data_1KD5
# 
_entry.id   1KD5 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.386 
_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   1KD5         pdb_00001kd5 10.2210/pdb1kd5/pdb 
NDB   AR0038       ?            ?                   
RCSB  RCSB014830   ?            ?                   
WWPDB D_1000014830 ?            ?                   
# 
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 2003-03-04 
2 'Structure model' 1 1 2008-04-27 
3 'Structure model' 1 2 2011-07-13 
4 'Structure model' 1 3 2024-02-07 
# 
_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' 'Refinement description'    
# 
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' software       
# 
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' '_software.name'                      
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        1KD5 
_pdbx_database_status.recvd_initial_deposition_date   2001-11-12 
_pdbx_database_status.deposit_site                    NDB 
_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_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Kacer, V.'       1 
'Scaringe, S.A.'  2 
'Scarsdale, J.N.' 3 
'Rife, J.P.'      4 
# 
_citation.id                        primary 
_citation.title                     'Crystal structures of r(GGUCACAGCCC)2.' 
_citation.journal_abbrev            'Acta Crystallogr.,Sect.D' 
_citation.journal_volume            59 
_citation.page_first                423 
_citation.page_last                 432 
_citation.year                      2003 
_citation.journal_id_ASTM           ABCRE6 
_citation.country                   DK 
_citation.journal_id_ISSN           0907-4449 
_citation.journal_id_CSD            0766 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   12595698 
_citation.pdbx_database_id_DOI      10.1107/S0907444902021911 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Kacer, V.'       1 ? 
primary 'Scaringe, S.A.'  2 ? 
primary 'Scarsdale, J.N.' 3 ? 
primary 'Rife, J.P.'      4 ? 
# 
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(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'" 3481.146 2   ? ? ? ? 
2 water   nat water                                       18.015   127 ? ? ? ? 
# 
_entity_poly.entity_id                      1 
_entity_poly.type                           polyribonucleotide 
_entity_poly.nstd_linkage                   no 
_entity_poly.nstd_monomer                   no 
_entity_poly.pdbx_seq_one_letter_code       GGUCACAGCCC 
_entity_poly.pdbx_seq_one_letter_code_can   GGUCACAGCCC 
_entity_poly.pdbx_strand_id                 A,B 
_entity_poly.pdbx_target_identifier         ? 
# 
_pdbx_entity_nonpoly.entity_id   2 
_pdbx_entity_nonpoly.name        water 
_pdbx_entity_nonpoly.comp_id     HOH 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1  G n 
1 2  G n 
1 3  U n 
1 4  C n 
1 5  A n 
1 6  C n 
1 7  A n 
1 8  G n 
1 9  C n 
1 10 C n 
1 11 C 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 
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 
HOH non-polymer   . WATER                        ? 'H2 O'            18.015  
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  G 1  1  1  G G A . n 
A 1 2  G 2  2  2  G G A . n 
A 1 3  U 3  3  3  U U A . n 
A 1 4  C 4  4  4  C C A . n 
A 1 5  A 5  5  5  A A A . n 
A 1 6  C 6  6  6  C C A . n 
A 1 7  A 7  7  7  A A A . n 
A 1 8  G 8  8  8  G G A . n 
A 1 9  C 9  9  9  C C A . n 
A 1 10 C 10 10 10 C C A . n 
A 1 11 C 11 11 11 C C A . n 
B 1 1  G 1  1  1  G G B . n 
B 1 2  G 2  2  2  G G B . n 
B 1 3  U 3  3  3  U U B . n 
B 1 4  C 4  4  4  C C B . n 
B 1 5  A 5  5  5  A A B . n 
B 1 6  C 6  6  6  C C B . n 
B 1 7  A 7  7  7  A A B . n 
B 1 8  G 8  8  8  G G B . n 
B 1 9  C 9  9  9  C C B . n 
B 1 10 C 10 10 10 C C B . n 
B 1 11 C 11 11 11 C C 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 HOH 1  27  27  HOH HOH A . 
C 2 HOH 2  28  28  HOH HOH A . 
C 2 HOH 3  31  31  HOH HOH A . 
C 2 HOH 4  34  34  HOH HOH A . 
C 2 HOH 5  35  35  HOH HOH A . 
C 2 HOH 6  36  36  HOH HOH A . 
C 2 HOH 7  37  37  HOH HOH A . 
C 2 HOH 8  38  38  HOH HOH A . 
C 2 HOH 9  41  41  HOH HOH A . 
C 2 HOH 10 42  42  HOH HOH A . 
C 2 HOH 11 46  46  HOH HOH A . 
C 2 HOH 12 47  47  HOH HOH A . 
C 2 HOH 13 51  51  HOH HOH A . 
C 2 HOH 14 53  53  HOH HOH A . 
C 2 HOH 15 54  54  HOH HOH A . 
C 2 HOH 16 56  56  HOH HOH A . 
C 2 HOH 17 59  59  HOH HOH A . 
C 2 HOH 18 60  60  HOH HOH A . 
C 2 HOH 19 63  63  HOH HOH A . 
C 2 HOH 20 64  64  HOH HOH A . 
C 2 HOH 21 65  65  HOH HOH A . 
C 2 HOH 22 67  67  HOH HOH A . 
C 2 HOH 23 71  71  HOH HOH A . 
C 2 HOH 24 73  73  HOH HOH A . 
C 2 HOH 25 75  75  HOH HOH A . 
C 2 HOH 26 78  78  HOH HOH A . 
C 2 HOH 27 79  79  HOH HOH A . 
C 2 HOH 28 82  82  HOH HOH A . 
C 2 HOH 29 87  87  HOH HOH A . 
C 2 HOH 30 88  88  HOH HOH A . 
C 2 HOH 31 92  92  HOH HOH A . 
