_asym_id 
_ndb_struct_na_base_pair.i_auth_seq_id 
_ndb_struct_na_base_pair.i_PDB_ins_code 
_ndb_struct_na_base_pair.j_auth_asym_id 
_ndb_struct_na_base_pair.j_auth_seq_id 
_ndb_struct_na_base_pair.j_PDB_ins_code 
_ndb_struct_na_base_pair.hbond_type_28 
_ndb_struct_na_base_pair.hbond_type_12 
1 A C   1  1_555 B G   23 1_555 0.009  -0.415 -0.063 6.887   -16.317 -6.167 1  A_C1:G23_B   A 1  ? B 23 ? 19 1 
1 A 5BU 2  1_555 B A   22 1_555 -0.582 -0.477 0.054  1.923   -22.520 5.873  2  A_5BU2:A22_B A 2  ? B 22 ? 20 1 
1 A U   3  1_555 B A   21 1_555 0.069  -0.098 0.158  2.777   -19.639 6.716  3  A_U3:A21_B   A 3  ? B 21 ? 20 1 
1 A G   4  1_555 B C   20 1_555 -0.611 -0.108 0.115  -3.029  -13.561 1.458  4  A_G4:C20_B   A 4  ? B 20 ? 19 1 
1 A C   5  1_555 B G   19 1_555 0.416  -0.244 0.336  -4.904  -11.987 -1.257 5  A_C5:G19_B   A 5  ? B 19 ? 19 1 
1 A U   6  1_555 B A   18 1_555 -0.390 -0.163 0.465  -12.427 -10.862 -0.766 6  A_U6:A18_B   A 6  ? B 18 ? 20 1 
1 A G   7  1_555 B C   17 1_555 -0.357 -0.226 0.152  3.172   -12.601 0.676  7  A_G7:C17_B   A 7  ? B 17 ? 19 1 
1 A G   9  1_555 B A   16 1_555 0.289  1.633  -0.346 27.128  -16.344 -6.131 8  A_G9:A16_B   A 9  ? B 16 ? 8  1 
1 A G   10 1_555 B C   15 1_555 -0.484 -0.317 0.334  -3.347  -11.617 3.535  9  A_G10:C15_B  A 10 ? B 15 ? 19 1 
1 A U   11 1_555 B A   14 1_555 -0.277 -0.171 0.025  -2.052  -6.553  -2.621 10 A_U11:A14_B  A 11 ? B 14 ? 20 1 
1 A G   12 1_555 B C   13 1_555 -0.051 -0.129 -0.269 -7.158  -14.017 1.105  11 A_G12:C13_B  A 12 ? B 13 ? 19 1 
1 A C   13 1_555 B G   12 1_555 0.404  -0.033 0.492  -4.021  -11.313 0.828  12 A_C13:G12_B  A 13 ? B 12 ? 19 1 
1 A A   14 1_555 B U   11 1_555 0.223  -0.305 0.719  11.618  -1.090  0.895  13 A_A14:U11_B  A 14 ? B 11 ? 20 1 
1 A C   15 1_555 B G   10 1_555 -0.142 0.018  0.290  4.292   -11.309 6.157  14 A_C15:G10_B  A 15 ? B 10 ? 19 1 
1 A A   16 1_555 B G   9  1_555 -0.643 1.399  -0.227 -17.436 -18.399 -1.027 15 A_A16:G9_B   A 16 ? B 9  ? 8  1 
1 A C   17 1_555 B G   7  1_555 0.330  0.000  0.363  -7.220  -3.107  -1.998 16 A_C17:G7_B   A 17 ? B 7  ? 19 1 
1 A A   18 1_555 B U   6  1_555 -0.266 -0.303 0.441  12.386  -4.405  5.710  17 A_A18:U6_B   A 18 ? B 6  ? 20 1 
1 A G   19 1_555 B C   5  1_555 -0.308 -0.390 0.052  8.208   -10.482 -3.375 18 A_G19:C5_B   A 19 ? B 5  ? 19 1 
1 A C   20 1_555 B G   4  1_555 0.468  -0.186 0.017  -0.952  -14.861 4.713  19 A_C20:G4_B   A 20 ? B 4  ? 19 1 