C 2 HOH 32 94  94  HOH HOH A . 
C 2 HOH 33 95  95  HOH HOH A . 
C 2 HOH 34 96  96  HOH HOH A . 
C 2 HOH 35 97  97  HOH HOH A . 
C 2 HOH 36 98  98  HOH HOH A . 
C 2 HOH 37 102 102 HOH HOH A . 
C 2 HOH 38 104 104 HOH HOH A . 
C 2 HOH 39 105 105 HOH HOH A . 
C 2 HOH 40 107 107 HOH HOH A . 
C 2 HOH 41 108 108 HOH HOH A . 
C 2 HOH 42 110 110 HOH HOH A . 
C 2 HOH 43 112 112 HOH HOH A . 
C 2 HOH 44 118 118 HOH HOH A . 
C 2 HOH 45 120 120 HOH HOH A . 
C 2 HOH 46 121 121 HOH HOH A . 
C 2 HOH 47 122 122 HOH HOH A . 
C 2 HOH 48 124 124 HOH HOH A . 
C 2 HOH 49 126 126 HOH HOH A . 
C 2 HOH 50 131 131 HOH HOH A . 
C 2 HOH 51 132 132 HOH HOH A . 
C 2 HOH 52 133 133 HOH HOH A . 
C 2 HOH 53 136 136 HOH HOH A . 
C 2 HOH 54 137 137 HOH HOH A . 
C 2 HOH 55 138 138 HOH HOH A . 
C 2 HOH 56 139 139 HOH HOH A . 
C 2 HOH 57 141 141 HOH HOH A . 
C 2 HOH 58 144 144 HOH HOH A . 
C 2 HOH 59 145 145 HOH HOH A . 
C 2 HOH 60 146 146 HOH HOH A . 
C 2 HOH 61 150 150 HOH HOH A . 
C 2 HOH 62 152 152 HOH HOH A . 
C 2 HOH 63 155 155 HOH HOH A . 
C 2 HOH 64 156 156 HOH HOH A . 
D 2 HOH 1  26  26  HOH HOH B . 
D 2 HOH 2  29  29  HOH HOH B . 
D 2 HOH 3  30  30  HOH HOH B . 
D 2 HOH 4  32  32  HOH HOH B . 
D 2 HOH 5  33  33  HOH HOH B . 
D 2 HOH 6  39  39  HOH HOH B . 
D 2 HOH 7  40  40  HOH HOH B . 
D 2 HOH 8  43  43  HOH HOH B . 
D 2 HOH 9  44  44  HOH HOH B . 
D 2 HOH 10 45  45  HOH HOH B . 
D 2 HOH 11 48  48  HOH HOH B . 
D 2 HOH 12 49  49  HOH HOH B . 
D 2 HOH 13 50  50  HOH HOH B . 
D 2 HOH 14 52  52  HOH HOH B . 
D 2 HOH 15 55  55  HOH HOH B . 
D 2 HOH 16 57  57  HOH HOH B . 
D 2 HOH 17 58  58  HOH HOH B . 
D 2 HOH 18 61  61  HOH HOH B . 
D 2 HOH 19 62  62  HOH HOH B . 
D 2 HOH 20 66  66  HOH HOH B . 
D 2 HOH 21 68  68  HOH HOH B . 
D 2 HOH 22 69  69  HOH HOH B . 
D 2 HOH 23 70  70  HOH HOH B . 
D 2 HOH 24 72  72  HOH HOH B . 
D 2 HOH 25 74  74  HOH HOH B . 
D 2 HOH 26 76  76  HOH HOH B . 
D 2 HOH 27 77  77  HOH HOH B . 
D 2 HOH 28 80  80  HOH HOH B . 
D 2 HOH 29 81  81  HOH HOH B . 
D 2 HOH 30 83  83  HOH HOH B . 
D 2 HOH 31 84  84  HOH HOH B . 
D 2 HOH 32 85  85  HOH HOH B . 
D 2 HOH 33 86  86  HOH HOH B . 
D 2 HOH 34 89  89  HOH HOH B . 
D 2 HOH 35 90  90  HOH HOH B . 
D 2 HOH 36 91  91  HOH HOH B . 
D 2 HOH 37 93  93  HOH HOH B . 
D 2 HOH 38 99  99  HOH HOH B . 
D 2 HOH 39 100 100 HOH HOH B . 
D 2 HOH 40 101 101 HOH HOH B . 
D 2 HOH 41 103 103 HOH HOH B . 
D 2 HOH 42 106 106 HOH HOH B . 
D 2 HOH 43 109 109 HOH HOH B . 
D 2 HOH 44 111 111 HOH HOH B . 
D 2 HOH 45 113 113 HOH HOH B . 
D 2 HOH 46 114 114 HOH HOH B . 
D 2 HOH 47 116 116 HOH HOH B . 
D 2 HOH 48 117 117 HOH HOH B . 
D 2 HOH 49 119 119 HOH HOH B . 
D 2 HOH 50 123 123 HOH HOH B . 
D 2 HOH 51 125 125 HOH HOH B . 
D 2 HOH 52 127 127 HOH HOH B . 
D 2 HOH 53 128 128 HOH HOH B . 
D 2 HOH 54 129 129 HOH HOH B . 
D 2 HOH 55 130 130 HOH HOH B . 
D 2 HOH 56 134 134 HOH HOH B . 
D 2 HOH 57 135 135 HOH HOH B . 
D 2 HOH 58 140 140 HOH HOH B . 
D 2 HOH 59 142 142 HOH HOH B . 
D 2 HOH 60 143 143 HOH HOH B . 
D 2 HOH 61 147 147 HOH HOH B . 
D 2 HOH 62 148 148 HOH HOH B . 
D 2 HOH 63 149 149 HOH HOH B . 
# 
loop_
_software.name 
_software.classification 
_software.version 
_software.citation_id 
_software.pdbx_ordinal 
DENZO     'data reduction' . ? 1 
SCALEPACK 'data scaling'   . ? 2 
SHARP     phasing          . ? 3 
SHELXL    refinement       . ? 4 
# 
_cell.entry_id           1KD5 
_cell.length_a           45.388 
_cell.length_b           45.388 
_cell.length_c           51.499 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        90.00 
_cell.Z_PDB              8 
_cell.pdbx_unique_axis   ? 
# 
_symmetry.entry_id                         1KD5 
_symmetry.space_group_name_H-M             'P 43' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     tetragonal 
_symmetry.Int_Tables_number                78 
# 
_exptl.entry_id          1KD5 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_percent_sol   61.6 
_exptl_crystal.density_Matthews      3.23 
_exptl_crystal.description           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, HANGING DROP' 
_exptl_crystal_grow.temp            293 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              6.4 
_exptl_crystal_grow.pdbx_details    
'50 mM tris HCl (pH 6.4), 1.4 M (NH4)2SO4, 20 mM MgCl2, 18 mM spermine, neomycin B, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 293K' 
_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.conc 
_exptl_crystal_grow_comp.volume 
_exptl_crystal_grow_comp.details 
1 1 1 'tris HCl'   ? ? ? 
1 2 1 '(NH4)2SO4'  ? ? ? 
1 3 1 MgCl2        ? ? ? 
1 4 1 spermine     ? ? ? 
1 5 1 'neomycin B' ? ? ? 
1 6 2 'tris HCl'   ? ? ? 
1 7 2 '(NH4)2SO4'  ? ? ? 
1 8 2 MgCl2        ? ? ? 
1 9 2 spermine     ? ? ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           98 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               CCD 
_diffrn_detector.type                   'ADSC QUANTUM 4' 
_diffrn_detector.pdbx_collection_date   2000-08-20 
_diffrn_detector.details                ? 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.monochromator                    ? 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.000 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      SYNCHROTRON 
_diffrn_source.type                        'NSLS BEAMLINE X8C' 
_diffrn_source.pdbx_synchrotron_site       NSLS 
_diffrn_source.pdbx_synchrotron_beamline   X8C 
_diffrn_source.pdbx_wavelength             ? 
_diffrn_source.pdbx_wavelength_list        1.000 
# 
_reflns.entry_id                     1KD5 
_reflns.observed_criterion_sigma_I   -3 
_reflns.observed_criterion_sigma_F   ? 
_reflns.d_resolution_low             25 
_reflns.d_resolution_high            1.58 
_reflns.number_obs                   14143 
_reflns.number_all                   14792 
_reflns.percent_possible_obs         95.6 
_reflns.pdbx_Rmerge_I_obs            0.058 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        17.7 
_reflns.B_iso_Wilson_estimate        ? 
_reflns.pdbx_redundancy              5.4 
_reflns.R_free_details               ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             1.58 
_reflns_shell.d_res_low              1.67 
_reflns_shell.percent_possible_all   91.7 
_reflns_shell.Rmerge_I_obs           0.558 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.meanI_over_sigI_obs    1.7 
_reflns_shell.pdbx_redundancy        2.2 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.number_unique_all      721 
_reflns_shell.pdbx_diffrn_id         ? 
_reflns_shell.pdbx_ordinal           1 
# 
_refine.entry_id                                 1KD5 
_refine.ls_number_reflns_obs                     13324 
_refine.ls_number_reflns_all                     ? 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          2.0 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.ls_d_res_low                             5.00 
_refine.ls_d_res_high                            1.58 
_refine.ls_percent_reflns_obs                    96.4 
_refine.ls_R_factor_obs                          0.1714 
_refine.ls_R_factor_all                          0.174 
_refine.ls_R_factor_R_work                       0.1714 
_refine.ls_R_factor_R_free                       0.226 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 9.93 
_refine.ls_number_reflns_R_free                  1324 
_refine.ls_number_parameters                     5286 
_refine.ls_number_restraints                     6608 
_refine.occupancy_min                            ? 
_refine.occupancy_max                            ? 
_refine.B_iso_mean                               ? 
_refine.aniso_B[1][1]                            ? 
_refine.aniso_B[2][2]                            ? 
_refine.aniso_B[3][3]                            ? 
_refine.aniso_B[1][2]                            ? 
_refine.aniso_B[1][3]                            ? 
_refine.aniso_B[2][3]                            ? 
_refine.solvent_model_details                    'MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-227' 
_refine.solvent_model_param_ksol                 ? 
_refine.solvent_model_param_bsol                 ? 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.details                                  
;Preliminary refinement in CNS. 
Restrained Anisotropic B factors as implemented in SHELXL-96
;
_refine.pdbx_starting_model                      ? 
_refine.pdbx_method_to_determine_struct          SIRAS 
_refine.pdbx_isotropic_thermal_model             'Restrained Anisotropic B factors as implemented in SHELXL-96' 
_refine.pdbx_stereochemistry_target_values       ? 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_R_Free_selection_details            random 
_refine.pdbx_overall_ESU_R_Free                  ? 
_refine.overall_SU_B                             ? 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.correlation_coeff_Fo_to_Fc               ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.overall_SU_R_free                        ? 
_refine.overall_SU_ML                            ? 
_refine.pdbx_overall_ESU_R                       ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.correlation_coeff_Fo_to_Fc_free          ? 
_refine.pdbx_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_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                        1KD5 
_refine_analyze.Luzzati_coordinate_error_obs    0.164 
_refine_analyze.Luzzati_sigma_a_obs             ? 
_refine_analyze.Luzzati_d_res_low_obs           5.00 
_refine_analyze.Luzzati_coordinate_error_free   ? 