1 A A   21 1_555 B U   3  1_555 -0.381 -0.118 0.021  -4.305  -12.047 4.038  20 A_A21:U3_B   A 21 ? B 3  ? 20 1 
1 A A   22 1_555 B 5BU 2  1_555 -0.056 -0.364 0.328  2.129   -16.645 4.228  21 A_A22:5BU2_B A 22 ? B 2  ? 20 1 
1 A G   23 1_555 B C   1  1_555 -0.259 -0.336 0.011  2.478   -10.851 -0.169 22 A_G23:C1_B   A 23 ? B 1  ? 19 1 
# 
loop_
_ndb_struct_na_base_pair_step.model_number 
_ndb_struct_na_base_pair_step.i_label_asym_id_1 
_ndb_struct_na_base_pair_step.i_label_comp_id_1 
_ndb_struct_na_base_pair_step.i_label_seq_id_1 
_ndb_struct_na_base_pair_step.i_symmetry_1 
_ndb_struct_na_base_pair_step.j_label_asym_id_1 
_ndb_struct_na_base_pair_step.j_label_comp_id_1 
_ndb_struct_na_base_pair_step.j_label_seq_id_1 
_ndb_struct_na_base_pair_step.j_symmetry_1 
_ndb_struct_na_base_pair_step.i_label_asym_id_2 
_ndb_struct_na_base_pair_step.i_label_comp_id_2 
_ndb_struct_na_base_pair_step.i_label_seq_id_2 
_ndb_struct_na_base_pair_step.i_symmetry_2 
_ndb_struct_na_base_pair_step.j_label_asym_id_2 
_ndb_struct_na_base_pair_step.j_label_comp_id_2 
_ndb_struct_na_base_pair_step.j_label_seq_id_2 
_ndb_struct_na_base_pair_step.j_symmetry_2 
_ndb_struct_na_base_pair_step.shift 
_ndb_struct_na_base_pair_step.slide 
_ndb_struct_na_base_pair_step.rise 
_ndb_struct_na_base_pair_step.tilt 
_ndb_struct_na_base_pair_step.roll 
_ndb_struct_na_base_pair_step.twist 
_ndb_struct_na_base_pair_step.x_displacement 
_ndb_struct_na_base_pair_step.y_displacement 
_ndb_struct_na_base_pair_step.helical_rise 
_ndb_struct_na_base_pair_step.inclination 
_ndb_struct_na_base_pair_step.tip 
_ndb_struct_na_base_pair_step.helical_twist 
_ndb_struct_na_base_pair_step.step_number 
_ndb_struct_na_base_pair_step.step_name 
_ndb_struct_na_base_pair_step.i_auth_asym_id_1 
_ndb_struct_na_base_pair_step.i_auth_seq_id_1 
_ndb_struct_na_base_pair_step.i_PDB_ins_code_1 
_ndb_struct_na_base_pair_step.j_auth_asym_id_1 
_ndb_struct_na_base_pair_step.j_auth_seq_id_1 
_ndb_struct_na_base_pair_step.j_PDB_ins_code_1 
_ndb_struct_na_base_pair_step.i_auth_asym_id_2 
_ndb_struct_na_base_pair_step.i_auth_seq_id_2 
_ndb_struct_na_base_pair_step.i_PDB_ins_code_2 
_ndb_struct_na_base_pair_step.j_auth_asym_id_2 
_ndb_struct_na_base_pair_step.j_auth_seq_id_2 
_ndb_struct_na_base_pair_step.j_PDB_ins_code_2 
1 A C   1  1_555 B G   23 1_555 A 5BU 2  1_555 B A   22 1_555 0.286  -1.314 3.334 -2.626  10.957 36.469 -3.347 -0.758 2.812 17.016 
4.079   38.113 1  AA_C15BU2:A22G23_BB A 1  ? B 23 ? A 2  ? B 22 ? 