_refine_analyze.Luzzati_sigma_a_free            ? 
_refine_analyze.Luzzati_d_res_low_free          ? 
_refine_analyze.number_disordered_residues      0 
_refine_analyze.occupancy_sum_hydrogen          0.00 
_refine_analyze.occupancy_sum_non_hydrogen      587.00 
_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   460 
_refine_hist.pdbx_number_atoms_ligand         0 
_refine_hist.number_atoms_solvent             127 
_refine_hist.number_atoms_total               587 
_refine_hist.d_res_high                       1.58 
_refine_hist.d_res_low                        5.00 
# 
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 
s_bond_d              0.013 ? ? ? 'X-RAY DIFFRACTION' ? 
s_angle_d             0.028 ? ? ? 'X-RAY DIFFRACTION' ? 
s_similar_dist        0.037 ? ? ? 'X-RAY DIFFRACTION' ? 
s_zero_chiral_vol     ?     ? ? ? 'X-RAY DIFFRACTION' ? 
s_anti_bump_dis_restr 0.016 ? ? ? 'X-RAY DIFFRACTION' ? 
# 
_pdbx_refine.entry_id                                    1KD5 
_pdbx_refine.R_factor_all_no_cutoff                      0.1714 
_pdbx_refine.R_factor_obs_no_cutoff                      0.1714 
_pdbx_refine.free_R_factor_no_cutoff                     0.226 
_pdbx_refine.free_R_val_test_set_size_perc_no_cutoff     ? 
_pdbx_refine.free_R_val_test_set_ct_no_cutoff            ? 
_pdbx_refine.R_factor_all_4sig_cutoff                    0.1569 
_pdbx_refine.R_factor_obs_4sig_cutoff                    0.1569 
_pdbx_refine.free_R_factor_4sig_cutoff                   0.226 
_pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff   13.9 
_pdbx_refine.free_R_val_test_set_ct_4sig_cutoff          1324 
_pdbx_refine.number_reflns_obs_4sig_cutoff               9475 
_pdbx_refine.number_reflns_obs_no_cutoff                 12429 
_pdbx_refine.pdbx_refine_id                              'X-RAY DIFFRACTION' 
_pdbx_refine.free_R_error_no_cutoff                      ? 
# 
_database_PDB_matrix.entry_id          1KD5 
_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]   0.000000 
_database_PDB_matrix.origx_vector[2]   0.000000 
_database_PDB_matrix.origx_vector[3]   0.000000 
# 
_struct.entry_id                  1KD5 
_struct.title                     'The Crystal Structure of r(GGUCACAGCCC)2 metal free form' 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        1KD5 
_struct_keywords.pdbx_keywords   RNA 
_struct_keywords.text            'RNA duplex, RNA' 
# 
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 ? 
# 
_struct_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    1KD5 
_struct_ref.pdbx_db_accession          1KD5 
_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 1KD5 A 1 ? 11 ? 1KD5 1 ? 11 ? 1 11 
2 1 1KD5 B 1 ? 11 ? 1KD5 1 ? 11 ? 1 11 
# 
_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 
# 
_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 
hydrog1  hydrog ? ? A G 1  N1 ? ? ? 1_555 B C 10 N3 ? ? A G 1  B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog2  hydrog ? ? A G 1  N2 ? ? ? 1_555 B C 10 O2 ? ? A G 1  B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog3  hydrog ? ? A G 1  O6 ? ? ? 1_555 B C 10 N4 ? ? A G 1  B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog4  hydrog ? ? A G 2  N1 ? ? ? 1_555 B C 9  N3 ? ? A G 2  B C 9  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog5  hydrog ? ? A G 2  N2 ? ? ? 1_555 B C 9  O2 ? ? A G 2  B C 9  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog6  hydrog ? ? A G 2  O6 ? ? ? 1_555 B C 9  N4 ? ? A G 2  B C 9  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog7  hydrog ? ? A U 3  N3 ? ? ? 1_555 B G 8  O6 ? ? A U 3  B G 8  1_555 ? ? ? ? ? ? TYPE_28_PAIR  ? ? ? 
hydrog8  hydrog ? ? A U 3  O2 ? ? ? 1_555 B G 8  N1 ? ? A U 3  B G 8  1_555 ? ? ? ? ? ? TYPE_28_PAIR  ? ? ? 
hydrog9  hydrog ? ? A C 4  O2 ? ? ? 1_555 B A 7  N6 ? ? A C 4  B A 7  1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? 
hydrog10 hydrog ? ? A A 5  N6 ? ? ? 1_555 B C 6  N3 ? ? A A 5  B C 6  1_555 ? ? ? ? ? ? TYPE_25_PAIR  ? ? ? 
hydrog11 hydrog ? ? A A 5  N7 ? ? ? 1_555 B C 6  N4 ? ? A A 5  B C 6  1_555 ? ? ? ? ? ? TYPE_25_PAIR  ? ? ? 
hydrog12 hydrog ? ? A C 6  N3 ? ? ? 1_555 B A 5  N6 ? ? A C 6  B A 5  1_555 ? ? ? ? ? ? TYPE_25_PAIR  ? ? ? 
hydrog13 hydrog ? ? A C 6  N4 ? ? ? 1_555 B A 5  N7 ? ? A C 6  B A 5  1_555 ? ? ? ? ? ? TYPE_25_PAIR  ? ? ? 
hydrog14 hydrog ? ? A A 7  N6 ? ? ? 1_555 B C 4  O2 ? ? A A 7  B C 4  1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? 
hydrog15 hydrog ? ? A G 8  N1 ? ? ? 1_555 B U 3  O2 ? ? A G 8  B U 3  1_555 ? ? ? ? ? ? TYPE_28_PAIR  ? ? ? 
hydrog16 hydrog ? ? A G 8  O6 ? ? ? 1_555 B U 3  N3 ? ? A G 8  B U 3  1_555 ? ? ? ? ? ? TYPE_28_PAIR  ? ? ? 
hydrog17 hydrog ? ? A C 9  N3 ? ? ? 1_555 B G 2  N1 ? ? A C 9  B G 2  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog18 hydrog ? ? A C 9  N4 ? ? ? 1_555 B G 2  O6 ? ? A C 9  B G 2  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog19 hydrog ? ? A C 9  O2 ? ? ? 1_555 B G 2  N2 ? ? A C 9  B G 2  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog20 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 1  N1 ? ? A C 10 B G 1  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog21 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 1  O6 ? ? A C 10 B G 1  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog22 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 1  N2 ? ? A C 10 B G 1  1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
# 
_struct_conn_type.id          hydrog 
_struct_conn_type.criteria    ? 
_struct_conn_type.reference   ? 
# 
_pdbx_validate_rmsd_bond.id                        1 
_pdbx_validate_rmsd_bond.PDB_model_num             1 
_pdbx_validate_rmsd_bond.auth_atom_id_1            N7 
_pdbx_validate_rmsd_bond.auth_asym_id_1            B 
_pdbx_validate_rmsd_bond.auth_comp_id_1            G 
_pdbx_validate_rmsd_bond.auth_seq_id_1             2 
_pdbx_validate_rmsd_bond.PDB_ins_code_1            ? 
_pdbx_validate_rmsd_bond.label_alt_id_1            ? 
_pdbx_validate_rmsd_bond.auth_atom_id_2            C8 
_pdbx_validate_rmsd_bond.auth_asym_id_2            B 
_pdbx_validate_rmsd_bond.auth_comp_id_2            G 
_pdbx_validate_rmsd_bond.auth_seq_id_2             2 
_pdbx_validate_rmsd_bond.PDB_ins_code_2            ? 
_pdbx_validate_rmsd_bond.label_alt_id_2            ? 
_pdbx_validate_rmsd_bond.bond_value                1.342 
_pdbx_validate_rmsd_bond.bond_target_value         1.305 
_pdbx_validate_rmsd_bond.bond_deviation            0.037 
_pdbx_validate_rmsd_bond.bond_standard_deviation   0.006 
_pdbx_validate_rmsd_bond.linker_flag               N 
# 
loop_
_pdbx_validate_rmsd_angle.id 
_pdbx_validate_rmsd_angle.PDB_model_num 
_pdbx_validate_rmsd_angle.auth_atom_id_1 
_pdbx_validate_rmsd_angle.auth_asym_id_1 
_pdbx_validate_rmsd_angle.auth_comp_id_1 
_pdbx_validate_rmsd_angle.auth_seq_id_1 
_pdbx_validate_rmsd_angle.PDB_ins_code_1 
_pdbx_validate_rmsd_angle.label_alt_id_1 
_pdbx_validate_rmsd_angle.auth_atom_id_2 
_pdbx_validate_rmsd_angle.auth_asym_id_2 
_pdbx_validate_rmsd_angle.auth_comp_id_2 
_pdbx_validate_rmsd_angle.auth_seq_id_2 
_pdbx_validate_rmsd_angle.PDB_ins_code_2 
_pdbx_validate_rmsd_angle.label_alt_id_2 
_pdbx_validate_rmsd_angle.auth_atom_id_3 
_pdbx_validate_rmsd_angle.auth_asym_id_3 
_pdbx_validate_rmsd_angle.auth_comp_id_3 
_pdbx_validate_rmsd_angle.auth_seq_id_3 
_pdbx_validate_rmsd_angle.PDB_ins_code_3 
_pdbx_validate_rmsd_angle.label_alt_id_3 
_pdbx_validate_rmsd_angle.angle_value 
_pdbx_validate_rmsd_angle.angle_target_value 
_pdbx_validate_rmsd_angle.angle_deviation 
_pdbx_validate_rmsd_angle.angle_standard_deviation 
_pdbx_validate_rmsd_angle.linker_flag 
1 1 C6    A C 4  ? ? N1    A C 4  ? ? C2 A C 4  ? ? 117.84 120.30 -2.46 0.40 N 
2 1 "O4'" A A 5  ? ? "C1'" A A 5  ? ? N9 A A 5  ? ? 113.83 108.50 5.33  0.70 N 
3 1 C2    A G 8  ? ? N3    A G 8  ? ? C4 A G 8  ? ? 115.71 111.90 3.81  0.50 N 
4 1 N3    A G 8  ? ? C4    A G 8  ? ? C5 A G 8  ? ? 124.71 128.60 -3.89 0.50 N 
5 1 C6    A C 10 ? ? N1    A C 10 ? ? C2 A C 10 ? ? 117.15 120.30 -3.15 0.40 N 
6 1 C2    B G 8  ? ? N3    B G 8  ? ? C4 B G 8  ? ? 115.56 111.90 3.66  0.50 N 
7 1 N3    B G 8  ? ? C4    B G 8  ? ? C5 B G 8  ? ? 125.08 128.60 -3.52 0.50 N 
# 
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 
A   OP3    O N N 1   
A   P      P N N 2   
A   OP1    O N N 3   
A   OP2    O N N 4   
A   "O5'"  O N N 5   
A   "C5'"  C N N 6   
A   "C4'"  C N R 7   
A   "O4'"  O N N 8   
A   "C3'"  C N S 9   
A   "O3'"  O N N 10  
A   "C2'"  C N R 11  
A   "O2'"  O N N 12  
A   "C1'"  C N R 13  