1 A 5BU 2  1_555 B A   22 1_555 A U   3  1_555 B A   21 1_555 -0.034 -0.986 3.213 -2.896  8.447  33.549 -2.883 -0.364 2.881 14.321 
4.910   34.684 2  AA_5BU2U3:A21A22_BB A 2  ? B 22 ? A 3  ? B 21 ? 
1 A U   3  1_555 B A   21 1_555 A G   4  1_555 B C   20 1_555 0.403  -1.746 3.176 0.390   12.012 28.569 -5.292 -0.689 2.279 23.092 
-0.750  30.945 3  AA_U3G4:C20A21_BB   A 3  ? B 21 ? A 4  ? B 20 ? 
1 A G   4  1_555 B C   20 1_555 A C   5  1_555 B G   19 1_555 -0.319 -1.477 3.351 -0.543  5.708  37.691 -2.980 0.420  3.107 8.773  
0.834   38.109 4  AA_G4C5:G19C20_BB   A 4  ? B 20 ? A 5  ? B 19 ? 
1 A C   5  1_555 B G   19 1_555 A U   6  1_555 B A   18 1_555 0.512  -1.403 3.194 1.337   12.903 29.693 -4.563 -0.708 2.412 23.799 
-2.466  32.344 5  AA_C5U6:A18G19_BB   A 5  ? B 19 ? A 6  ? B 18 ? 
1 A U   6  1_555 B A   18 1_555 A G   7  1_555 B C   17 1_555 0.702  -1.503 2.664 4.830   12.527 32.134 -3.949 -0.623 2.036 21.496 
-8.288  34.757 6  AA_U6G7:C17A18_BB   A 6  ? B 18 ? A 7  ? B 17 ? 
1 A G   7  1_555 B C   17 1_555 A G   9  1_555 B A   16 1_555 -1.672 0.022  2.866 6.660   2.801  41.252 -0.215 2.924  2.574 3.940  
-9.366  41.852 7  AA_G7G9:A16C17_BB   A 7  ? B 17 ? A 9  ? B 16 ? 
1 A G   9  1_555 B A   16 1_555 A G   10 1_555 B C   15 1_555 0.123  -2.379 3.622 -9.962  11.256 34.521 -5.159 -1.487 2.616 17.951 
15.887  37.560 8  AA_G9G10:C15A16_BB  A 9  ? B 16 ? A 10 ? B 15 ? 
1 A G   10 1_555 B C   15 1_555 A U   11 1_555 B A   14 1_555 -0.545 -1.750 3.097 3.330   5.197  34.440 -3.618 1.359  2.749 8.691  
-5.568  34.973 9  AA_G10U11:A14C15_BB A 10 ? B 15 ? A 11 ? B 14 ? 
1 A U   11 1_555 B A   14 1_555 A G   12 1_555 B C   13 1_555 0.499  -1.605 3.308 4.854   10.787 29.825 -4.741 -0.080 2.631 19.996 
-8.998  32.036 10 AA_U11G12:C13A14_BB A 11 ? B 14 ? A 12 ? B 13 ? 
1 A G   12 1_555 B C   13 1_555 A C   13 1_555 B G   12 1_555 0.092  -1.426 3.133 -4.913  2.515  32.565 -2.910 -0.944 2.972 4.444  
8.683   33.016 11 AA_G12C13:G12C13_BB A 12 ? B 13 ? A 13 ? B 12 ? 
1 A C   13 1_555 B G   12 1_555 A A   14 1_555 B U   11 1_555 -0.227 -1.778 2.549 -3.482  2.347  30.174 -3.741 -0.098 2.417 4.481  
6.647   30.458 12 AA_C13A14:U11G12_BB A 13 ? B 12 ? A 14 ? B 11 ? 