A   N9     N Y N 14  
A   C8     C Y N 15  
A   N7     N Y N 16  
A   C5     C Y N 17  
A   C6     C Y N 18  
A   N6     N N N 19  
A   N1     N Y N 20  
A   C2     C Y N 21  
A   N3     N Y N 22  
A   C4     C Y N 23  
A   HOP3   H N N 24  
A   HOP2   H N N 25  
A   "H5'"  H N N 26  
A   "H5''" H N N 27  
A   "H4'"  H N N 28  
A   "H3'"  H N N 29  
A   "HO3'" H N N 30  
A   "H2'"  H N N 31  
A   "HO2'" H N N 32  
A   "H1'"  H N N 33  
A   H8     H N N 34  
A   H61    H N N 35  
A   H62    H N N 36  
A   H2     H N N 37  
C   OP3    O N N 38  
C   P      P N N 39  
C   OP1    O N N 40  
C   OP2    O N N 41  
C   "O5'"  O N N 42  
C   "C5'"  C N N 43  
C   "C4'"  C N R 44  
C   "O4'"  O N N 45  
C   "C3'"  C N S 46  
C   "O3'"  O N N 47  
C   "C2'"  C N R 48  
C   "O2'"  O N N 49  
C   "C1'"  C N R 50  
C   N1     N N N 51  
C   C2     C N N 52  
C   O2     O N N 53  
C   N3     N N N 54  
C   C4     C N N 55  
C   N4     N N N 56  
C   C5     C N N 57  
C   C6     C N N 58  
C   HOP3   H N N 59  
C   HOP2   H N N 60  
C   "H5'"  H N N 61  
C   "H5''" H N N 62  
C   "H4'"  H N N 63  
C   "H3'"  H N N 64  
C   "HO3'" H N N 65  
C   "H2'"  H N N 66  
C   "HO2'" H N N 67  
C   "H1'"  H N N 68  
C   H41    H N N 69  
C   H42    H N N 70  
C   H5     H N N 71  
C   H6     H N N 72  
G   OP3    O N N 73  
G   P      P N N 74  
G   OP1    O N N 75  
G   OP2    O N N 76  
G   "O5'"  O N N 77  
G   "C5'"  C N N 78  
G   "C4'"  C N R 79  
G   "O4'"  O N N 80  
G   "C3'"  C N S 81  
G   "O3'"  O N N 82  
G   "C2'"  C N R 83  
G   "O2'"  O N N 84  
G   "C1'"  C N R 85  
G   N9     N Y N 86  
G   C8     C Y N 87  
G   N7     N Y N 88  
G   C5     C Y N 89  
G   C6     C N N 90  
G   O6     O N N 91  
G   N1     N N N 92  
G   C2     C N N 93  
G   N2     N N N 94  
G   N3     N N N 95  
G   C4     C Y N 96  
G   HOP3   H N N 97  
G   HOP2   H N N 98  
G   "H5'"  H N N 99  
G   "H5''" H N N 100 
G   "H4'"  H N N 101 
G   "H3'"  H N N 102 
G   "HO3'" H N N 103 
G   "H2'"  H N N 104 
G   "HO2'" H N N 105 
G   "H1'"  H N N 106 
G   H8     H N N 107 
G   H1     H N N 108 
G   H21    H N N 109 
G   H22    H N N 110 
HOH O      O N N 111 
HOH H1     H N N 112 
HOH H2     H N N 113 
U   OP3    O N N 114 
U   P      P N N 115 
U   OP1    O N N 116 
U   OP2    O N N 117 
U   "O5'"  O N N 118 
U   "C5'"  C N N 119 
U   "C4'"  C N R 120 
U   "O4'"  O N N 121 
U   "C3'"  C N S 122 
U   "O3'"  O N N 123 
U   "C2'"  C N R 124 
U   "O2'"  O N N 125 
U   "C1'"  C N R 126 
U   N1     N N N 127 
U   C2     C N N 128 
U   O2     O N N 129 
U   N3     N N N 130 
U   C4     C N N 131 
U   O4     O N N 132 
U   C5     C N N 133 
U   C6     C N N 134 
U   HOP3   H N N 135 
U   HOP2   H N N 136 
U   "H5'"  H N N 137 
U   "H5''" H N N 138 
U   "H4'"  H N N 139 
U   "H3'"  H N N 140 
U   "HO3'" H N N 141 
U   "H2'"  H N N 142 
U   "HO2'" H N N 143 
U   "H1'"  H N N 144 
U   H3     H N N 145 
U   H5     H N N 146 
U   H6     H N N 147 
# 
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 
A   OP3   P      sing N N 1   
A   OP3   HOP3   sing N N 2   
A   P     OP1    doub N N 3   
A   P     OP2    sing N N 4   
A   P     "O5'"  sing N N 5   
A   OP2   HOP2   sing N N 6   
A   "O5'" "C5'"  sing N N 7   
A   "C5'" "C4'"  sing N N 8   
A   "C5'" "H5'"  sing N N 9   
A   "C5'" "H5''" sing N N 10  
A   "C4'" "O4'"  sing N N 11  
A   "C4'" "C3'"  sing N N 12  
A   "C4'" "H4'"  sing N N 13  
A   "O4'" "C1'"  sing N N 14  
A   "C3'" "O3'"  sing N N 15  
A   "C3'" "C2'"  sing N N 16  
A   "C3'" "H3'"  sing N N 17  
A   "O3'" "HO3'" sing N N 18  
A   "C2'" "O2'"  sing N N 19  
A   "C2'" "C1'"  sing N N 20  
A   "C2'" "H2'"  sing N N 21  
A   "O2'" "HO2'" sing N N 22  
A   "C1'" N9     sing N N 23  
A   "C1'" "H1'"  sing N N 24  
A   N9    C8     sing Y N 25  
A   N9    C4     sing Y N 26  
A   C8    N7     doub Y N 27  
A   C8    H8     sing N N 28  
A   N7    C5     sing Y N 29  
A   C5    C6     sing Y N 30  
A   C5    C4     doub Y N 31  
A   C6    N6     sing N N 32  
A   C6    N1     doub Y N 33  
A   N6    H61    sing N N 34  
A   N6    H62    sing N N 35  
A   N1    C2     sing Y N 36  
A   C2    N3     doub Y N 37  
A   C2    H2     sing N N 38  
A   N3    C4     sing Y N 39  
C   OP3   P      sing N N 40  
C   OP3   HOP3   sing N N 41  
C   P     OP1    doub N N 42  
C   P     OP2    sing N N 43  
C   P     "O5'"  sing N N 44  
C   OP2   HOP2   sing N N 45  
C   "O5'" "C5'"  sing N N 46  
C   "C5'" "C4'"  sing N N 47  
C   "C5'" "H5'"  sing N N 48  
C   "C5'" "H5''" sing N N 49  
C   "C4'" "O4'"  sing N N 50  
C   "C4'" "C3'"  sing N N 51  
C   "C4'" "H4'"  sing N N 52  
C   "O4'" "C1'"  sing N N 53  
C   "C3'" "O3'"  sing N N 54  
C   "C3'" "C2'"  sing N N 55  
C   "C3'" "H3'"  sing N N 56  
C   "O3'" "HO3'" sing N N 57  
C   "C2'" "O2'"  sing N N 58  
C   "C2'" "C1'"  sing N N 59  
C   "C2'" "H2'"  sing N N 60  
C   "O2'" "HO2'" sing N N 61  
C   "C1'" N1     sing N N 62  
C   "C1'" "H1'"  sing N N 63  
C   N1    C2     sing N N 64  
C   N1    C6     sing N N 65  
C   C2    O2     doub N N 66  
C   C2    N3     sing N N 67  
C   N3    C4     doub N N 68  
C   C4    N4     sing N N 69  
C   C4    C5     sing N N 70  
C   N4    H41    sing N N 71  
C   N4    H42    sing N N 72  
C   C5    C6     doub N N 73  
C   C5    H5     sing N N 74  
C   C6    H6     sing N N 75  
G   OP3   P      sing N N 76  
G   OP3   HOP3   sing N N 77  
G   P     OP1    doub N N 78  
G   P     OP2    sing N N 79  
G   P     "O5'"  sing N N 80  
G   OP2   HOP2   sing N N 81  
G   "O5'" "C5'"  sing N N 82  
G   "C5'" "C4'"  sing N N 83  
G   "C5'" "H5'"  sing N N 84  
G   "C5'" "H5''" sing N N 85  
G   "C4'" "O4'"  sing N N 86  
G   "C4'" "C3'"  sing N N 87  
G   "C4'" "H4'"  sing N N 88  
G   "O4'" "C1'"  sing N N 89  
G   "C3'" "O3'"  sing N N 90  
G   "C3'" "C2'"  sing N N 91  
G   "C3'" "H3'"  sing N N 92  
G   "O3'" "HO3'" sing N N 93  
G   "C2'" "O2'"  sing N N 94  
G   "C2'" "C1'"  sing N N 95  
G   "C2'" "H2'"  sing N N 96  
G   "O2'" "HO2'" sing N N 97  
G   "C1'" N9     sing N N 98  
G   "C1'" "H1'"  sing N N 99  
G   N9    C8     sing Y N 100 
G   N9    C4     sing Y N 101 
G   C8    N7     doub Y N 102 
G   C8    H8     sing N N 103 
G   N7    C5     sing Y N 104 
G   C5    C6     sing N N 105 
G   C5    C4     doub Y N 106 
G   C6    O6     doub N N 107 
G   C6    N1     sing N N 108 
G   N1    C2     sing N N 109 
G   N1    H1     sing N N 110 
G   C2    N2     sing N N 111 
G   C2    N3     doub N N 112 
G   N2    H21    sing N N 113 
G   N2    H22    sing N N 114 
G   N3    C4     sing N N 115 
HOH O     H1     sing N N 116 
HOH O     H2     sing N N 117 
U   OP3   P      sing N N 118 
U   OP3   HOP3   sing N N 119 
U   P     OP1    doub N N 120 
U   P     OP2    sing N N 121 
U   P     "O5'"  sing N N 122 
U   OP2   HOP2   sing N N 123 
U   "O5'" "C5'"  sing N N 124 
U   "C5'" "C4'"  sing N N 125 
U   "C5'" "H5'"  sing N N 126 
U   "C5'" "H5''" sing N N 127 
U   "C4'" "O4'"  sing N N 128 
U   "C4'" "C3'"  sing N N 129 
U   "C4'" "H4'"  sing N N 130 
U   "O4'" "C1'"  sing N N 131 
U   "C3'" "O3'"  sing N N 132 
U   "C3'" "C2'"  sing N N 133 
U   "C3'" "H3'"  sing N N 134 
U   "O3'" "HO3'" sing N N 135 
U   "C2'" "O2'"  sing N N 136 
U   "C2'" "C1'"  sing N N 137 
U   "C2'" "H2'"  sing N N 138 
U   "O2'" "HO2'" sing N N 139 
U   "C1'" N1     sing N N 140 
U   "C1'" "H1'"  sing N N 141 
U   N1    C2     sing N N 142 
U   N1    C6     sing N N 143 
U   C2    O2     doub N N 144 
U   C2    N3     sing N N 145 
U   N3    C4     sing N N 146 
U   N3    H3     sing N N 147 
U   C4    O4     doub N N 148 
U   C4    C5     sing N N 149 
U   C5    C6     doub N N 150 
U   C5    H5     sing N N 151 
U   C6    H6     sing N N 152 
# 
loop_
_ndb_struct_conf_na.entry_id 
_ndb_struct_conf_na.feature 
1KD5 'double helix'         
1KD5 'a-form double helix'  
1KD5 '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 G 1  1_555 B C 10 1_555 -0.202 0.050  -0.348 -9.606  -7.684  0.061   1  A_G1:C10_B A 1  ? B 10 ? 19 1 