1 A A   14 1_555 B U   11 1_555 A C   15 1_555 B G   10 1_555 0.624  -1.692 3.286 5.488   4.899  32.333 -3.777 -0.186 3.066 8.658  
-9.698  33.138 13 AA_A14C15:G10U11_BB A 14 ? B 11 ? A 15 ? B 10 ? 
1 A C   15 1_555 B G   10 1_555 A A   16 1_555 B G   9  1_555 -0.240 -1.873 3.221 7.076   13.568 34.022 -4.516 1.201  2.247 21.868 
-11.405 37.212 14 AA_C15A16:G9G10_BB  A 15 ? B 10 ? A 16 ? B 9  ? 
1 A A   16 1_555 B G   9  1_555 A C   17 1_555 B G   7  1_555 0.817  -0.109 3.541 -11.115 -3.941 39.720 0.291  -2.412 3.205 -5.651 
15.938  41.366 15 AA_A16C17:G7G9_BB   A 16 ? B 9  ? A 17 ? B 7  ? 
1 A C   17 1_555 B G   7  1_555 A A   18 1_555 B U   6  1_555 0.288  -1.199 2.445 -2.884  14.077 30.299 -3.634 -0.819 1.703 25.226 
5.169   33.461 16 AA_C17A18:U6G7_BB   A 17 ? B 7  ? A 18 ? B 6  ? 
1 A A   18 1_555 B U   6  1_555 A G   19 1_555 B C   5  1_555 -0.265 -1.477 3.333 2.881   8.710  33.271 -3.792 0.877  2.836 14.863 
-4.917  34.478 17 AA_A18G19:C5U6_BB   A 18 ? B 6  ? A 19 ? B 5  ? 
1 A G   19 1_555 B C   5  1_555 A C   20 1_555 B G   4  1_555 0.996  -1.618 3.505 2.626   2.875  36.671 -2.972 -1.196 3.434 4.554  
-4.159  36.870 18 AA_G19C20:G4C5_BB   A 19 ? B 5  ? A 20 ? B 4  ? 
1 A C   20 1_555 B G   4  1_555 A A   21 1_555 B U   3  1_555 -0.852 -1.558 3.049 0.082   13.973 28.130 -5.058 1.589  2.060 26.759 
-0.158  31.347 19 AA_C20A21:U3G4_BB   A 20 ? B 4  ? A 21 ? B 3  ? 
1 A A   21 1_555 B U   3  1_555 A A   22 1_555 B 5BU 2  1_555 -0.145 -0.637 3.148 -1.559  10.446 31.638 -2.738 0.010  2.806 18.524 
2.765   33.312 20 AA_A21A22:5BU2U3_BB A 21 ? B 3  ? A 22 ? B 2  ? 
1 A A   22 1_555 B 5BU 2  1_555 A G   23 1_555 B C   1  1_555 0.108  -1.505 3.246 1.880   13.608 31.929 -4.414 0.079  2.426 23.429 
-3.236  34.688 21 AA_A22G23:C15BU2_BB A 22 ? B 2  ? A 23 ? B 1  ? 
# 
_atom_sites.entry_id                    1Y90 
_atom_sites.fract_transf_matrix[1][1]   0.016926 
_atom_sites.fract_transf_matrix[1][2]   0.009772 
_atom_sites.fract_transf_matrix[1][3]   0.000000 
_atom_sites.fract_transf_matrix[2][1]   0.000000 
_atom_sites.fract_transf_matrix[2][2]   0.019545 
_atom_sites.fract_transf_matrix[2][3]   0.000000 
_atom_sites.fract_transf_matrix[3][1]   0.000000 
_atom_sites.fract_transf_matrix[3][2]   0.000000 
_atom_sites.fract_transf_matrix[3][3]   0.015709 
_atom_sites.fract_transf_vector[1]      0.00000 
_atom_sites.fract_transf_vector[2]      0.00000 
_atom_sites.fract_transf_vector[3]      0.00000 
# 
loop_
_atom_type.symbol 
BR 
C  
MN 
N  
O  
P  
# 
loop_