1 A G 2  1_555 B C 9  1_555 -0.243 -0.001 -0.259 -12.963 -11.629 -0.210  2  A_G2:C9_B  A 2  ? B 9  ? 19 1 
1 A U 3  1_555 B G 8  1_555 2.396  -0.484 0.137  -9.446  -3.829  -4.030  3  A_U3:G8_B  A 3  ? B 8  ? 28 ? 
1 A C 4  1_555 B A 7  1_555 7.095  -4.159 0.444  -9.748  7.287   -9.293  4  A_C4:A7_B  A 4  ? B 7  ? ?  6 
1 A A 5  1_555 B C 6  1_555 -3.187 0.056  -0.185 -2.824  -11.622 -97.780 5  A_A5:C6_B  A 5  ? B 6  ? 25 4 
1 A C 6  1_555 B A 5  1_555 3.103  0.024  -0.089 3.771   -9.922  -96.196 6  A_C6:A5_B  A 6  ? B 5  ? 25 4 
1 A A 7  1_555 B C 4  1_555 -7.126 -4.218 0.455  10.141  8.747   -9.472  7  A_A7:C4_B  A 7  ? B 4  ? ?  6 
1 A G 8  1_555 B U 3  1_555 -2.377 -0.485 0.081  8.327   -2.648  -3.801  8  A_G8:U3_B  A 8  ? B 3  ? 28 ? 
1 A C 9  1_555 B G 2  1_555 0.239  0.052  -0.248 13.895  -12.247 -0.129  9  A_C9:G2_B  A 9  ? B 2  ? 19 1 
1 A C 10 1_555 B G 1  1_555 0.197  0.025  -0.280 8.637   -5.644  -0.064  10 A_C10:G1_B A 10 ? 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 G 1 1_555 B C 10 1_555 A G 2  1_555 B C 9 1_555 0.040  -2.034 3.495 1.262  5.169  30.994  -4.740 0.167   3.122 9.585  -2.340  
31.436  1 AA_G1G2:C9C10_BB A 1 ? B 10 ? A 2  ? B 9 ? 
1 A G 2 1_555 B C 9  1_555 A U 3  1_555 B G 8 1_555 0.087  -1.313 3.246 -0.248 4.146  41.901  -2.245 -0.146  3.107 5.780  0.346   
42.097  2 AA_G2U3:G8C9_BB  A 2 ? B 9  ? A 3  ? B 8 ? 
1 A U 3 1_555 B G 8  1_555 A C 4  1_555 B A 7 1_555 0.345  -1.227 3.456 7.304  6.592  57.617  -1.618 0.047   3.327 6.785  -7.518  
58.380  3 AA_U3C4:A7G8_BB  A 3 ? B 8  ? A 4  ? B 7 ? 
1 A C 4 1_555 B A 7  1_555 A A 5  1_555 B C 6 1_555 -5.470 -1.011 2.983 3.231  -1.642 -11.601 7.100  -21.266 4.161 7.873  15.498  
-12.152 4 AA_C4A5:C6A7_BB  A 4 ? B 7  ? A 5  ? B 6 ? 
1 A A 5 1_555 B C 6  1_555 A C 6  1_555 B A 5 1_555 0.001  -3.751 3.228 -0.297 -4.249 66.128  -3.258 -0.013  3.436 -3.890 0.272   
66.250  5 AA_A5C6:A5C6_BB  A 5 ? B 6  ? A 6  ? B 5 ? 
1 A C 6 1_555 B A 5  1_555 A A 7  1_555 B C 4 1_555 5.442  -1.008 2.978 -3.171 -2.500 -11.432 8.279  21.325  4.021 12.067 -15.305 
-12.121 6 AA_C6A7:C4A5_BB  A 6 ? B 5  ? A 7  ? B 4 ? 
1 A A 7 1_555 B C 4  1_555 A G 8  1_555 B U 3 1_555 -0.354 -1.208 3.474 -7.299 6.903  58.470  -1.590 -0.031  3.344 7.010  7.412   
59.252  7 AA_A7G8:U3C4_BB  A 7 ? B 4  ? A 8  ? B 3 ? 
1 A G 8 1_555 B U 3  1_555 A C 9  1_555 B G 2 1_555 -0.086 -1.322 3.207 -0.048 3.876  41.185  -2.271 0.117   3.076 5.495  0.068   
41.359  8 AA_G8C9:G2U3_BB  A 8 ? B 3  ? A 9  ? B 2 ? 
1 A C 9 1_555 B G 2  1_555 A C 10 1_555 B G 1 1_555 -0.053 -2.070 3.539 -1.719 5.351  31.265  -4.794 -0.228  3.148 9.829  3.157   
31.753  9 AA_C9C10:G1G2_BB A 9 ? B 2  ? A 10 ? B 1 ? 
# 
_atom_sites.entry_id                    1KD5 
_atom_sites.fract_transf_matrix[1][1]   0.022032 
_atom_sites.fract_transf_matrix[1][2]   0.000000 
_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]   0.022032 
_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]   0.019418 
_atom_sites.fract_transf_vector[1]      0.000000 
_atom_sites.fract_transf_vector[2]      0.000000 
_atom_sites.fract_transf_vector[3]      0.000000 
# 
loop_
_atom_type.symbol 
C 
N 
O 
P 
# 
loop_